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Conserved domains on  [gi|262527218|ref|NP_001155288|]
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RNA binding motif protein 10-like [Mus musculus]

Protein Classification

G patch domain-containing protein; zinc finger Ran-binding domain-containing protein( domain architecture ID 10986442)

G patch domain-containing protein similar to Saccharomyces cerevisiae protein PXR1 that is involved in rRNA-processing at A0, A1 and A2 sites through its action in U18 and U24 snoRNA 3'-end final trimming, and pre-mRNA-splicing factor SPP382 that is involved in pre-mRNA splicing and spliceosome disassembly| zinc finger Ran-binding domain-containing protein similar to Homo sapiens zinc finger Ran-binding domain-containing protein 2 (ZRANB2) that regulates alternative splicing via a direct interaction with pre-mRNA at sites that resemble the consensus 5' splice site

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM2_RBM10 cd12754
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This ...
221-307 1.13e-54

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM2 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


:

Pssm-ID: 410148 [Multi-domain]  Cd Length: 87  Bit Score: 183.29  E-value: 1.13e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 221 ASDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 300
Cdd:cd12754    1 ANDTIILRNLNPHSTMDSILSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 80

                 ....*..
gi 262527218 301 NVEFAKG 307
Cdd:cd12754   81 NVEFAKG 87
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
67-134 8.14e-39

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).


The actual alignment was detected with superfamily member cd12753:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 84  Bit Score: 138.53  E-value: 8.14e-39
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 262527218  67 EIRGQLKSHGVKAREVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEANQHSLNILGQKVSMHYSDPNP 134
Cdd:cd12753   17 DIRGQLQAHGVQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLTILGQKVSMHYSDPKP 84
OCRE_RBM10 cd16167
OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G ...
486-549 1.94e-29

OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), is a paralogue of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.


:

Pssm-ID: 293886  Cd Length: 64  Bit Score: 111.31  E-value: 1.94e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 262527218 486 YPVPDVSTYQYDETSGYYYDSQTGLYYDPNYQYYYNAQSQQYLYWDGEWRTYIPALEQSADGHK 549
Cdd:cd16167    1 YPVPDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQTQQYLYWDGERRTYVPASEQGADGHK 64
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
780-824 1.18e-17

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


:

Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 77.16  E-value: 1.18e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 262527218  780 SDNIGSRMLQAMGWKEGSGLGRKKQGIVTPIEAQTRVPGSGLGAR 824
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
140-162 2.31e-07

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


:

Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 47.31  E-value: 2.31e-07
                           10        20
                   ....*....|....*....|...
gi 262527218   140 WLCNKCGVQNFKRREKCFKCGMP 162
Cdd:smart00547   3 WECPACTFLNFASRSKCFACGAP 25
 
Name Accession Description Interval E-value
RRM2_RBM10 cd12754
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This ...
221-307 1.13e-54

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM2 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 410148 [Multi-domain]  Cd Length: 87  Bit Score: 183.29  E-value: 1.13e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 221 ASDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 300
Cdd:cd12754    1 ANDTIILRNLNPHSTMDSILSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 80

                 ....*..
gi 262527218 301 NVEFAKG 307
Cdd:cd12754   81 NVEFAKG 87
RRM1_RBM10 cd12753
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This ...
67-134 8.14e-39

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 410147 [Multi-domain]  Cd Length: 84  Bit Score: 138.53  E-value: 8.14e-39
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 262527218  67 EIRGQLKSHGVKAREVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEANQHSLNILGQKVSMHYSDPNP 134
Cdd:cd12753   17 DIRGQLQAHGVQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLTILGQKVSMHYSDPKP 84
OCRE_RBM10 cd16167
OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G ...
486-549 1.94e-29

OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), is a paralogue of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 293886  Cd Length: 64  Bit Score: 111.31  E-value: 1.94e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 262527218 486 YPVPDVSTYQYDETSGYYYDSQTGLYYDPNYQYYYNAQSQQYLYWDGEWRTYIPALEQSADGHK 549
Cdd:cd16167    1 YPVPDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQTQQYLYWDGERRTYVPASEQGADGHK 64
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
780-824 1.18e-17

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 77.16  E-value: 1.18e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 262527218  780 SDNIGSRMLQAMGWKEGSGLGRKKQGIVTPIEAQTRVPGSGLGAR 824
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
778-823 3.95e-16

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 72.58  E-value: 3.95e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 262527218   778 LGSDNIGSRMLQAMGWKEGSGLGRKKQGIVTPIEAQTRVPGSGLGA 823
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGA 46
OCRE pfam17780
OCRE domain; The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with ...
490-540 2.95e-09

OCRE domain; The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts. The structure of the domain consists of an anti-parallel arrangement of six beta strands.


