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Conserved domains on  [gi|11072029|gb|AAG28908|]
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F12A21.10 [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM3_EAR1_like cd12530
RNA recognition motif 3 (RRM3) found in terminal EAR1-like proteins; This subgroup corresponds ...
336-439 4.24e-62

RNA recognition motif 3 (RRM3) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM3 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.


:

Pssm-ID: 240974  Cd Length: 101  Bit Score: 198.53  E-value: 4.24e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 336 RTTVMIKNIPNKYTQKLLLKMLDTHCKDCNQSVikEGNKTPMSSYDFVYLPIDFSNKSNVGYGFVNMTSPEAVWRLYKSF 415
Cdd:cd12530   1 RTTLMIKNIPNKYSQKLLLDMLDTHCIQCNQHI--EDSSQPVSSYDFVYLPIDFKNKCNLGYAFVNFTSPEATWRFYKAF 78
                        90       100
                ....*....|....*....|....
gi 11072029 416 HNQHWRDFtTTRKICEVTYARIQG 439
Cdd:cd12530  79 HNQQWEEF-NSRKICQITYARVQG 101
RRM2_EAR1_like cd12527
RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds ...
182-252 2.06e-40

RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.


:

Pssm-ID: 409947 [Multi-domain]  Cd Length: 71  Bit Score: 140.37  E-value: 2.06e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 11072029 182 QGSLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQ 252
Cdd:cd12527   1 QGSLVILNLLPAVSSFTLREIFQVYGDVKDVRETPLKPSQRFVEFFDVRDAARALHEMNGKEIFGKRLVIE 71
RRM1_EAR1_like cd12526
RNA recognition motif 1 (RRM1) found in terminal EAR1-like proteins; This subgroup corresponds ...
79-141 6.16e-34

RNA recognition motif 1 (RRM1) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM1 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.


:

Pssm-ID: 409946 [Multi-domain]  Cd Length: 71  Bit Score: 122.64  E-value: 6.16e-34
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029  79 TRAVMLLQVPATVTETSLRRDMELFGEVRGVQMERAHEGIVIFHFYNLINSQRAFNEIRYRHM 141
Cdd:cd12526   1 TRSVLLSPVPPHVPETDLRRDLEAFGEVRAVQMERFREGVVTVHFYDLRHAERAFAEIRTRHY 63
 
Name Accession Description Interval E-value
RRM3_EAR1_like cd12530
RNA recognition motif 3 (RRM3) found in terminal EAR1-like proteins; This subgroup corresponds ...
336-439 4.24e-62

RNA recognition motif 3 (RRM3) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM3 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.


Pssm-ID: 240974  Cd Length: 101  Bit Score: 198.53  E-value: 4.24e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 336 RTTVMIKNIPNKYTQKLLLKMLDTHCKDCNQSVikEGNKTPMSSYDFVYLPIDFSNKSNVGYGFVNMTSPEAVWRLYKSF 415
Cdd:cd12530   1 RTTLMIKNIPNKYSQKLLLDMLDTHCIQCNQHI--EDSSQPVSSYDFVYLPIDFKNKCNLGYAFVNFTSPEATWRFYKAF 78
                        90       100
                ....*....|....*....|....
gi 11072029 416 HNQHWRDFtTTRKICEVTYARIQG 439
Cdd:cd12530  79 HNQQWEEF-NSRKICQITYARVQG 101
RRM2_EAR1_like cd12527
RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds ...
182-252 2.06e-40

RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.


Pssm-ID: 409947 [Multi-domain]  Cd Length: 71  Bit Score: 140.37  E-value: 2.06e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 11072029 182 QGSLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQ 252
Cdd:cd12527   1 QGSLVILNLLPAVSSFTLREIFQVYGDVKDVRETPLKPSQRFVEFFDVRDAARALHEMNGKEIFGKRLVIE 71
RRM1_EAR1_like cd12526
RNA recognition motif 1 (RRM1) found in terminal EAR1-like proteins; This subgroup corresponds ...
79-141 6.16e-34

RNA recognition motif 1 (RRM1) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM1 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.


Pssm-ID: 409946 [Multi-domain]  Cd Length: 71  Bit Score: 122.64  E-value: 6.16e-34
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029  79 TRAVMLLQVPATVTETSLRRDMELFGEVRGVQMERAHEGIVIFHFYNLINSQRAFNEIRYRHM 141
Cdd:cd12526   1 TRSVLLSPVPPHVPETDLRRDLEAFGEVRAVQMERFREGVVTVHFYDLRHAERAFAEIRTRHY 63
RRM_2 pfam04059
RNA recognition motif 2;
336-448 8.81e-33

RNA recognition motif 2;


Pssm-ID: 112856  Cd Length: 97  Bit Score: 120.36  E-value: 8.81e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029   336 RTTVMIKNIPNKYTQKLLLKMLDTHCKdcnqsvikegnktpmSSYDFVYLPIDFSNKSNVGYGFVNMTSPEAVWRLYKSF 415
Cdd:pfam04059   1 RTTLMIKNIPNKYTQKMLLAAIDEKNK---------------GTYDFLYLPIDFKNKCNVGYAFINMIEPQSIIPFGKAF 65
                          90       100       110
                  ....*....|....*....|....*....|...
gi 11072029   416 HNQHWRDFtTTRKICEVTYARIQGLESLREHFK 448
Cdd:pfam04059  66 NGKKWEKF-NSEKVASLAYARIQGKDALIAHFQ 97
RRM smart00360
RNA recognition motif;
184-251 6.14e-11

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 58.37  E-value: 6.14e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029    184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQR-----FVEFFDVRDAAKALRVMNGKVISGKPMVI 251
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKskgfaFVEFESEEDAEKALEALNGKELDGRPLKV 73
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
86-251 8.34e-09

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 57.89  E-value: 8.34e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029    86 QVPATVTETSLRRDMELFGEVRGVQMERAHEG-IVIFHFYNLINSQ---RAFNEIRYRHMQQQEQQQHFHFTTARGLVSG 161
Cdd:TIGR01628 185 NLDPSVNEDKLRELFAKFGEITSAAVMKDGSGrSRGFAFVNFEKHEdaaKAVEEMNGKKIGLAKEGKKLYVGRAQKRAER 264
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029   162 HSLWAHfVFPQLNAVPEGNNQGS-LVIMNLEPTVSSSTLRHIFQVYGEVKQVR----ETPCKREQRFVEFFDVRDAAKAL 236
Cdd:TIGR01628 265 EAELRR-KFEELQQERKMKAQGVnLYVKNLDDTVTDEKLRELFSECGEITSAKvmldEKGVSRGFGFVCFSNPEEANRAV 343
                         170
                  ....*....|....*
gi 11072029   237 RVMNGKVISGKPMVI 251
Cdd:TIGR01628 344 TEMHGRMLGGKPLYV 358
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
185-249 3.34e-08

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 50.31  E-value: 3.34e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029   185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVReTPCKREQR-----FVEFFDVRDAAKALRVMNGKVISGKPM 249
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIR-LVRDETGRskgfaFVEFEDEEDAEKAIEALNGKELGGREL 69
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
189-256 5.55e-07

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 47.40  E-value: 5.55e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 11072029 189 NLEPTVSSSTLRHIFQVYGEVKQV-----RETpcKREQR--FVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:COG0724   8 NLPYSVTEEDLRELFSEYGEVTSVklitdRET--GRSRGfgFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARP 80
hnRNP-R-Q TIGR01648
heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...
156-256 8.48e-05

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.


Pssm-ID: 273732 [Multi-domain]  Cd Length: 578  Bit Score: 45.38  E-value: 8.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029   156 RGLVSGH-SLWAHFVF-----PQLNAVPEGNNQGS-LVIMNLEPTVSSSTLRHIFQVY--GEVKQVRETpckREQRFVEF 226
Cdd:TIGR01648 200 RKLMPGRiQLWGHVIAvdwaePEEEVDEDVMAKVKiLYVRNLMTTTTEEIIEKSFSEFkpGKVERVKKI---RDYAFVHF 276
                          90       100       110
                  ....*....|....*....|....*....|
gi 11072029   227 FDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:TIGR01648 277 EDREDAVKAMDELNGKELEGSEIEVTLAKP 306
 
Name Accession Description Interval E-value
RRM3_EAR1_like cd12530
RNA recognition motif 3 (RRM3) found in terminal EAR1-like proteins; This subgroup corresponds ...
336-439 4.24e-62

RNA recognition motif 3 (RRM3) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM3 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.


