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Conserved domains on  [gi|1063729863|ref|NP_001330679|]
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RNA-binding (RRM/RBD/RNP motifs) family protein with retrovirus zinc finger-like domain-containing protein [Arabidopsis thaliana]

Protein Classification

RNA-binding protein( domain architecture ID 10350394)

RNA-binding protein containing an RNA recognition motif (RRM) and a zinc finger CCHC (ZCCHC) domain; similar to Danio rerio serine and arginine rich splicing factor 7a

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM super family cl34019
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
1-51 1.52e-14

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


The actual alignment was detected with superfamily member COG0724:

Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 67.05  E-value: 1.52e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEPKLGR 51
Cdd:COG0724    34 ITDRETGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPREER 84
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
90-105 1.50e-05

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


:

Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 40.97  E-value: 1.50e-05
                          10
                  ....*....|....*.
gi 1063729863  90 CFKCGRVGHWARDCPS 105
Cdd:pfam00098   3 CYNCGEPGHIARDCPK 18
U2AF_lg super family cl36941
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
132-218 6.75e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


The actual alignment was detected with superfamily member TIGR01642:

Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 37.57  E-value: 6.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729863 132 DRYADRDRY-VDRERYIDDRYDGAARYGARDRFDSREAYIPRDRYASDRYAAPADRFAGGDRYSRGSDRYPPGSYDKARS 210
Cdd:TIGR01642  32 SRFRDRHRRsRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKR 111

                  ....*...
gi 1063729863 211 FERDIAPS 218
Cdd:TIGR01642 112 SLWDIKPP 119
 
Name Accession Description Interval E-value
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
1-51 1.52e-14

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 67.05  E-value: 1.52e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEPKLGR 51
Cdd:COG0724    34 ITDRETGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPREER 84
RRM2_Hrp1p cd12330
RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
1-48 1.79e-11

RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409767 [Multi-domain]  Cd Length: 78  Bit Score: 58.87  E-value: 1.79e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIrEMHGRDFGDRVISVNRAEPK 48
Cdd:cd12330    32 MLDHDTGRSRGFGFVTFDSESAVEKVL-SKGFHELGGKKVEVKRATPK 78
RRM smart00360
RNA recognition motif;
1-42 4.28e-10

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 54.91  E-value: 4.28e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1063729863    1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISV 42
Cdd:smart00360  32 VRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
4-40 3.16e-08

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


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 49.54  E-value: 3.16e-08
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1063729863   4 RDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVI 40
Cdd:pfam00076  33 DETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
1-51 7.08e-07

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


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 49.81  E-value: 7.08e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1063729863   1 MLErDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEPKLGR 51
Cdd:TIGR01628 318 MLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQR 367
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
1-62 1.75e-06

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 46.57  E-value: 1.75e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA--EPKLGRDDGESHGSRGG 62
Cdd:PLN03134   67 IVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAndRPSAPRAYGGGGGYSGG 130
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
90-105 1.50e-05

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 40.97  E-value: 1.50e-05
                          10
                  ....*....|....*.
gi 1063729863  90 CFKCGRVGHWARDCPS 105
Cdd:pfam00098   3 CYNCGEPGHIARDCPK 18
ZnF_C2HC smart00343
zinc finger;
90-105 2.23e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.50  E-value: 2.23e-05
                           10
                   ....*....|....*.
gi 1063729863   90 CFKCGRVGHWARDCPS 105
Cdd:smart00343   2 CYNCGKEGHIARDCPS 17
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
132-218 6.75e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 37.57  E-value: 6.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729863 132 DRYADRDRY-VDRERYIDDRYDGAARYGARDRFDSREAYIPRDRYASDRYAAPADRFAGGDRYSRGSDRYPPGSYDKARS 210
Cdd:TIGR01642  32 SRFRDRHRRsRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKR 111

                  ....*...
gi 1063729863 211 FERDIAPS 218
Cdd:TIGR01642 112 SLWDIKPP 119
 
Name Accession Description Interval E-value
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
1-51 1.52e-14

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 67.05  E-value: 1.52e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEPKLGR 51
Cdd:COG0724    34 ITDRETGRSRGFGFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPREER 84
RRM2_Hrp1p cd12330
RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
1-48 1.79e-11

RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409767 [Multi-domain]  Cd Length: 78  Bit Score: 58.87  E-value: 1.79e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIrEMHGRDFGDRVISVNRAEPK 48
Cdd:cd12330    32 MLDHDTGRSRGFGFVTFDSESAVEKVL-SKGFHELGGKKVEVKRATPK 78
RRM smart00360
RNA recognition motif;
1-42 4.28e-10