Pssm-ID: 465502  Cd Length: 51  Bit Score: 53.40  E-value: 2.95e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 262527218  490 DVSTYQYDETSGYYYDSQTGLYYDPNYQYYYNAQSQQYLYWDGEWRTYIPA 540
Cdd:pfam17780   1 DSSGYVYDEASGYYYDPTTGYYYDPNTGLYYDPATGKYYTYDEETKSYVPH 51
RRM smart00360
RNA recognition motif;
224-302 7.31e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 52.98  E-value: 7.31e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 262527218   224 TIILRNLNPHSTMDSILGALAPYAVLSSsnVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQAlhppLTIDGKTINV 302
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVES--VRLVRDKETGKSKGFAFVEFESEEDAEKALEALNG----KELDGRPLKV 73
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
224-306 9.54e-08

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 50.10  E-value: 9.54e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 224 TIILRNLNPHSTMDSILGALAPY-AVLSssnVRVIKDKQTQLNRGFAFIQLSTIVEAAqllQILQALHpPLTIDGKTINV 302
Cdd:COG0724    3 KIYVGNLPYSVTEEDLRELFSEYgEVTS---VKLITDRETGRSRGFGFVEMPDDEEAQ---AAIEALN-GAELMGRTLKV 75

                 ....
gi 262527218 303 EFAK 306
Cdd:COG0724   76 NEAR 79
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
140-162 2.31e-07

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 47.31  E-value: 2.31e-07
                           10        20
                   ....*....|....*....|...
gi 262527218   140 WLCNKCGVQNFKRREKCFKCGMP 162
Cdd:smart00547   3 WECPACTFLNFASRSKCFACGAP 25
RRM smart00360
RNA recognition motif;
67-125 1.71e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 43.35  E-value: 1.71e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 262527218    67 EIRGQLKSHGvKAREVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEANqHSLNILGQKV 125
Cdd:smart00360  15 ELRELFSKFG-KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL-NGKELDGRPL 71
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
140-164 2.00e-05

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 41.95  E-value: 2.00e-05
                          10        20
                  ....*....|....*....|....*
gi 262527218  140 WLCNKCGVQNFKRREKCFKCGMPKS 164
Cdd:pfam00641   5 WDCSKCLVQNFATSTKCVACQAPKP 29
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
184-304 2.35e-04

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 44.16  E-value: 2.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218  184 GRRELSQGLLPQLQPYQAQGVLTSQA----LSQGSE-PSSENASDTIILRNLNPhSTMDSILGAL-APYAVLSssNVRVI 257
Cdd:TIGR01661 226 LAHQQQQHAVAQQHAAQRASPPATDGqtagLAAGAQiSASDGAGYCIFVYNLSP-DTDETVLWQLfGPFGAVQ--NVKII 302
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 262527218  258 KDKQTQLNRGFAFIQLSTIVEAAQLLQILQAlhppLTIDGKTINVEF 304
Cdd:TIGR01661 303 RDLTTNQCKGYGFVSMTNYDEAAMAILSLNG----YTLGNRVLQVSF 345
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
66-102 3.10e-03

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 37.38  E-value: 3.10e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 262527218  66 AEIRGQLKSHGvKAREVRLMRNKSSGQSQGFAFVEFS 102
Cdd:COG0724   16 EDLRELFSEYG-EVTSVKLITDRETGRSRGFGFVEMP 51
 
Name Accession Description Interval E-value
RRM2_RBM10 cd12754
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This ...
221-307 1.13e-54

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM2 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 410148 [Multi-domain]  Cd Length: 87  Bit Score: 183.29  E-value: 1.13e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 221 ASDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 300
Cdd:cd12754    1 ANDTIILRNLNPHSTMDSILSALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 80

                 ....*..
gi 262527218 301 NVEFAKG 307
Cdd:cd12754   81 NVEFAKG 87
RRM2_RBM5_like cd12562
RNA recognition motif 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; ...
221-306 1.56e-51

RNA recognition motif 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409978 [Multi-domain]  Cd Length: 86  Bit Score: 174.75  E-value: 1.56e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 221 ASDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTI 300
Cdd:cd12562    1 ANDTIILRNINPHTTVDSILGALAPYAVLSSSNVRLIKDKQTQLNRGFAFVQLSSPIEASQLLQILQSLHPPLTIDGKTI 80

                 ....*.
gi 262527218 301 NVEFAK 306
Cdd:cd12562   81 NVDFAK 86
RRM2_RBM5 cd12755
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup ...
222-306 5.15e-41

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM2 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.