Pssm-ID: 240974  Cd Length: 101  Bit Score: 198.53  E-value: 4.24e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 336 RTTVMIKNIPNKYTQKLLLKMLDTHCKDCNQSVikEGNKTPMSSYDFVYLPIDFSNKSNVGYGFVNMTSPEAVWRLYKSF 415
Cdd:cd12530   1 RTTLMIKNIPNKYSQKLLLDMLDTHCIQCNQHI--EDSSQPVSSYDFVYLPIDFKNKCNLGYAFVNFTSPEATWRFYKAF 78
                        90       100
                ....*....|....*....|....
gi 11072029 416 HNQHWRDFtTTRKICEVTYARIQG 439
Cdd:cd12530  79 HNQQWEEF-NSRKICQITYARVQG 101
RRM2_EAR1_like cd12527
RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds ...
182-252 2.06e-40

RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.


Pssm-ID: 409947 [Multi-domain]  Cd Length: 71  Bit Score: 140.37  E-value: 2.06e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 11072029 182 QGSLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQ 252
Cdd:cd12527   1 QGSLVILNLLPAVSSFTLREIFQVYGDVKDVRETPLKPSQRFVEFFDVRDAARALHEMNGKEIFGKRLVIE 71
RRM3_MEI2_like cd12531
RNA recognition motif 3 (RRM3) found in plant Mei2-like proteins; This subgroup corresponds to ...
339-439 3.55e-35

RNA recognition motif 3 (RRM3) found in plant Mei2-like proteins; This subgroup corresponds to the RRM3 of Mei2-like proteins, representing an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 240975 [Multi-domain]  Cd Length: 86  Bit Score: 126.74  E-value: 3.55e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 339 VMIKNIPNKYTQKLLLKMLDTHCKDcnqsvikegnktpmsSYDFVYLPIDFSNKSNVGYGFVNMTSPEAVWRLYKSFHNQ 418
Cdd:cd12531   1 LMIKNIPNKYTQKMLLAAIDEKHRG---------------TYDFFYLPIDFKNKCNVGYAFINMISPELIVPFYKAFNGK 65
                        90       100
                ....*....|....*....|.
gi 11072029 419 HWRDFtTTRKICEVTYARIQG 439
Cdd:cd12531  66 KWEKF-NSEKVCSLAYARIQG 85
RRM3_MEI2_EAR1_like cd12277
RNA recognition motif 3 (RRM3) found in Mei2-like proteins and terminal EAR1-like proteins; ...
339-439 1.94e-34

RNA recognition motif 3 (RRM3) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM3 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 409719 [Multi-domain]  Cd Length: 86  Bit Score: 124.66  E-value: 1.94e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 339 VMIKNIPNKYTQKLLLKMLDTHCKDcnqsvikegnktpmSSYDFVYLPIDFSNKSNVGYGFVNMTSPEAVWRLYKSFHNQ 418
Cdd:cd12277   1 VMLRNIPNKYTQEMLLQEIDEHGKG--------------GAYDFFYLPLDFKTKCNVGYAFINFINPEAAERFYKAFNGK 66
                        90       100
                ....*....|....*....|.
gi 11072029 419 HWRDFtTTRKICEVTYARIQG 439
Cdd:cd12277  67 KWKNF-PSKKVCDISYARLQG 86
RRM1_EAR1_like cd12526
RNA recognition motif 1 (RRM1) found in terminal EAR1-like proteins; This subgroup corresponds ...
79-141 6.16e-34

RNA recognition motif 1 (RRM1) found in terminal EAR1-like proteins; This subgroup corresponds to the RRM1 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins.


Pssm-ID: 409946 [Multi-domain]  Cd Length: 71  Bit Score: 122.64  E-value: 6.16e-34
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029  79 TRAVMLLQVPATVTETSLRRDMELFGEVRGVQMERAHEGIVIFHFYNLINSQRAFNEIRYRHM 141
Cdd:cd12526   1 TRSVLLSPVPPHVPETDLRRDLEAFGEVRAVQMERFREGVVTVHFYDLRHAERAFAEIRTRHY 63
RRM_2 pfam04059
RNA recognition motif 2;
336-448 8.81e-33

RNA recognition motif 2;


Pssm-ID: 112856  Cd Length: 97  Bit Score: 120.36  E-value: 8.81e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029   336 RTTVMIKNIPNKYTQKLLLKMLDTHCKdcnqsvikegnktpmSSYDFVYLPIDFSNKSNVGYGFVNMTSPEAVWRLYKSF 415
Cdd:pfam04059   1 RTTLMIKNIPNKYTQKMLLAAIDEKNK---------------GTYDFLYLPIDFKNKCNVGYAFINMIEPQSIIPFGKAF 65
                          90       100       110
                  ....*....|....*....|....*....|...
gi 11072029   416 HNQHWRDFtTTRKICEVTYARIQGLESLREHFK 448
Cdd:pfam04059  66 NGKKWEKF-NSEKVASLAYARIQGKDALIAHFQ 97
RRM3_MEI2_fungi cd12532
RNA recognition motif 3 (RRM3) found in fungal Mei2-like proteins; This subgroup corresponds ...
336-441 1.59e-30

RNA recognition motif 3 (RRM3) found in fungal Mei2-like proteins; This subgroup corresponds to the RRM3 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif.


Pssm-ID: 409949  Cd Length: 90  Bit Score: 114.04  E-value: 1.59e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 336 RTTVMIKNIPNKYTQKLLLKMLDTHCKDCnqsvikegnktpmssYDFVYLPIDFSNKSNVGYGFVNMTSPEAVWRLYKSF 415
Cdd:cd12532   1 RTTCMIKNIPNKFTQQMLKEYLDETNKGT---------------YDFVYLRIDFKNNCNVGYAFINFTEPESIVTFYKAR 65
                        90       100
                ....*....|....*....|....*.
gi 11072029 416 HNQHWRDFtTTRKICEVTYARIQGLE 441
Cdd:cd12532  66 QGKKWNKF-NSEKICDISYANIQGKD 90
RRM2_MEI2_EAR1_like cd12276
RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; ...
182-252 7.72e-25

RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 409718 [Multi-domain]  Cd Length: 71  Bit Score: 97.71  E-value: 7.72e-25
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 11072029 182 QGSLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQ 252
Cdd:cd12276   1 QGTLLVFNLDAPVSNDELKSLFSKFGEIKEIRPTPDKPSQKFVEFYDVRDAEAALDGLNGRELLGGKLKVA 71
RRM2_MEI2_like cd12529
RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to ...
182-252 2.25e-24

RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins; This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409948 [Multi-domain]  Cd Length: 71  Bit Score: 96.42  E-value: 2.25e-24
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 11072029 182 QGSLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQ 252
Cdd:cd12529   1 QGTLVVFNLDPSISNDDLHQIFGAYGEIKEIRETPNKRHHKFIEFYDVRSAEAALKALNKSEIAGKRIKLE 71
RRM1_MEI2_EAR1_like cd12275
RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins; ...
79-141 1.57e-14

RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 240721 [Multi-domain]  Cd Length: 71  Bit Score: 68.35  E-value: 1.57e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029  79 TRAVMLLQVPATVTETSLRRDMELFGEVRGVQMERAHEGIVIFHFYNLINSQRAFNEIRYRHM 141
Cdd:cd12275   1 SRSLFVINVPRDVTESTLRRLFEVYGDVRGVQTERISEGIVTVHFYDIRDAKRAVRELCGRHM 63
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
185-252 1.39e-11

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 59.99  E-value: 1.39e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVReTPCKREQR-----FVEFFDVRDAAKALRVMNGKVISGKPMVIQ 252
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVR-IVRDRDGKskgfaFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM smart00360
RNA recognition motif;
184-251 6.14e-11

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 58.37  E-value: 6.14e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029    184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQR-----FVEFFDVRDAAKALRVMNGKVISGKPMVI 251
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKskgfaFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
198-255 1.18e-10

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 57.54  E-value: 1.18e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 198 TLRHIFQVYGEVKQV--RETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12246  19 SLYALFSQFGPVLDIvaSKSLKMRGQAFVVFKDVESATNALRALQGFPFYGKPMRIQYAK 78
RRM1_MEI2_like cd12524
RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to ...
185-256 5.36e-10

RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins; This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear.


Pssm-ID: 409944 [Multi-domain]  Cd Length: 77  Bit Score: 55.75  E-value: 5.36e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVReTPCKreQR---FVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12524   4 LFVRNINSSVEDEELRALFEQFGEIRTLY-TACK--HRgfiMVSYYDIRAAQSAKRALQGTELGGRKLDIHFSIP 75
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
185-254 3.67e-09

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.