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 54.91  E-value: 4.28e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1063729863    1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISV 42
Cdd:smart00360  32 VRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
4-45 6.15e-10

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: 54.48  E-value: 6.15e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1063729863   4 RDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd21608    35 RETGRSRGFGFVTFSTAEAAEAAIDALNGKELDGRSIVVNEA 76
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
2-45 2.01e-09

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 52.91  E-value: 2.01e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1063729863   2 LERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12399    32 MDRETKRPRGFGFVELQEEESAEKAIAKLDGTDFMGRTIRVNEA 75
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
4-40 3.16e-08

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


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 49.54  E-value: 3.16e-08
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1063729863   4 RDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVI 40
Cdd:pfam00076  33 DETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGREL 69
RRM2_PUB1 cd12619
RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated ...
1-45 1.46e-07

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


Pssm-ID: 410031 [Multi-domain]  Cd Length: 80  Bit Score: 47.88  E-value: 1.46e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12619    34 MWDQKTGRSRGYGFVSFRSQQDAQNAINSMNGKWLGSRPIRCNWA 78
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
1-43 2.31e-07

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: 47.28  E-value: 2.31e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVN 43
Cdd:cd00590    30 IVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
5-48 2.35e-07

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 47.17  E-value: 2.35e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1063729863   5 DTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEPK 48
Cdd:cd12380    37 DSGKSKGFGFVNFENHEAAQKAVEELNGKELNGKKLYVGRAQKK 80
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
1-45 3.82e-07

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


Pssm-ID: 409816 [Multi-domain]  Cd Length: 80  Bit Score: 46.63  E-value: 3.82e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12382    34 MKDRETNKSRGFAFVTFESPADAKDAARDMNGKELDGKAIKVEQA 78
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
3-48 5.22e-07

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: 46.32  E-value: 5.22e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1063729863   3 ERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEPK 48
Cdd:cd12449    35 DRETQRSRGFGFVTFENPDDAKDAMMAMNGKSLDGRQIRVDQAGKS 80
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
1-51 7.08e-07

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


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 49.81  E-value: 7.08e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1063729863   1 MLErDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEPKLGR 51
Cdd:TIGR01628 318 MLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQR 367
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
1-45 8.85e-07

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 45.59  E-value: 8.85e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12398    33 VTDRETGKPKGYGFCEFRDAETALSAVRNLNGYELNGRPLRVDFA 77
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
3-48 1.49e-06

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


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 45.28  E-value: 1.49e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1063729863   3 ERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEPK 48
Cdd:cd12413    34 DKGKDKCRGFGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKKK 79
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
1-62 1.75e-06

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 46.57  E-value: 1.75e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA--EPKLGRDDGESHGSRGG 62
Cdd:PLN03134   67 IVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAndRPSAPRAYGGGGGYSGG 130
RRM1_PSRP2_like cd21609
RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 ...
1-49 2.72e-06

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


Pssm-ID: 410188 [Multi-domain]  Cd Length: 80  Bit Score: 44.33  E-value: 2.72e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEPKL 49
Cdd:cd21609    32 MYDRYTGRSRGFGFVTMGSVEDAKAAIEKLNGTEVGGREIKVNITEKPL 80
RRM2_SECp43_like cd12345
RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
1-45 2.91e-06

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


Pssm-ID: 409781 [Multi-domain]  Cd Length: 80  Bit Score: 44.18  E-value: 2.91e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12345    35 VMDPVTGRSKGYGFVRFGDESEQDRALTEMQGVYLGSRPIRVSPA 79
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
1-43 4.91e-06

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


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 43.37  E-value: 4.91e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVN 43
Cdd:cd12362    31 FVDKNTGRSKGFGFVSYDNPLSAQAAIKAMNGFQVGGKRLKVQ 73
RRM2_SF3B4 cd12335
RNA recognition motif 2 (RRM2) found in splicing factor 3B subunit 4 (SF3B4) and similar ...
1-48 1.28e-05

RNA recognition motif 2 (RRM2) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins; This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145.