Pssm-ID: 410149 [Multi-domain]  Cd Length: 86  Bit Score: 145.07  E-value: 5.15e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 222 SDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTIN 301
Cdd:cd12755    2 SDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSALEASQLLQILQSLHPPLKIDGKTIG 81

                 ....*
gi 262527218 302 VEFAK 306
Cdd:cd12755   82 VDFAK 86
RRM1_RBM10 cd12753
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This ...
67-134 8.14e-39

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 410147 [Multi-domain]  Cd Length: 84  Bit Score: 138.53  E-value: 8.14e-39
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 262527218  67 EIRGQLKSHGVKAREVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEANQHSLNILGQKVSMHYSDPNP 134
Cdd:cd12753   17 DIRGQLQAHGVQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLTILGQKVSMHYSDPKP 84
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
222-305 4.36e-31

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 116.60  E-value: 4.36e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 222 SDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTIN 301
Cdd:cd12313    2 TNVLILRGLDVLTTEEDILSALQAHADLPIKDVRLIRDKLTGTSRGFAFVEFSSLEDATQVMDALQNLLPPFKIDGRVVS 81

                 ....
gi 262527218 302 VEFA 305
Cdd:cd12313   82 VSYA 85
OCRE_RBM10 cd16167
OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G ...
486-549 1.94e-29

OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins; RBM10, also called G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), is a paralogue of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 293886  Cd Length: 64  Bit Score: 111.31  E-value: 1.94e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 262527218 486 YPVPDVSTYQYDETSGYYYDSQTGLYYDPNYQYYYNAQSQQYLYWDGEWRTYIPALEQSADGHK 549
Cdd:cd16167    1 YPVPDVSTYQYDETSGYYYDPQTGLYYDPNSQYYYNAQTQQYLYWDGERRTYVPASEQGADGHK 64
RRM1_RBM5_like cd12561
RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; ...
66-130 4.27e-29

RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409977 [Multi-domain]  Cd Length: 81  Bit Score: 110.92  E-value: 4.27e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 262527218  66 AEIRGQLKSHGVKAREVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEANQHSLNILGQKVSMHYS 130
Cdd:cd12561   17 EDIRNALVSHGVQPKDVRLMRRKTTGASRGFAFVEFMSLEEATRWMEANQGKLQLQGYKITLHYS 81
OCRE_RBM5 cd16168
OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins; RBM5 is also called ...
488-542 4.90e-22

OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins; RBM5 is also called protein G15, H37, putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9. It is a known modulator of apoptosis. It acts as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both of them specifically binds poly(G) RNA. RBM5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.


Pssm-ID: 293887  Cd Length: 56  Bit Score: 89.78  E-value: 4.90e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 262527218 488 VPDVSTYQYDETSGYYYDSQTGLYYDPNYQYYYNAQSQQYLYWDGEWRTYIPALE 542
Cdd:cd16168    2 VPDTSTYQYDESSGYYYDPITGLYYDPNSQYYYNSLTQQYLYWDGEKQTYLPAAE 56
OCRE_RBM5_like cd16162
OCRE domain found in RNA-binding protein RBM5, RBM10, and similar proteins; RBM5 is a known ...
487-540 1.83e-20

OCRE domain found in RNA-binding protein RBM5, RBM10, and similar proteins; RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing, and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 293881  Cd Length: 56  Bit Score: 85.44  E-value: 1.83e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 262527218 487 PVPDVSTYQYDETSGYYYDSQTGLYYDPNYQYYYNAQSQQYLYWDGEWRTYIPA 540
Cdd:cd16162    1 PPPDPSTYQYDETSGYYYDPTTGLYYDPNSQYFYNSQTQQYLYWDQTKKTYVPV 54
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
68-130 4.40e-20

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 85.40  E-value: 4.40e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 262527218  68 IRGQLKSH-GVKAREVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEANQHS---LNILGQKVSMHYS 130
Cdd:cd12313   19 ILSALQAHaDLPIKDVRLIRDKLTGTSRGFAFVEFSSLEDATQVMDALQNLlppFKIDGRVVSVSYA 85
RRM2_RBM6 cd12563
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup ...
222-307 8.82e-20

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6); This subgroup corresponds to the RRM2 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


Pssm-ID: 409979 [Multi-domain]  Cd Length: 87  Bit Score: 84.51  E-value: 8.82e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 222 SDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHPPLTIDGKTIN 301
Cdd:cd12563    2 SKTIMLKRIYRSTPPEVIVEVLEPYVRLTTANVRIIKNKTGPMGHTYGFIDLDSHAEALRLVKLLQNLDPPLYIDGRRVY 81

                 ....*.
gi 262527218 302 VEFAKG 307
Cdd:cd12563   82 VNVATG 87
RRM1_RBM5 cd12752
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup ...
66-132 3.09e-18

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM1 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.