Pssm-ID: 409685 [Multi-domain]  Cd Length: 82  Bit Score: 53.39  E-value: 3.67e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCK---------REQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12239   4 LYVKNLSKRVSEKDLKYIFGRFVDSSSEEKNMFDirlmtegrmKGQAFITFPSEELAEKALNLTNGYVLHGKPMVVQFA 82
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
86-251 8.34e-09

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 57.89  E-value: 8.34e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029    86 QVPATVTETSLRRDMELFGEVRGVQMERAHEG-IVIFHFYNLINSQ---RAFNEIRYRHMQQQEQQQHFHFTTARGLVSG 161
Cdd:TIGR01628 185 NLDPSVNEDKLRELFAKFGEITSAAVMKDGSGrSRGFAFVNFEKHEdaaKAVEEMNGKKIGLAKEGKKLYVGRAQKRAER 264
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029   162 HSLWAHfVFPQLNAVPEGNNQGS-LVIMNLEPTVSSSTLRHIFQVYGEVKQVR----ETPCKREQRFVEFFDVRDAAKAL 236
Cdd:TIGR01628 265 EAELRR-KFEELQQERKMKAQGVnLYVKNLDDTVTDEKLRELFSECGEITSAKvmldEKGVSRGFGFVCFSNPEEANRAV 343
                         170
                  ....*....|....*
gi 11072029   237 RVMNGKVISGKPMVI 251
Cdd:TIGR01628 344 TEMHGRMLGGKPLYV 358
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
185-249 3.34e-08

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 50.31  E-value: 3.34e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029   185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVReTPCKREQR-----FVEFFDVRDAAKALRVMNGKVISGKPM 249
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIR-LVRDETGRskgfaFVEFEDEEDAEKAIEALNGKELGGREL 69
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
184-256 3.49e-08

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 50.32  E-value: 3.49e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETpckREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12251   3 VLYVRNLMLSTTEEKLRELFSEYGKVERVKKI---KDYAFVHFEERDDAVKAMEEMNGKELEGSEIEVSLAKP 72
RRM1_PUB1 cd12614
RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated ...
189-251 1.17e-07

RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410026 [Multi-domain]  Cd Length: 74  Bit Score: 48.97  E-value: 1.17e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11072029 189 NLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQR----FVEFFDVRDAAKALRVMNGKVISGKPMVI 251
Cdd:cd12614   5 NLDPRVTEDLLQEIFAVTGPVENCKIIPDKNSKGvnygFVEYYDRRSAEIAIQTLNGRQIFGQEIKV 71
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
185-249 1.85e-07

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 48.56  E-value: 1.85e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQ---VRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPM 249
Cdd:cd12352   1 LYVGNLDRQVTEDLILQLFSQIGPCKSckmITEHGGNDPYCFVEFYEHNHAAAALQAMNGRKILGKEV 68
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
185-248 2.86e-07

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 47.93  E-value: 2.86e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVReTPCKREQR-----FVEFFDVRDAAKALRVMNGKVISGKP 248
Cdd:cd12414   2 LIVRNLPFKCTEDDLKKLFSKFGKVLEVT-IPKKPDGKlrgfaFVQFTNVADAAKAIKGMNGKKIKGRP 69
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
189-256 5.55e-07

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 47.40  E-value: 5.55e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 11072029 189 NLEPTVSSSTLRHIFQVYGEVKQV-----RETpcKREQR--FVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:COG0724   8 NLPYSVTEEDLRELFSEYGEVTSVklitdRET--GRSRGfgFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARP 80
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
185-252 6.09e-07

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 46.88  E-value: 6.09e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQV---REtPCKREQR---FVEFFDVRDAAKALRVMNGKVISGKPMVIQ 252
Cdd:cd12311   1 LKVDNLTYRTTPDDLRRVFEKYGEVGDVyipRD-RYTRESRgfaFVRFYDKRDAEDAIDAMDGAELDGRELRVQ 73
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
185-255 7.04e-07

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 46.91  E-value: 7.04e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQV-----RETPCKREQR---FVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12355   2 LWIGNLDPRLTEYHLLKLLSKYGKIKKFdflfhKTGPLKGQPRgycFVTFETKEEAEKAIECLNGKLALGKKLVVRWAH 80
RRM3_hnRNPQ cd12495
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q ...
185-256 7.21e-07

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q); This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains.


Pssm-ID: 409918 [Multi-domain]  Cd Length: 72  Bit Score: 46.91  E-value: 7.21e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVRETpckREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12495   4 LFVRNLANTVTEEILEKAFSQFGKLERVKKL---KDYAFIHFDERDGAVKAMDEMNGKDLEGENIEIVFAKP 72
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
184-256 1.12e-06

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 46.43  E-value: 1.12e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQ---VRE---TPCkREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12413   1 TLFVRNLPYDTTDEQLEELFSDVGPVKRcfvVKDkgkDKC-RGFGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKK 78
RRM_SRSF3_like cd12373
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...
187-256 1.28e-06

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 409808 [Multi-domain]  Cd Length: 73  Bit Score: 46.08  E-value: 1.28e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029 187 IMNLEPTVSSSTLRHIFQVYGEVKQV---RETPckrEQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12373   4 VGNLGPRVTKRELEDAFEKYGPLRNVwvaRNPP---GFAFVEFEDPRDAEDAVRALDGRRICGSRVRVELSRG 73
RRM2_Spen cd12309
RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily ...
184-255 1.57e-06

RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family; This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 240755 [Multi-domain]  Cd Length: 79  Bit Score: 45.85  E-value: 1.57e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVretPCKREQR-------FVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12309   4 TLFVGNLEITITEEELRRAFERYGVVEDV---DIKRPPRgqgnayaFVKFLNLDMAHRAKVAMSGQYIGRNQIKIGYGK 79
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
185-252 1.89e-06

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.


Pssm-ID: 409852 [Multi-domain]  Cd Length: 75  Bit Score: 45.65  E-value: 1.89e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVR----ETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQ 252
Cdd:cd12418   3 VRVSNLHPDVTEEDLRELFGRVGPVKSVKinydRSGRSTGTAYVVFERPEDAEKAIKQFDGVLLDGQPMKVE 74
RRM3_RBM46 cd12496
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 46 (RBM46); This ...
185-256 3.06e-06

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 46 (RBM46); This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409919 [Multi-domain]  Cd Length: 74  Bit Score: 45.00  E-value: 3.06e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVY--GEVKQVRETpckREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12496   4 LYVRNLMISTTEETIKAEFNKFkpGVVERVKKL---RDYAFVHFFNREDAVAAMSVMNGKCIDGASIEVTLAKP 74
RRM1_MEI2_EAR1_like cd12275
RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins; ...
184-242 3.23e-06

RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins; This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins.


Pssm-ID: 240721 [Multi-domain]  Cd Length: 71  Bit Score: 44.86  E-value: 3.23e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVrETPCKREQ-RFVEFFDVRDAAKALRVMNGK 242
Cdd:cd12275   3 SLFVINVPRDVTESTLRRLFEVYGDVRGV-QTERISEGiVTVHFYDIRDAKRAVRELCGR 61
RRM3_hnRNPR cd12494
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R ...
185-256 3.78e-06

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R); This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains.


Pssm-ID: 409917 [Multi-domain]  Cd Length: 72  Bit Score: 44.63  E-value: 3.78e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVRETpckREQRFVEFFDvRDAA-KALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12494   4 LFVRNLATTVTEEILEKTFSQFGKLERVKKL---KDYAFVHFED-RDAAvKAMDEMNGKEVEGEEIEIVLAKP 72
RRM1_SRSF4_like cd12337
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and ...
187-256 3.79e-06

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 409774 [Multi-domain]  Cd Length: 70  Bit Score: 44.62  E-value: 3.79e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 187 IMNLEPTVSSSTLRHIFQVYGevkQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12337   4 IGRLPYRARERDVERFFRGYG---RIRDINLKNGFGFVEFEDPRDADDAVYELNGKELCGERVIVEHARG 70
RRM1_I_PABPs cd12378
RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily ...
184-254 4.25e-06

RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409812 [Multi-domain]  Cd Length: 80  Bit Score: 44.93  E-value: 4.25e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQR-----FVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12378   1 SLYVGDLHPDVTEAMLYEKFSPAGPVLSIRVCRDAVTRRslgyaYVNFQQPADAERALDTLNFDVIKGKPIRIMWS 76
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
185-256 4.54e-06

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 44.98  E-value: 4.54e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQV-----RETPCKREQR---FVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12223   4 LYVGNLPPSVTEEVLLREFGRFGPLASVkimwpRTEEERRRNRncgFVAFMSRADAERAMRELNGKDVMGYELKLGWGKA 83
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
185-252 5.11e-06

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 44.47  E-value: 5.11e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQV-----RETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQ 252
Cdd:cd12365   1 LHVGKLTRNVTKDHLKEIFSVYGTVKNVdlpidREPNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVTVE 73
RRM3_ACF cd12498
RNA recognition motif 3 (RRM3) found in vertebrate APOBEC-1 complementation factor (ACF); This ...
185-256 6.33e-06

RNA recognition motif 3 (RRM3) found in vertebrate APOBEC-1 complementation factor (ACF); This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1.