Pssm-ID: 410146 [Multi-domain]  Cd Length: 87  Bit Score: 79.98  E-value: 3.09e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 262527218  66 AEIRGQLKS-HGVKAREVRLMRNKSsGQSQGFAFVEFSHLQDTTRWMEANQHSLNILGQKVSMHYSDP 132
Cdd:cd12752   20 NDIRELIESfEGPQPADVRLMKRKT-GVSRGFAFVEFYHLQDATSWMEANQKKLVIQGKTIAMHYSNP 86
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
780-824 1.18e-17

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 77.16  E-value: 1.18e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 262527218  780 SDNIGSRMLQAMGWKEGSGLGRKKQGIVTPIEAQTRVPGSGLGAR 824
Cdd:pfam01585   1 TSNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDRRGLGAE 45
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
778-823 3.95e-16

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 72.58  E-value: 3.95e-16
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 262527218   778 LGSDNIGSRMLQAMGWKEGSGLGRKKQGIVTPIEAQTRVPGSGLGA 823
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGA 46
OCRE pfam17780
OCRE domain; The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with ...
490-540 2.95e-09

OCRE domain; The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts. The structure of the domain consists of an anti-parallel arrangement of six beta strands.


Pssm-ID: 465502  Cd Length: 51  Bit Score: 53.40  E-value: 2.95e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 262527218  490 DVSTYQYDETSGYYYDSQTGLYYDPNYQYYYNAQSQQYLYWDGEWRTYIPA 540
Cdd:pfam17780   1 DSSGYVYDEASGYYYDPTTGYYYDPNTGLYYDPATGKYYTYDEETKSYVPH 51
RRM smart00360
RNA recognition motif;
224-302 7.31e-09

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 52.98  E-value: 7.31e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 262527218   224 TIILRNLNPHSTMDSILGALAPYAVLSSsnVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQAlhppLTIDGKTINV 302
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVES--VRLVRDKETGKSKGFAFVEFESEEDAEKALEALNG----KELDGRPLKV 73
G-patch_2 pfam12656
G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ...
781-827 7.97e-09

G-patch domain; Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ATP-dependent DExH-box splicing factor Prp2. As this interaction involves the G-patch sequence in Spp2 and is required for the recruitment of Prp2 to the spliceosome before the first catalytic step of splicing, it is proposed that Spp2 might be an accessory factor that confers spliceosome specificity on Prp2.


Pssm-ID: 432700 [Multi-domain]  Cd Length: 61  Bit Score: 52.67  E-value: 7.97e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 262527218  781 DNIGSRMLQAMGWKEGSGLGRKKQGIVTPIEAQTRVPGSGLGARGSS 827
Cdd:pfam12656  15 EEFGAAMLRGMGWKPGQGIGKNKKGDVKPKEYKRRPGGLGLGAKPAE 61
OCRE cd16074
OCRE domain; The OCRE (OCtamer REpeat) domain contains 5 repeats of an 8-residue motif, which ...
489-539 4.88e-08

OCRE domain; The OCRE (OCtamer REpeat) domain contains 5 repeats of an 8-residue motif, which were shown to form beta-strands. Based on the architectures of proteins containing OCRE domains, a role in RNA metabolism and/or signalling has been proposed.


Pssm-ID: 293880  Cd Length: 54  Bit Score: 49.98  E-value: 4.88e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 262527218 489 PDVSTYQYDETSGYYYDSQTGLYYDPNYQYYYNAQSQQYLYWDGEWRTYIP 539
Cdd:cd16074    3 PDPSGFVFDPNSGYYYDPSTGLYYDPNTGYYYDPTSGTYYIWDDELGAYVP 53
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
224-306 9.54e-08

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 50.10  E-value: 9.54e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 224 TIILRNLNPHSTMDSILGALAPY-AVLSssnVRVIKDKQTQLNRGFAFIQLSTIVEAAqllQILQALHpPLTIDGKTINV 302
Cdd:COG0724    3 KIYVGNLPYSVTEEDLRELFSEYgEVTS---VKLITDRETGRSRGFGFVEMPDDEEAQ---AAIEALN-GAELMGRTLKV 75

                 ....
gi 262527218 303 EFAK 306
Cdd:COG0724   76 NEAR 79
RRM1_RBM5_like cd12561
RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; ...
221-279 1.94e-07

RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409977 [Multi-domain]  Cd Length: 81  Bit Score: 49.29  E-value: 1.94e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 262527218 221 ASDTIILRNLNPHSTMDSILGALAPYAVlSSSNVRVIKDKQTQLNRGFAFIQLSTIVEA 279
Cdd:cd12561    1 PNNTIMLRGLPLSVTEEDIRNALVSHGV-QPKDVRLMRRKTTGASRGFAFVEFMSLEEA 58
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
140-162 2.31e-07

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 47.31  E-value: 2.31e-07
                           10        20
                   ....*....|....*....|...
gi 262527218   140 WLCNKCGVQNFKRREKCFKCGMP 162
Cdd:smart00547   3 WECPACTFLNFASRSKCFACGAP 25
RRM1_RBM6 cd12314
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This ...
76-129 7.75e-07

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6); This subfamily corresponds to the RRM1 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.


Pssm-ID: 409753 [Multi-domain]  Cd Length: 78  Bit Score: 47.57  E-value: 7.75e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 262527218  76 GVKAREVRLmRNKSSGQSQGFAFVEFSHLQDTTRWMEANQHSLNILGQKVSMHY 129
Cdd:cd12314   26 GMPVKNLKL-KNYVPGYDYDYVCVEFSLLEDAIGCMEANQGTLKIGTKEVTLEY 78
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
225-303 3.36e-06

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: 45.35  E-value: 3.36e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 262527218 225 IILRNLNPHSTMDSILGALAPYAVLSSsnVRVIKDKQTQlNRGFAFIQLSTIVEAAQLLQILQAlhppLTIDGKTINVE 303
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVS--VRIVRDRDGK-SKGFAFVEFESPEDAEKALEALNG----TELGGRPLKVS 72
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
229-305 1.44e-05

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: 1.44e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 262527218 229 NLNPHSTMDSILGALAPY-AVLSssnVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQAlhppLTIDGKTINVEFA 305
Cdd:cd21608    6 NLSWDTTEDDLRDLFSEFgEVES---AKVITDRETGRSRGFGFVTFSTAEAAEAAIDALNG----KELDGRSIVVNEA 76
RRM1_RBM10 cd12753
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This ...
222-305 1.60e-05

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 410147 [Multi-domain]  Cd Length: 84  Bit Score: 43.77  E-value: 1.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 222 SDTIILRNLNPHSTMDSILGALAPYAVlSSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQAlhpPLTIDGKTIN 301
Cdd:cd12753    1 SNIIMLRMLPQSATENDIRGQLQAHGV-QPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQH---SLTILGQKVS 76

                 ....
gi 262527218 302 VEFA 305
Cdd:cd12753   77 MHYS 80
RRM smart00360
RNA recognition motif;
67-125 1.71e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 43.35  E-value: 1.71e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 262527218    67 EIRGQLKSHGvKAREVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEANqHSLNILGQKV 125
Cdd:smart00360  15 ELRELFSKFG-KVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL-NGKELDGRPL 71
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
140-164 2.00e-05

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 41.95  E-value: 2.00e-05
                          10        20
                  ....*....|....*....|....*
gi 262527218  140 WLCNKCGVQNFKRREKCFKCGMPKS 164
Cdd:pfam00641   5 WDCSKCLVQNFATSTKCVACQAPKP 29
OCRE_SUA_like cd16166
OCRE domain found in Suppressor of ABI3-5 (SUA) and similar proteins; SUA is an RNA-binding ...
491-540 3.61e-05

OCRE domain found in Suppressor of ABI3-5 (SUA) and similar proteins; SUA is an RNA-binding protein located in the nucleus and expressed in all plant tissues. It functions as a splicing factor that influences seed maturation by controlling alternative splicing of ABI3. The suppression of the cryptic ABI3 intron indicates a role of SUA in mRNA processing. SUA also interacts with the prespliceosomal component U2AF65, the larger subunit of the conserved pre-mRNA splicing factor U2AF. SUA contains two RNA recognition motifs surrounding a zinc finger domain, an OCtamer REpeat (OCRE) domain, and a Gly-rich domain close to the C-terminus.


Pssm-ID: 293885  Cd Length: 54  Bit Score: 41.90  E-value: 3.61e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 262527218 491 VSTYQYDETSGYYYDSQTGLYYDPNYQYYYNAQSQQYLYWDGEWRTYIPA 540
Cdd:cd16166    5 PSGFVYDPASGYYYDASSGYYYDANTGLYYDAASGRWYSYDEETGQYVEV 54
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
67-117 2.04e-04

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: 40.68  E-value: 2.04e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 262527218  67 EIRGQLKSHGvKAREVRLMRnKSSGQSQGFAFVEFSHLQDTTRWMEANQHS 117
Cdd:cd12320   16 EIRELFSPFG-QLKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEALKST 64
RRM3_Hu cd12377
RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to ...
224-304 2.23e-04

RNA recognition motif 3 (RRM3) found in the Hu proteins family; This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the 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. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein 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 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: 409811 [Multi-domain]  Cd Length: 76  Bit Score: 40.38  E-value: 2.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 224 TIILRNLNPHSTmDSILGAL-APYAVLSssNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQAlhppLTIDGKTINV 302
Cdd:cd12377    1 CIFVYNLAPDAD-ESLLWQLfGPFGAVQ--NVKIIRDFTTNKCKGYGFVTMTNYDEAAVAIASLNG----YRLGGRVLQV 73

                 ..
gi 262527218 303 EF 304
Cdd:cd12377   74 SF 75
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
184-304 2.35e-04

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 44.16  E-value: 2.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218  184 GRRELSQGLLPQLQPYQAQGVLTSQA----LSQGSE-PSSENASDTIILRNLNPhSTMDSILGAL-APYAVLSssNVRVI 257
Cdd:TIGR01661 226 LAHQQQQHAVAQQHAAQRASPPATDGqtagLAAGAQiSASDGAGYCIFVYNLSP-DTDETVLWQLfGPFGAVQ--NVKII 302
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 262527218  258 KDKQTQLNRGFAFIQLSTIVEAAQLLQILQAlhppLTIDGKTINVEF 304
Cdd:TIGR01661 303 RDLTTNQCKGYGFVSMTNYDEAAMAILSLNG----YTLGNRVLQVSF 345
RRM1_RBM5 cd12752
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup ...
219-305 3.03e-04

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM1 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.


Pssm-ID: 410146 [Multi-domain]  Cd Length: 87  Bit Score: 40.31  E-value: 3.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 219 ENASDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKdKQTQLNRGFAFIQLSTIVEAAQLLQILQALhppLTIDGK 298
Cdd:cd12752    2 EKESKTIMLRGLPINITENDIRELIESFEGPQPADVRLMK-RKTGVSRGFAFVEFYHLQDATSWMEANQKK---LVIQGK 77

                 ....*..
gi 262527218 299 TINVEFA 305
Cdd:cd12752   78 TIAMHYS 84
RRM1_RBM39_like cd12283
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
78-125 3.04e-04

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is 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: 409725 [Multi-domain]  Cd Length: 73  Bit Score: 39.91  E-value: 3.04e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 262527218  78 KAREVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEANQHSLniLGQKV 125
Cdd:cd12283   25 KVRDVRLIMDRNSRRSKGVAYVEFYDVESVPLALALTGQRL--LGQPI 70
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
253-305 3.29e-04

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: 40.11  E-value: 3.29e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 262527218 253 NVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHppltIDGKTINVEFA 305
Cdd:cd12447   28 SARVITDRGSGRSKGYGYVDFATPEAAQKALAAMSGKE----IDGRQINVDFS 76
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
252-308 3.66e-04

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: 39.77  E-value: 3.66e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 262527218 252 SNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQAlhppLTIDGKTINVEFAKGS 308
Cdd:cd12449   28 SEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNG----KSLDGRQIRVDQAGKS 80
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
80-106 4.38e-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: 39.91  E-value: 4.38e-04
                         10        20
                 ....*....|....*....|....*..
gi 262527218  80 REVRLMRNKSSGQSQGFAFVEFSHLQD 106
Cdd:cd12236   29 KRVRLVRDKKTGKSRGYAFIEFEHERD 55
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
67-125 5.79e-04

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: 39.19  E-value: 5.79e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 262527218  67 EIRGQLKSHGvKAREVRLMRNKSsGQSQGFAFVEFSHLQDTTRWMEANQHSLnILGQKV 125
Cdd:cd00590   14 DLRELFSKFG-EVVSVRIVRDRD-GKSKGFAFVEFESPEDAEKALEALNGTE-LGGRPL 69
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
250-305 5.90e-04

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 409798 [Multi-domain]  Cd Length: 80  Bit Score: 39.14  E-value: 5.90e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 262527218 250 SSSNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQAlhppLTIDGKTINVEFA 305
Cdd:cd12363   27 PIEKVQVVYDQQTGRSRGFGFVYFESVEDAKEAKERLNG----QEIDGRRIRVDYS 78
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
224-305 7.58e-04

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 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: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 39.12  E-value: 7.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 224 TIILRNLNPHSTMDSILGALAPYAVLSSsnVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQI--LQALHPPLTIDGKTIN 301
Cdd:cd12415    2 TVFIRNLSFDTTEEDLKEFFSKFGEVKY--ARIVLDKDTGHSKGTAFVQFKTKESADKCIEAanDESEDGGLVLDGRKLI 79

                 ....
gi 262527218 302 VEFA 305
Cdd:cd12415   80 VSLA 83
RRM_CFIm68_CFIm59 cd12372
RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or ...
66-129 8.57e-04

RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins; This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping.