Pssm-ID: 409921 [Multi-domain]  Cd Length: 83  Bit Score: 44.53  E-value: 6.33e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVY--GEVKQVRETpckREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12498  11 LYVRNLMLSTTEETIEKEFSNIkpGAVERVKKI---RDYAFVHFYNREDAVNAMNALNGKVIDGSPIEVTLAKP 81
RRM3_PTBP1 cd12695
RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 1 (PTB) ...
185-261 6.38e-06

RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 1 (PTB); This subgroup corresponds to the RRM3 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence show that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution.


Pssm-ID: 410095 [Multi-domain]  Cd Length: 93  Bit Score: 44.61  E-value: 6.38e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 185 LVIMNLEP-TVSSSTLRHIFQVYGEVKQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPM--------VIQFSR 255
Cdd:cd12695   2 LLVSNLNPeRVTPQCLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGQKLHGKPIritlskhqTVQLPR 81
                        90
                ....*....|
gi 11072029 256 PG----GLTK 261
Cdd:cd12695  82 EGqedqGLTK 91
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
189-251 7.98e-06

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 43.70  E-value: 7.98e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11072029 189 NLEPTVSSSTLRHIFQVYGEVKQV-----RETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVI 251
Cdd:cd21608   6 NLSWDTTEDDLRDLFSEFGEVESAkvitdRETGRSRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVV 73
RRM3_SHARP cd12350
RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
184-249 1.25e-05

RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409786 [Multi-domain]  Cd Length: 74  Bit Score: 43.17  E-value: 1.25e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQV--RETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPM 249
Cdd:cd12350   4 TLFIGNLEKTTTYGDLRNIFERFGEIIDIdiKKQNGNPQYAFLQYCDIASVVKAIKKMDGEYLGNNRL 71
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
80-249 1.33e-05

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 47.61  E-value: 1.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029    80 RAVMLLQVPATVTETSLRRDMELFGEVRGVQM-----ERAHEGIVIFHFYNLINSQRAFNeiryrhmqqqeqqqhfhftt 154
Cdd:TIGR01622 115 RTVFVQQLAARARERDLYEFFSKVGKVRDVQIikdrnSRRSKGVGYVEFYDVDSVQAALA-------------------- 174
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029   155 arglVSGHSLWAHFVFPQLN------AVPEGNNQGS----------LVIMNLEPTVSSSTLRHIFQVYGEVKQVR----- 213
Cdd:TIGR01622 175 ----LTGQKLLGIPVIVQLSeaeknrAARAATETSGhhpnsipfhrLYVGNLHFNITEQDLRQIFEPFGEIEFVQlqkdp 250
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 11072029   214 ETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPM 249
Cdd:TIGR01622 251 ETGRSKGYGFIQFRDAEQAKEALEKMNGFELAGRPI 286
RRM2_SREK1 cd12260
RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 ...
184-255 1.41e-05

RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins; This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site.


Pssm-ID: 409705 [Multi-domain]  Cd Length: 85  Bit Score: 43.45  E-value: 1.41e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVR--ETPCKREQR-FVEFFDVRDAAKALRvMNGKVISGKPMVIQFSR 255
Cdd:cd12260   6 TVYVGNLDPSTTADQLLEFFSQAGEVKYVRmaGDETQPTRYaFVEFAEQTSVINALK-LNGKMFGGRPLKVNHSN 79
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
185-251 1.65e-05

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 42.77  E-value: 1.65e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPcKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVI 251
Cdd:cd12340   2 LFVRPFPPDTSESAIREIFSPYGPVKEVKMLS-DSNFAFVEFEELEDAIRAKDSVHGRVLNNEPLYV 67
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
179-249 2.26e-05

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 42.64  E-value: 2.26e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11072029 179 GNNqgsLVIMNLEPTVSSSTLRHIFQVYGEV---KQVRETpcKREQR---FVEFFDVRDAAKALRVMNGKVISGKPM 249
Cdd:cd12381   1 GVN---LYVKNLDDTIDDEKLREEFSPFGTItsaKVMTDE--GGRSKgfgFVCFSSPEEATKAVTEMNGRIIGGKPL 72
RRM2_PUB1 cd12619
RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated ...
184-249 2.46e-05

RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins; This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 410031 [Multi-domain]  Cd Length: 80  Bit Score: 42.48  E-value: 2.46e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVR-----ETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPM 249
Cdd:cd12619   3 NIFVGDLSPEVTDAALFNAFSDFPSCSDARvmwdqKTGRSRGYGFVSFRSQQDAQNAINSMNGKWLGSRPI 73
RRM_SRSF10_SRSF12 cd12312
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...
184-255 2.87e-05

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 240758 [Multi-domain]  Cd Length: 84  Bit Score: 42.36  E-value: 2.87e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVReTPC---KREQR---FVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12312   2 SLFVRNVADDTRPDDLRREFGRYGPIVDVY-IPLdfyTRRPRgfaYIQFEDVRDAEDALYYLDRTRFLGREIEIQFAQ 78
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
185-249 4.39e-05

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 41.84  E-value: 4.39e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQV---RETPCKREQ--RFVEFFDVRDAAKALRVMNGKVISGKPM 249
Cdd:cd12284   1 LYVGSLHFNITEDMLRGIFEPFGKIEFVqlqKDPETGRSKgyGFIQFRDAEDAKKALEQLNGFELAGRPM 70
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
190-248 4.71e-05

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 41.54  E-value: 4.71e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 11072029 190 LEPTVSSSTLRHIFQVYGEVKQVRETPCKReQRFVEFFDVRDAAKALRVMNGKVISGKP 248
Cdd:cd12346   9 LDPNVTEEDLRVLFGPFGEIVYVKIPPGKG-CGFVQFVNRASAEAAIQKLQGTPIGGSR 66
RRM2_Prp24 cd12297
RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
185-256 4.86e-05

RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409738 [Multi-domain]  Cd Length: 78  Bit Score: 41.59  E-value: 4.86e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVReTPCKR---EQRF--VEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12297   3 LWVTNFPPSYDERSIRDLFGDYGVILSVR-LPSLRyntSRRFcyIDFTSPESARAAVELLNGLLEEGYTLVVKISDP 78
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
185-254 6.16e-05

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409759 [Multi-domain]  Cd Length: 76  Bit Score: 41.45  E-value: 6.16e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVReTPCKREQR-----FVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12320   3 LIVKNVPFEATRKEIRELFSPFGQLKSVR-LPKKFDGShrgfaFVEFVTKQEAQNAMEALKSTHLYGRHLVLEYA 76
RRM5_MRD1 cd12570
RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 ...
183-254 6.37e-05

RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 241014 [Multi-domain]  Cd Length: 76  Bit Score: 41.34  E-value: 6.37e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11072029 183 GSLVIMNLEPTVSSSTLRHIFQVYGEVKQVReTPCKREQR-----FVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12570   1 TKILVKNLPFEATKKDVRTLFSSYGQLKSVR-VPKKFDQSargfaFVEFSTAKEALNAMNALKDTHLLGRRLVLQYA 76
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
79-140 6.95e-05

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 41.23  E-value: 6.95e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11072029  79 TRAVMLLQVPATVTETSLRRDMELFGEVRGVQMERaHEGIVIFHFYNLINSQRAFNEIRYRH 140
Cdd:cd12262   3 SRNVYVGNLDDSLTEEEIRGILEKYGEIESIKILK-EKNCAFVNYLNIANAIKAVQELPIKN 63
RRM_Nab3p cd12342
RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) ...
185-256 7.11e-05

RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins; This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues.


Pssm-ID: 240788 [Multi-domain]  Cd Length: 71  Bit Score: 40.89  E-value: 7.11e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 11072029 185 LVIMNLePT--VSSSTLRHIFQVYGEVKQVRetpCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12342   2 LFIGNL-PTkrVSKEDLFRIFSPYGHLMQIV---IKNAFGFVQFDSPQSCRNAIECEQGEMNRGKKLHLEVSKS 71
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
183-247 8.38e-05

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.


Pssm-ID: 409883 [Multi-domain]  Cd Length: 80  Bit Score: 41.31  E-value: 8.38e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 183 GSLVIMNLEPTVSSSTLRHIFQVYGEVKQV-----RETPCKREQRFVEFFDVRDAAKALRVMNGKVISGK 247
Cdd:cd12449   1 GKLFVGGLSFDTNEQSLEEVFSKYGQISEVvvvkdRETQRSRGFGFVTFENPDDAKDAMMAMNGKSLDGR 70
hnRNP-R-Q TIGR01648
heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...
156-256 8.48e-05

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.