Pssm-ID: 409807 [Multi-domain]  Cd Length: 76  Bit Score: 38.83  E-value: 8.57e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 262527218  66 AEIRGQLKSHGV-KAREVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEA-NQHSLNilGQKVSMHY 129
Cdd:cd12372   13 EDLEGACASFGVvDVKEIKFFEHKANGKSKGYAYVEFASPAAAAAVKEKlEKREFN--GRPCVVTP 76
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
224-305 9.24e-04

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: 38.75  E-value: 9.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 224 TIILRNLNPHSTMDSILGALAPYAVLSSsnVRVIKdKQTQLNRGFAFIQLSTIVEAAQLLQILQALHppltIDGKTINVE 303
Cdd:cd12320    2 KLIVKNVPFEATRKEIRELFSPFGQLKS--VRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEALKSTH----LYGRHLVLE 74

                 ..
gi 262527218 304 FA 305
Cdd:cd12320   75 YA 76
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
81-116 1.05e-03

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 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: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 38.54  E-value: 1.05e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 262527218  81 EVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEANQH 116
Cdd:cd12448   27 SVRLPTDRETGQPKGFGYVDFSTIDSAEAAIDALGG 62
RRM1_Hu_like cd12375
RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
80-113 1.10e-03

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is 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. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein 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 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. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. 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 to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 409810 [Multi-domain]  Cd Length: 76  Bit Score: 38.54  E-value: 1.10e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 262527218  80 REVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEA 113
Cdd:cd12375   27 ESCKLVRDKITGQSLGYGFVNYRDPNDARKAINT 60
RRM_eIF4H cd12401
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and ...
75-114 1.18e-03

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins; This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation.


Pssm-ID: 409835 [Multi-domain]  Cd Length: 84  Bit Score: 38.42  E-value: 1.18e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 262527218  75 HGVKAREVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEAN 114
Cdd:cd12401   27 KDLKVRSVRLVRDRETDKFKGFCYVEFEDLESLKEALEYD 66
RRM4_RBM28_like cd12416
RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
76-121 1.54e-03

RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM4 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: 409850 [Multi-domain]  Cd Length: 98  Bit Score: 38.74  E-value: 1.54e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 262527218  76 GVKAREVRLMRNK------SSGQSQGFAFVEFShlqdttrwmeANQHSLNIL 121
Cdd:cd12416   33 GVKIKEVKVMRDKkrlnsdGKGRSKGYGFVEFT----------EHEHALKAL 74
RRM1_FCA cd12633
RNA recognition motif 1 (RRM1) found in plant flowering time control protein FCA and similar ...
67-131 1.73e-03

RNA recognition motif 1 (RRM1) found in plant flowering time control protein FCA and similar proteins; This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. 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: 241077 [Multi-domain]  Cd Length: 80  Bit Score: 38.02  E-value: 1.73e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 262527218  67 EIRGQLKSHGvKAREVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEA--NQHSLNILGQKVSMHYSD 131
Cdd:cd12633   15 EVRPMFEEHG-NVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAlhNQRTLPGGASPVQVRYAD 80
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
225-303 2.65e-03

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 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: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 37.39  E-value: 2.65e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 262527218 225 IILRNLNPHSTMDSILGALAPYAVLSSsnVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQALHppltIDGKTINVE 303
Cdd:cd12448    1 LFVGNLPFSATQDALYEAFSQHGSIVS--VRLPTDRETGQPKGFGYVDFSTIDSAEAAIDALGGEY----IDGRPIRLD 73
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
57-125 2.86e-03

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.


Pssm-ID: 409834 [Multi-domain]  Cd Length: 74  Bit Score: 37.20  E-value: 2.86e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218  57 YDDSSEEqsaeIRGQLKSHGvKAREVRLMRNKSSGQSQGFAFVEFShlqDTTRWMEA-NQHSLNILGQKV 125
Cdd:cd12400   10 YDTTAED----LKEHFKKAG-EPPSVRLLTDKKTGKSKGCAFVEFD---NQKALQKAlKLHHTSLGGRKI 71
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
225-305 2.88e-03

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: 37.15  E-value: 2.88e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 225 IILRNLnPHSTMDSILGAL-APY-AVLSssnVRVIKDKQTQLnRGFAFIQLSTIVEAAQLLQILQAlhppLTIDGKTINV 302
Cdd:cd12414    2 LIVRNL-PFKCTEDDLKKLfSKFgKVLE---VTIPKKPDGKL-RGFAFVQFTNVADAAKAIKGMNG----KKIKGRPVAV 72

                 ...
gi 262527218 303 EFA 305
Cdd:cd12414   73 DWA 75
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
66-102 3.10e-03

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 37.38  E-value: 3.10e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 262527218  66 AEIRGQLKSHGvKAREVRLMRNKSSGQSQGFAFVEFS 102
Cdd:COG0724   16 EDLRELFSEYG-EVTSVKLITDRETGRSRGFGFVEMP 51
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
81-102 3.33e-03

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: 37.15  E-value: 3.33e-03
                         10        20
                 ....*....|....*....|..
gi 262527218  81 EVRLMRNKSSGQSQGFAFVEFS 102
Cdd:cd21608   28 SAKVITDRETGRSRGFGFVTFS 49
RRM1_SECp43 cd12610
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43); ...
76-140 4.92e-03

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43); This subgroup corresponds to the RRM1 of SECp43, 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.


Pssm-ID: 410022 [Multi-domain]  Cd Length: 84  Bit Score: 36.92  E-value: 4.92e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 262527218  76 GVKAREVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMeanqHSLNilGQKVSmhYSDPNPKINENW 140
Cdd:cd12610   24 GETVLSVKIIRNRVTGGPAGYCFVEFADEATAERCL----HKLN--GKPIP--GSNPPKRFKLNH 80
RRM1_SECp43_like cd12344
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
252-300 5.03e-03

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: 36.90  E-value: 5.03e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 262527218 252 SNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQilqalhpplTIDGKTI 300
Cdd:cd12344   28 VSVKIIRNKQTGKSAGYCFVEFATQEAAEQALE---------HLNGKPI 67
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
225-303 5.52e-03

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: 36.47  E-value: 5.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 262527218 225 IILRNLNPHSTMDSILGALAPYAVLSSSNV-RVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQAlhpplTIDGKTINVE 303
Cdd:cd12298    3 IRVRNLDFELDEEALRGIFEKFGEIESINIpKKQKNRKGRHNNGFAFVTFEDADSAESALQLNGT-----LLDNRKISVS 77
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
72-129 6.10e-03

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 36.27  E-value: 6.10e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 262527218  72 LKSHGVKA---REVRLMRNKSSGQSQGFAFVEFSHLQDTTRWMEaNQHSLNILGQKVSMHY 129
Cdd:cd12397   15 LRKHFAPAgkiRKVRMATFEDSGKCKGFAFVDFKEIESATNAVK-GPINHSLNGRDLRVEY 74
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
253-282 6.34e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 36.32  E-value: 6.34e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 262527218 253 NVRVIKDKQTQLNRGFAFIQLSTIvEAAQL 282
Cdd:cd12395   28 AVRIVRDRETGIGKGFGYVLFKDK-DSVDL 56
RRM1_SECp43_like cd12344
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
82-112 6.49e-03

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: 36.51  E-value: 6.49e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 262527218  82 VRLMRNKSSGQSQGFAFVEFSHLQDTTRWME 112
Cdd:cd12344   30 VKIIRNKQTGKSAGYCFVEFATQEAAEQALE 60
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
82-112 7.22e-03

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: 36.06  E-value: 7.22e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 262527218  82 VRLMRNKSSGQSQGFAFVEFSHLQDTTRWME 112
Cdd:cd12284   28 VQLQKDPETGRSKGYGFIQFRDAEDAKKALE 58
RRM1_hnRNPA_hnRNPD_like cd12325
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and ...
84-119 8.74e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.


Pssm-ID: 409763 [Multi-domain]  Cd Length: 72  Bit Score: 35.58  E-value: 8.74e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 262527218  84 LMRNKSSGQSQGFAFVEFSHLQDTTRWMEANQHSLN 119
Cdd:cd12325   30 VMKDPATGRSRGFGFVTFKDPSSVDAVLAARPHTLD 65
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
252-287 9.54e-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: 35.95  E-value: 9.54e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 262527218 252 SNVRVIKDKQTQLNRGFAFIQLSTIVEAAQLLQILQ 287
Cdd:cd12408   27 SRVYLAKDKETGQSKGFAFVTFETREDAERAIEKLN 62
 
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.
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