Pssm-ID: 273732 [Multi-domain]  Cd Length: 578  Bit Score: 45.38  E-value: 8.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029   156 RGLVSGH-SLWAHFVF-----PQLNAVPEGNNQGS-LVIMNLEPTVSSSTLRHIFQVY--GEVKQVRETpckREQRFVEF 226
Cdd:TIGR01648 200 RKLMPGRiQLWGHVIAvdwaePEEEVDEDVMAKVKiLYVRNLMTTTTEEIIEKSFSEFkpGKVERVKKI---RDYAFVHF 276
                          90       100       110
                  ....*....|....*....|....*....|
gi 11072029   227 FDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:TIGR01648 277 EDREDAVKAMDELNGKELEGSEIEVTLAKP 306
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
185-256 9.34e-05

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 41.16  E-value: 9.34e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCK----REQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12392   5 LFVKGLPFSCTKEELEELFKQHGTVKDVRLVTYRngkpKGLAYVEYENEADASQAVLKTDGTEIKDHTISVAISNP 80
RRM_ABT1_like cd12263
RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar ...
199-247 9.99e-05

RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar proteins; This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 could be a transcription cofactor that can bind to DNA in a sequence-independent manner. The yeast ABT1 homolog, ESF2, is a component of 90S preribosomes and 5' ETS-based RNPs. It is previously identified as a putative partner of the TATA-element binding protein. However, it is primarily localized to the nucleolus and physically associates with pre-rRNA processing factors. ESF2 may play a role in ribosome biogenesis. It is required for normal pre-rRNA processing, as well as for SSU processome assembly and function. Both ABT1 and ESF2 contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409707 [Multi-domain]  Cd Length: 98  Bit Score: 41.42  E-value: 9.99e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11072029 199 LRHIFQVYGEVKQV---RETPCKREQR--------------FVEFFDVRDAAKALRVMNGKVISGK 247
Cdd:cd12263  17 LRQLLSQYGEVGRIylqPEDPSKRKKRkkkggnkkkkftegWVEFEDKKVAKRVAESLNNTPIGGK 82
RRM1_SXL cd12649
RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
185-258 1.07e-04

RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 241093 [Multi-domain]  Cd Length: 81  Bit Score: 40.85  E-value: 1.07e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQvretpCK--REQR--------FVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12649   3 LIVNYLPQDLTDREFRALFRAIGPVNT-----CKivRDKKtgysygfgFVDFTSEEDAQRAIKTLNGLQLQNKRLKVAYA 77

                ....
gi 11072029 255 RPGG 258
Cdd:cd12649  78 RPGG 81
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
184-254 1.12e-04

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 40.67  E-value: 1.12e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVReTPCKREQR---------FVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12318   2 TLFVKNLNFKTTEEALKKHFEKCGPIRSVT-IAKKKDPKgpllsmgygFVEFKSPEAAQKALKQLQGTVLDGHALELKIS 80
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
194-255 1.22e-04

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 41.07  E-value: 1.22e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11072029 194 VSSSTLRHIFQVYGEVKQVR-----ETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12236  13 TTESKLRREFEKYGPIKRVRlvrdkKTGKSRGYAFIEFEHERDMKAAYKHADGKKIDGRRVLVDVER 79
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
184-255 1.26e-04

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 40.51  E-value: 1.26e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029 184 SLVIMNLEP-TVSSSTLRHIFQVYGEVKQVRetpCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12233   1 TLFVVGFDPgTTREEDIEKLFEPFGPLVRCD---IRKTFAFVEFEDSEDATKALEALHGSRIDGSVLTVEFVK 70
RRM4_Prp24 cd12299
RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
184-247 1.55e-04

RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM4 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409740 [Multi-domain]  Cd Length: 71  Bit Score: 39.92  E-value: 1.55e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYG-EVKQVRETPCKrEQRFVEFFDVRDAAKALRVMNGKVISGK 247
Cdd:cd12299   2 TIGLFNLSDTVNEEQIRAFFEKIGpDIRKILLVPDH-EGALVEFEDESDAGKASLSLDGSQFQGK 65
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
189-247 2.56e-04

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 39.51  E-value: 2.56e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 11072029 189 NLEPTVSSSTLRHIFQVYGEVKQVrETPCKREQR------FVEFFDVRDAAKALRVMNGKVISGK 247
Cdd:cd12347   5 GLAEEVDEKVLHAAFIPFGDIVDI-QIPLDYETEkhrgfaFVEFEEAEDAAAAIDNMNESELFGR 68
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
189-248 2.61e-04

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 39.57  E-value: 2.61e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 189 NLEPTVSSSTLRHIFQVYGEVKQVRETPCKrEQRFVEFFDVRDAAKALRVMNGKVISGKP 248
Cdd:cd12354   7 NITKGLTEALLQQTFSPFGQILEVRVFPDK-GYAFIRFDSHEAATHAIVSVNGTIINGQA 65
RRM1_TIAR cd12616
RNA recognition motif 1 (RRM1) found in nucleolysin TIAR and similar proteins; This subgroup ...
184-254 3.00e-04

RNA recognition motif 1 (RRM1) found in nucleolysin TIAR and similar proteins; This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410028 [Multi-domain]  Cd Length: 81  Bit Score: 39.69  E-value: 3.00e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYG---EVKQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12616   1 TLYVGNLSRDVTEVLILQLFSQIGpckSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA 74
RRM_SF3B14 cd12241
RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar ...
185-253 3.24e-04

RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins; This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409687 [Multi-domain]  Cd Length: 77  Bit Score: 39.53  E-value: 3.24e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVR--ETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQF 253
Cdd:cd12241   5 LYVRNLPYKISSEELYDLFGKYGAIRQIRigNTKETRGTAFVVYEDIFDAKNACDHLSGFNVCNRYLVVLY 75
RRM2_PTBP1_hnRNPL_like cd12422
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
185-260 3.27e-04

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs.


Pssm-ID: 409856 [Multi-domain]  Cd Length: 85  Bit Score: 39.48  E-value: 3.27e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 185 LVIM-NLEPTVSSSTLRHIFQVYGEV-KQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGK--PMVIQFSRPGGLT 260
Cdd:cd12422   3 LVTVtNLLYPVTVDVLHQVFSPYGAVeKIVIFEKGTGVQALVQFDSVESAEAAKKALNGRNIYDGccTLDIQFSRLKELT 82
RRM_SRSF10 cd12559
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and ...
184-255 3.52e-04

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins; This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 409975 [Multi-domain]  Cd Length: 95  Bit Score: 39.66  E-value: 3.52e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVReTPCKREQR------FVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12559   7 SLFVRNVADDTRSEDLRREFGRYGPIVDVY-VPLDFYTRrprgfaYVQFEDVRDAEDALHNLDRKWICGRQIEIQFAQ 83
RRM1_SRSF5 cd12595
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 ...
187-255 3.81e-04

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 (SRSF5); This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain.


Pssm-ID: 410008 [Multi-domain]  Cd Length: 70  Bit Score: 39.16  E-value: 3.81e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 11072029 187 IMNLEPTVSSSTLRHIFQVYGevkQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12595   4 IGRLNPAAREKDVERFFKGYG---RIRDIDLKRGFGFVEFEDPRDADDAVYELDGKELCNERVTIEHAR 69
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
187-248 4.09e-04

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 39.17  E-value: 4.09e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 11072029 187 IMNLEPTVSSSTLRHIFQVYGEVKQVReTPCKREQR---------FVEFFDVRDAAKALRvMNGKVISGKP 248
Cdd:cd12298   5 VRNLDFELDEEALRGIFEKFGEIESIN-IPKKQKNRkgrhnngfaFVTFEDADSAESALQ-LNGTLLDNRK 73
RRM_5 pfam13893
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
171-265 4.23e-04

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins.


Pssm-ID: 433561 [Multi-domain]  Cd Length: 125  Bit Score: 40.16  E-value: 4.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029   171 PQLNAVPEGnnqGSLVIMNLEP-TVSSSTLRHIFQVYGEVKQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPM 249
Cdd:pfam13893  18 PGAAGVAGN---SVLMVYGLNPdRVNCDKLFNLFCLYGNVARVKFMKNKKGTAMVQMGDASQVQRAIQHLNGHPLFGKRL 94
                          90
                  ....*....|....*.
gi 11072029   250 VIQFSRPGGLTKKLFF 265
Cdd:pfam13893  95 QIILSKQQAVSYALPF 110
RRM_snRNP35 cd12237
RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein ...
179-255 4.51e-04

RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.


Pssm-ID: 409683 [Multi-domain]  Cd Length: 94  Bit Score: 39.62  E-value: 4.51e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 179 GNNQGSLVIMNLEPTVSSSTLRHIFQVYGEVKQVR-----ETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQF 253
Cdd:cd12237   1 GDPRLTLFVGRLSLQTTEEKLKEVFSRYGDIRRLRlvrdiVTGFSKRYAFIEYKEERDALHAYRDAKKLVIDQYEIFVDF 80

                ..
gi 11072029 254 SR 255
Cdd:cd12237  81 EC 82
RRM1_TIA1 cd12615
RNA recognition motif 1 (RRM1) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
184-254 4.88e-04

RNA recognition motif 1 (RRM1) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410027 [Multi-domain]  Cd Length: 74  Bit Score: 38.86  E-value: 4.88e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYG---EVKQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12615   1 TLYVGNLSRDVTEALILQLFSQIGpckNCKMIMDTAGNDPYCFVEFHEHRHAAAALAAMNGRKIMGKEVKVNWA 74
RRM_U2AF35B cd12539
RNA recognition motif (RRM) found in splicing factor U2AF 35 kDa subunit B (U2AF35B); This ...
223-254 5.18e-04

RNA recognition motif (RRM) found in splicing factor U2AF 35 kDa subunit B (U2AF35B); This subgroup corresponds to the RRM of U2AF35B, also termed zinc finger CCCH domain-containing protein 60 (C3H60), which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. Members in this family are mainly found in plant. They show high sequence homology to vertebrates U2AF35 that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. U2AF35B contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants.


Pssm-ID: 409955 [Multi-domain]  Cd Length: 102  Bit Score: 39.30  E-value: 5.18e-04
                        10        20        30
                ....*....|....*....|....*....|..
gi 11072029 223 FVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12539  70 YVKFRDEEHAAAALKALQGRFYAGRPIIVEFS 101
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
183-249 5.58e-04

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 409816 [Multi-domain]  Cd Length: 80  Bit Score: 38.93  E-value: 5.58e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11072029 183 GSLVIMNLEPTVSSSTLRHIFQVYGEVKQV-----RETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPM 249
Cdd:cd12382   2 GKLFIGGLNTETNEKALEAVFGKYGRIVEVllmkdRETNKSRGFAFVTFESPADAKDAARDMNGKELDGKAI 73
RRM_SKAR cd12681
RNA recognition motif (RRM) found in S6K1 Aly/REF-like target (SKAR) and similar proteins; ...
185-249 5.82e-04

RNA recognition motif (RRM) found in S6K1 Aly/REF-like target (SKAR) and similar proteins; This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410082 [Multi-domain]  Cd Length: 69  Bit Score: 38.41  E-value: 5.82e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVR-ETPCKREqrfVEFFDVRDAAKALRVMNGKVISGKPM 249
Cdd:cd12681   3 LTVSNLHPSVTEDDIVELFSVIGALKRARlVRPGVAE---VVYVRREDAITAIKKYNNRELDGQPM 65
RRM_RBM42 cd12383
RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This ...
189-255 5.92e-04

RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409817 [Multi-domain]  Cd Length: 83  Bit Score: 38.80  E-value: 5.92e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11072029 189 NLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQR-----FVEFFDVRDAAKALRVMNGKVISGKPmvIQFSR 255
Cdd:cd12383  13 DLGNEVTDEVLARAFSKYPSFQKAKVIRDKRTGKskgygFVSFKDPNDYLKALREMNGKYVGNRP--IKLRK 82
RRM3_PTBP1_like cd12423
RNA recognition motif 3 (RRM3) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...
185-255 7.46e-04

RNA recognition motif 3 (RRM3) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409857 [Multi-domain]  Cd Length: 74  Bit Score: 38.37  E-value: 7.46e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11072029 185 LVIMNL-EPTVSSSTLRHIFQVYGEVKQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12423   2 LLVSNLnEEMVTPDALFTLFGVYGDVLRVKILFNKKDTALIQMADPQQAQTALQHLNGIKLFGKPIRVTLSK 73
RRM1_SRSF6 cd12596
RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 6 ...
187-255 7.58e-04

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6); This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides.


Pssm-ID: 410009 [Multi-domain]  Cd Length: 72  Bit Score: 38.40  E-value: 7.58e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 11072029 187 IMNLEPTVSSSTLRHIFQVYGevkQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12596   6 IGRLSYHVREKDIQRFFSGYG---KLLEVDLKNGYGFVEFEDSRDADDAVYELNGKELCGERVIVEHAR 71
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
189-247 7.70e-04

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 38.42  E-value: 7.70e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11072029 189 NLEPTVSSSTLRHIFQVYGEVKQV-----RETpckREQR---FVEFFDVRDAAKALRVMNGKVISGK 247
Cdd:cd12393   8 NLPFSLTNNDLHQIFSKYGKVVKVtilkdKET---RKSKgvaFVLFLDRESAHNAVRAMNNKELFGR 71
RRM1_SHARP cd12348
RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
185-235 7.72e-04

RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409784 [Multi-domain]  Cd Length: 75  Bit Score: 38.36  E-value: 7.72e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQR----FVEFFDVRDAAKA 235
Cdd:cd12348   2 LWVGNLPENVREEKIIEHFKRFGRVESVKILPKRGSEGgvaaFVDFVDIKSAQKA 56
RRM1_MEI2_fungi cd12525
RNA recognition motif 1 (RRM1) found in fungal Mei2-like proteins; This subgroup corresponds ...
77-137 7.90e-04

RNA recognition motif 1 (RRM1) found in fungal Mei2-like proteins; This subgroup corresponds to the RRM1 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif.


Pssm-ID: 409945 [Multi-domain]  Cd Length: 91  Bit Score: 38.53  E-value: 7.90e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11072029  77 TPTRAVMLLQVPATVTETSLRRDMELFGEVRGVQMER-AHEGIVIFHFYNLINSQRAFNEIR 137
Cdd:cd12525   5 VPTRYLKVTGVPKDVSTSNLKEIFEKMGDVKGIFVKKlLSKGIVIVSFHDLRQAIKAYKDLQ 66
RRM2_MEI2_fungi cd12528
RNA recognition motif 2 (RRM2) found in fungal Mei2-like proteins; This subgroup corresponds ...
178-244 8.55e-04

RNA recognition motif 2 (RRM2) found in fungal Mei2-like proteins; This subgroup corresponds to the RRM2 of fungal Mei2-like proteins.The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif.


Pssm-ID: 240972 [Multi-domain]  Cd Length: 81  Bit Score: 38.24  E-value: 8.55e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 178 EGNNQGSLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKRE---QRFVEFFDVRDAAKALRVMNGKVI 244
Cdd:cd12528   4 EGQILISVQGDSHNSDLVKNSLQNLLSTFGDLKAFKSLPSQQDnvkEFICEFFDTRDADNAVDELNGRVV 73
RRM1_SECp43_like cd12344
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
190-248 8.57e-04

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 409780 [Multi-domain]  Cd Length: 82  Bit Score: 38.44  E-value: 8.57e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11072029 190 LEPTVSSSTLRHIFQVYGE----VKQVREtpcKREQR-----FVEFFDVRDAAKALRVMNGKVISGKP 248
Cdd:cd12344   7 LEPWMDEAYISSCFAKTGEevvsVKIIRN---KQTGKsagycFVEFATQEAAEQALEHLNGKPIPNTQ 71
RRM1_CoAA cd12608
RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator ...
185-254 9.91e-04

RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator/modulator (CoAA); This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs.


Pssm-ID: 410020 [Multi-domain]  Cd Length: 69  Bit Score: 37.86  E-value: 9.91e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVretPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12608   3 IFVGNVDEDTSQEELSALFEPYGAVLSC---AVMKQFAFVHMRGEAAADRAIRELNGRELHGRALVVEES 69
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
184-254 1.09e-03

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 37.80  E-value: 1.09e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVR-----ETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12447   1 TLFVGGLSWNVDDPWLKKEFEKYGGVISARvitdrGSGRSKGYGYVDFATPEAAQKALAAMSGKEIDGRQINVDFS 76
RRM1_SNF cd12476
RNA recognition motif 1 (RRM1) found in Drosophila melanogaster sex determination protein SNF ...
184-255 1.16e-03

RNA recognition motif 1 (RRM1) found in Drosophila melanogaster sex determination protein SNF and similar proteins; This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently.


Pssm-ID: 409905 [Multi-domain]  Cd Length: 85  Bit Score: 37.97  E-value: 1.16e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11072029 184 SLVIMNLEPTVSSSTLRH----IFQVYGEVKQV--RETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12476   8 TIYINNLNEKVKKEELKKslyaIFSQFGQILDIvaLKTLKMRGQAFVIFKDISSATNALRSMQGFPFYDKPMRIAYSK 85
RRM2_U1A_like cd12247
RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily ...
185-252 1.22e-03

RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding.


Pssm-ID: 409693 [Multi-domain]  Cd Length: 72  Bit Score: 37.54  E-value: 1.22e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPcKREQRFVEFFDVRDAAKALRVMNG-KVISGKPMVIQ 252
Cdd:cd12247   5 LFLQNLPEETTKEMLEMLFNQFPGFKEVRLVP-RRGIAFVEFETEEQATVALQALQGfKITPGHAMKIS 72
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
183-251 1.22e-03

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 37.78  E-value: 1.22e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 11072029 183 GSLVIMNLEPTVSSSTLRHIFQVYGEVKQV-----RETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVI 251
Cdd:cd12566   3 GRLFLRNLPYSTKEDDLQKLFSKFGEVSEVhvpidKKTKKSKGFAYVLFLDPEDAVQAYNELDGKVFQGRLIHI 76
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
184-241 1.22e-03

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 37.49  E-value: 1.22e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQV-----RETPCKREQRFVEFFDVRDAAKALRVMNG 241
Cdd:cd12408   1 TIRVTNLSEDATEEDLRELFRPFGPISRVylakdKETGQSKGFAFVTFETREDAERAIEKLNG 63
RRM2_SECp43_like cd12345
RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
184-249 1.28e-03

RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 409781 [Multi-domain]  Cd Length: 80  Bit Score: 37.63  E-value: 1.28e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQ-VYGEVKQVR--ETPCKREQR---FVEFFDVRDAAKALRVMNGKVISGKPM 249
Cdd:cd12345   3 SLFVGDLAPDVTDYQLYETFSaRYPSVRGAKvvMDPVTGRSKgygFVRFGDESEQDRALTEMQGVYLGSRPI 74
RRM3_PTBP2 cd12696
RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 2 ...
173-255 1.40e-03

RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2); This subgroup corresponds to the RRM3 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410096 [Multi-domain]  Cd Length: 107  Bit Score: 38.43  E-value: 1.40e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 173 LNAVPEGNNqGSLVIMNL-EPTVSSSTLRHIFQVYGEVKQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVI 251
Cdd:cd12696   5 MPGVSAGGN-TVLLVSNLnEEMVTPQSLFTLFGVYGDVQRVKILYNKKDSALIQMADGNQSQLAMSHLNGQKMYGKIIRV 83

                ....
gi 11072029 252 QFSR 255
Cdd:cd12696  84 TLSK 87
RRM2_NGR1_NAM8_like cd12613
RNA recognition motif 2 (RRM2) found in yeast negative growth regulatory protein NGR1, yeast ...
184-251 1.41e-03

RNA recognition motif 2 (RRM2) found in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins; This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 410025 [Multi-domain]  Cd Length: 80  Bit Score: 37.49  E-value: 1.41e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQ-VYGEVKQVR-----ETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVI 251
Cdd:cd12613   3 SIFVGDLSPTTNESDLVSLFQsRFPSCKSAKimtdpVTGVSRGYGFVRFSDENDQQRALIEMQGKYCQGRPLRI 76
RRM3_Crp79_Mug28 cd21622
RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, ...
185-254 1.41e-03

RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the three RRM motif.


Pssm-ID: 410201 [Multi-domain]  Cd Length: 92  Bit Score: 38.12  E-value: 1.41e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11072029 185 LVIMNLEPTV--SSSTLRHIFQVYGEVKQ-----VRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd21622   6 LFVKNLDDTVitNKEDLEQLFSPFGQIVSsylatYPGTGISKGFGFVAFSKPEDAAKAKETLNGVMVGRKRIFVSYA 82
RRM4_MRD1 cd12319
RNA recognition motif 4 (RRM4) found in yeast multiple RNA-binding domain-containing protein 1 ...
223-255 1.84e-03

RNA recognition motif 4 (RRM4) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409758 [Multi-domain]  Cd Length: 84  Bit Score: 37.46  E-value: 1.84e-03
                        10        20        30
                ....*....|....*....|....*....|...
gi 11072029 223 FVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12319  51 FVGFKTKEQAQAALKAMDGFVLDGHKLEVKFSH 83
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
184-244 1.92e-03

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 37.17  E-value: 1.92e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029 184 SLVIMN--LEPTVSSSTLRHIFQVYGEVKQVRETPCKrEQRFVEFFDVRDAAKALRVMNGKVI 244
Cdd:cd12431   3 HLVVANggLGNGVSREQLLEVFEKYGTVEDIVMLPGK-PYSFVSFKSVEEAAKAYNALNGKEL 64
RRM_scw1_like cd12245
RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar ...
185-255 1.94e-03

RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar proteins; This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins.


Pssm-ID: 409691 [Multi-domain]  Cd Length: 79  Bit Score: 37.22  E-value: 1.94e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVR-----ETPCKreqrFVEFFDVRDAAKALRVMNGKVISGK---PMVIQFSR 255
Cdd:cd12245   5 LFVANLGPNVSEQELRQLFSRQPGFRRLRmhnkgGGPVC----FVEFEDVPFATQALNHLQGAILSSSdrgGIRIEYAK 79
RRM_occluded pfam16842
Occluded RNA-recognition motif; This family is an unusual, usually C-terminal, RNA-recognition ...
184-261 2.03e-03

Occluded RNA-recognition motif; This family is an unusual, usually C-terminal, RNA-recognition motif found in fungi. In yeast it is the fourth RRM domain on the essential splicing factor Prp24. Structurally, it has a non-canonical RRM fold with the expected beta-aloha-beta-beta-alpha-beta RRM-fold is flanked by N- and C-terminal alpha-helices. These two additional flanking alpha-helices occlude the beta-sheet face. The electropositive surface thereby presented is an alternative RNA-binding surface that allows both binding and unwinding of the U6 small nuclear RNA's internal stem loop, at least in vitro.


Pssm-ID: 465282 [Multi-domain]  Cd Length: 79  Bit Score: 37.10  E-value: 2.03e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 11072029   184 SLVIMNLEPTVSSSTLRHIFQVY-GEVKQVRETPcKREQRFVEFFDVRDAAKALRVMNGKVISGKpmVIQFSRPGGLTK 261
Cdd:pfam16842   3 TISLLPLPDTVNDARIRALVEEKeGPIVKIVLVP-DHQGAIVEFKDVADAGKASLALDGSEFEGR--KLRCGTVNDLKK 78
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
185-246 2.04e-03

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 40.95  E-value: 2.04e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11072029   185 LVIMNLEPTVSSSTLRHIFQVYGEVKQ--VRETPCKREQRF--VEFFDVRDAAKALRVMNGKVISG 246
Cdd:TIGR01628 181 LYVKNLDPSVNEDKLRELFAKFGEITSaaVMKDGSGRSRGFafVNFEKHEDAAKAVEEMNGKKIGL 246
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
185-256 2.18e-03

RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins; PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 37.01  E-value: 2.18e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQV-----RETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd21609   2 LYVGNIPRNVTSEELAKIFEEAGTVEIAevmydRYTGRSRGFGFVTMGSVEDAKAAIEKLNGTEVGGREIKVNITEK 78
RRM2_FCA cd12637
RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar ...
185-256 2.43e-03

RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain.


Pssm-ID: 410045 [Multi-domain]  Cd Length: 81  Bit Score: 36.97  E-value: 2.43e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQV-----RETPCKREQRFVEFFDVRDAAKALRVMNGKVISG---KPMVIQFSRP 256
Cdd:cd12637   2 LFVGSLPKTATEQEVRDLFEAYGEVEEVylmkdPVTQQGTGCAFVKFAYKEEALAAIRSLNGTVTFDgcsRPVEVRFAES 81
RRM_SRSF7 cd12646
RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 7 (SRSF7); ...
189-254 2.44e-03

RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 7 (SRSF7); This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 410050 [Multi-domain]  Cd Length: 77  Bit Score: 36.86  E-value: 2.44e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 11072029 189 NLEPTVSSSTLRHIFQVYGEVKQV---RETPckrEQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12646   6 NLGTGAGKGELERAFSYYGPLRTVwiaRNPP---GFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS 71
RRM1_SRSF1 cd12597
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
179-255 2.48e-03

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides.


Pssm-ID: 410010 [Multi-domain]  Cd Length: 79  Bit Score: 37.13  E-value: 2.48e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 179 GNNQGSLVIMNLEPTVSSSTLRHIFQVYGEV-----KQVRETPckrEQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQF 253
Cdd:cd12597   1 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIrdidlKNRRGGP---PFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF 77

                ..
gi 11072029 254 SR 255
Cdd:cd12597  78 PR 79
RRM2_TIA1_like cd12353
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...
189-247 2.52e-03

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409789 [Multi-domain]  Cd Length: 75  Bit Score: 36.60  E-value: 2.52e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 11072029 189 NLEPTVSSSTLRHIFQVYGEV---KQVRETPCKREQ--RFVEFFDVRDAAKALRVMNGKVISGK 247
Cdd:cd12353   6 DLSPEIETEDLKEAFAPFGEIsdaRVVKDTQTGKSKgyGFVSFVKKEDAENAIQGMNGQWLGGR 69
RRM1_HuR cd12769
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen R (HuR); This subgroup ...
182-256 2.57e-03

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen R (HuR); This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410162 [Multi-domain]  Cd Length: 82  Bit Score: 36.94  E-value: 2.57e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 182 QGSLVIMNLEP-TVSSSTLRHIFQVYGEV---KQVRETPCKRE--QRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12769   1 GRTNLIVNYLPqNMTQDELRSLFSSIGEVesaKLIRDKVAGHSlgYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR 80

                .
gi 11072029 256 P 256
Cdd:cd12769  81 P 81
RRM1_HuB cd12771
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup ...
180-256 2.76e-03

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410164 [Multi-domain]  Cd Length: 83  Bit Score: 37.01  E-value: 2.76e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 180 NNQGSLVIMNLEPTVSSSTLRHIFQVYGEV---KQVRE--TPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12771   2 DSKTNLIVNYLPQNMTQEELKSLFGSIGEIescKLVRDkiTGQSLGYGFVNYIEPKDAEKAINTLNGLRLQTKTIKVSYA 81

                ..
gi 11072029 255 RP 256
Cdd:cd12771  82 RP 83
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
184-255 2.86e-03

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 36.61  E-value: 2.86e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPcKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12262   5 NVYVGNLDDSLTEEEIRGILEKYGEIESIKILK-EKNCAFVNYLNIANAIKAVQELPIKNPKFKKVRINYGK 75
RRM2_RBM15B cd12556
RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from ...
177-255 2.97e-03

RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate; This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.


Pssm-ID: 409972 [Multi-domain]  Cd Length: 85  Bit Score: 36.82  E-value: 2.97e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 11072029 177 PEGNNQGS--LVIMNLEPTVSSSTLRHIFQVYGEVKQVretPCKREQR-------FVEFFDVRDAAKALRVMNGKVISGK 247
Cdd:cd12556   1 PEDDQRATrnLFIGNLDHNVSEVELRRAFEKYGIIEEV---VIKRPARgqggayaFLKFQNLDMAHRAKVAMSGRVIGRN 77

                ....*...
gi 11072029 248 PMVIQFSR 255
Cdd:cd12556  78 PIKIGYGK 85
RRM1_U1A cd12477
RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A); ...
184-255 3.55e-03

RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A); This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import.


Pssm-ID: 409906 [Multi-domain]  Cd Length: 89  Bit Score: 36.88  E-value: 3.55e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11072029 184 SLVIMNLEPTVSSSTLRH----IFQVYGEVKQ--VRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12477   5 TIYINNLNEKIKKDELKKslhaIFSRFGQILDilVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK 82
RRM2_MRN1 cd12523
RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This ...
79-136 4.01e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409943 [Multi-domain]  Cd Length: 78  Bit Score: 36.26  E-value: 4.01e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 11072029  79 TRAVMLLQVPATVTETSLRRDMELFGEVRGVQMERaHEGIVIFHFYNLINSQRAFNEI 136
Cdd:cd12523   3 SRNVYLGNLPESITEEELREDLEKFGPIDQIKIVK-EKNIAFVHFLSIANAIKVVTTL 59
RRM3_ROD1 cd12697
RNA recognition motif 3 (RRM3) found in vertebrate regulator of differentiation 1 (Rod1); This ...
185-255 4.18e-03

RNA recognition motif 3 (RRM3) found in vertebrate regulator of differentiation 1 (Rod1); This subgroup corresponds to the RRM3 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities.


Pssm-ID: 410097 [Multi-domain]  Cd Length: 76  Bit Score: 36.10  E-value: 4.18e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 11072029 185 LVIMNLEP-TVSSSTLRHIFQVYGEVKQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12697   3 LLVSNLNPdAITPHGLFILFGVYGDVLRVKIMFNKKENALVQMADATQAQIAMSHLNGQRLYGKVLRATLSK 74
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
184-256 5.69e-03

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 35.90  E-value: 5.69e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQ--VRETPCKREQR---FVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRP 256
Cdd:cd12674   2 TLFVRNLPFDVTLESLTDFFSDIGPVKHavVVTDPETKKSRgygFVSFSTHDDAEEALAKLKNRKLSGHILKLDFAKP 79
RRM2_Nop4p cd12675
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
185-254 6.27e-03

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410076 [Multi-domain]  Cd Length: 83  Bit Score: 35.92  E-value: 6.27e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11072029 185 LVIMNLEPTVSS-STLRHIFQVYGEVKQVrETPCKREQR-----FVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12675   3 LIIRNLPWSIKKpVHLKKLFGRYGKVVEA-TIPRKKGGKlsgfaFVTMKGRKNAEEALESVNGLEIDGRPVAVDWA 77
RRM2_SHARP cd12349
RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and ...
185-252 6.39e-03

RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins; This subfamily corresponds to the RRM2 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins.


Pssm-ID: 409785 [Multi-domain]  Cd Length: 74  Bit Score: 35.46  E-value: 6.39e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 11072029 185 LVIMNLEPTVSSSTLR----HIFQVYGEVKQVReTPCKREQRF--VEFFDVRDAAKALRVMNGKVISGKPMVIQ 252
Cdd:cd12349   2 IKVRNLPVRSSDTSLKdglfHEFKKHGKVTSVK-VHGQGEERYaiVFFRRPEDAEKALEVSKGKLFFGMQIEVT 74
RRM_SRSF3 cd12645
RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 3 (SRSF3); ...
189-254 6.68e-03

RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 3 (SRSF3); This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.


Pssm-ID: 241089 [Multi-domain]  Cd Length: 81  Bit Score: 35.79  E-value: 6.68e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11072029 189 NLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFS 254
Cdd:cd12645  11 NLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS 76
RRM2_RBM15 cd12555
RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This ...
184-255 6.81e-03

RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15); This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties.


Pssm-ID: 409971 [Multi-domain]  Cd Length: 87  Bit Score: 35.99  E-value: 6.81e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQR----FVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12555   9 TLFLGNLDITVTENDLRRAFDRFGVITEVDIKRPGRGQTstygFLKFENLDMAHRAKLAMSGKVIGRNPIKIGYGK 84
RRM_SRSF12 cd12560
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 12 (SRSF12) and ...
184-255 7.42e-03

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins; This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.


Pssm-ID: 409976 [Multi-domain]  Cd Length: 84  Bit Score: 35.75  E-value: 7.42e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11072029 184 SLVIMNLEPTVSSSTLRHIFQVYGEVKQVR-----ETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSR 255
Cdd:cd12560   2 SLFVRNVADATRPEDLRREFGRYGPIVDVYipldfYNRRPRGFAYIQFEDVRDAEDALYNLNRKWVCGRQIEIQFAQ 78
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
189-249 7.76e-03

RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409825 [Multi-domain]  Cd Length: 72  Bit Score: 35.28  E-value: 7.76e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 11072029 189 NLEPTVSSSTLRHIFQVYGEVKQVReTPCKREQRF-----VEFFDVRDAAKALRvMNGKVISGKPM 249
Cdd:cd12391   6 NLDYSVPEDKIREIFSGCGEITDVR-LVKNYKGKSkgycyVEFKDEESAQKALK-LDRQPVEGRPM 69
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
189-253 8.26e-03

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues.


Pssm-ID: 409775 [Multi-domain]  Cd Length: 72  Bit Score: 35.42  E-value: 8.26e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 11072029 189 NLEPTVSSSTLRHIFQVYGEVKQV--RETPCKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQF 253
Cdd:cd12338   6 NLPGDIRERDIEDLFYKYGPILAIdlKNRRRGPPFAFVEFEDPRDAEDAIRGRDGYDFDGYRLRVEF 72
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
185-252 9.46e-03

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 34.90  E-value: 9.46e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPCKREQR-----FVEFFDVRDAAKALRVMNGKVISGKPMVIQ 252
Cdd:cd12362   1 LFVYHLPNEFTDQDLYQLFAPFGNVVSAKVFVDKNTGRskgfgFVSYDNPLSAQAAIKAMNGFQVGGKRLKVQ 73
RRM1_VICKZ cd12358
RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds ...
185-257 9.95e-03

RNA recognition motif 1 (RRM1) found in the VICKZ family proteins; Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains.


Pssm-ID: 240804 [Multi-domain]  Cd Length: 73  Bit Score: 35.04  E-value: 9.95e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 11072029 185 LVIMNLEPTVSSSTLRHIFQVYGEVKQVRETPcKREQRFVEFFDVRDAAKALRVMNGKVISGKPMVIQFSRPG 257
Cdd:cd12358   1 LYIGNLSSDVNESDLRQLFEEHKIPVSSVLVK-KGGYAFVDCPDQSWADKAIEKLNGKILQGKVIEVEHSVPK 72
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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