Pssm-ID: 409772 [Multi-domain]  Cd Length: 83  Bit Score: 42.73  E-value: 1.28e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEPK 48
Cdd:cd12335    35 MRDPDTGNSKGFGFVSFDSFEASDAAIEAMNGQYLCNRPITVSYAFKK 82
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
90-105 1.50e-05

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 40.97  E-value: 1.50e-05
                          10
                  ....*....|....*.
gi 1063729863  90 CFKCGRVGHWARDCPS 105
Cdd:pfam00098   3 CYNCGEPGHIARDCPK 18
RRM1_hnRNPA_hnRNPD_like cd12325
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and ...
1-33 1.56e-05

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: 42.13  E-value: 1.56e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1063729863   1 MLERDTGRSRGFGFITFAD----RRAMDESIREMHGR 33
Cdd:cd12325    31 MKDPATGRSRGFGFVTFKDpssvDAVLAARPHTLDGR 67
ZnF_C2HC smart00343
zinc finger;
90-105 2.23e-05

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 40.50  E-value: 2.23e-05
                           10
                   ....*....|....*.
gi 1063729863   90 CFKCGRVGHWARDCPS 105
Cdd:smart00343   2 CYNCGKEGHIARDCPS 17
RRM2_DAZAP1 cd12327
RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) ...
1-47 3.40e-05

RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins; This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain.


Pssm-ID: 409765 [Multi-domain]  Cd Length: 80  Bit Score: 41.33  E-value: 3.40e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIrEMHGRDFGDRVISVNRAEP 47
Cdd:cd12327    35 MYDAEKQRSRGFGFITFEDEQSVDQAV-NMHFHDIMGKKVEVKRAEP 80
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
3-45 4.96e-05

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: 40.57  E-value: 4.96e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1063729863   3 ERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12408    34 DKETGQSKGFAFVTFETREDAERAIEKLNGFGYDNLILSVEWA 76
RRM1_Hrp1p cd12577
RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 ...
1-48 5.30e-05

RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins; This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y.


Pssm-ID: 409991 [Multi-domain]  Cd Length: 76  Bit Score: 40.56  E-value: 5.30e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDfgDRVISVNRAEPK 48
Cdd:cd12577    31 MKDSATGRSRGFGFLTFEDPSSVNEVMKKEHVLD--GKIIDPKRAIPR 76
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
3-42 5.61e-05

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: 40.67  E-value: 5.61e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1063729863   3 ERDTGRSRGFGFITFADRRAMDESIReMHGRDFGDRVISV 42
Cdd:cd12400    35 DKKTGKSKGCAFVEFDNQKALQKALK-LHHTSLGGRKINV 73
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
1-43 8.38e-05

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


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 40.30  E-value: 8.38e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063729863   1 MLERDTGRSRGFGFITFAD----RRAMDesirEMHGRDFGDRVISVN 43
Cdd:cd12284    31 QKDPETGRSKGYGFIQFRDaedaKKALE----QLNGFELAGRPMKVG 73
RRM2_NUCLs cd12451
RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This ...
3-45 9.46e-05

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409885 [Multi-domain]  Cd Length: 79  Bit Score: 40.09  E-value: 9.46e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1063729863   3 ERDTGRSRGFGFITFADRRAMDESiREMHGRDFGDRVISVNRA 45
Cdd:cd12451    38 DRETGELKGFAYIEFSTKEAKEKA-LELNGSDIAGGNLVVDEA 79
RRM2_NGR1_NAM8_like cd12613
RNA recognition motif 2 (RRM2) found in yeast negative growth regulatory protein NGR1, yeast ...
1-45 9.75e-05

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


Pssm-ID: 410025 [Multi-domain]  Cd Length: 80  Bit Score: 40.19  E-value: 9.75e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12613    35 MTDPVTGVSRGYGFVRFSDENDQQRALIEMQGKYCQGRPLRISYA 79
RRM_RBM42 cd12383
RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins; This ...
3-45 1.12e-04

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


Pssm-ID: 409817 [Multi-domain]  Cd Length: 83  Bit Score: 39.96  E-value: 1.12e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1063729863   3 ERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12383    41 DKRTGKSKGYGFVSFKDPNDYLKALREMNGKYVGNRPIKLRKS 83
RRM2_PUF60 cd12371
RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
6-45 1.26e-04

RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409806 [Multi-domain]  Cd Length: 77  Bit Score: 39.58  E-value: 1.26e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1063729863   6 TGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12371    38 TGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQYLRVGRA 77
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
2-42 1.85e-04

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 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: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 39.25  E-value: 1.85e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1063729863   2 LERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISV 42
Cdd:cd12316    33 LDKQTKRSKGFAFVLFVIPEDAVKAYQELDGSIFQGRLLHV 73
RRM2_TIA1_like cd12353
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...
6-43 2.14e-04

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


Pssm-ID: 409789 [Multi-domain]  Cd Length: 75  Bit Score: 38.91  E-value: 2.14e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1063729863   6 TGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVN 43
Cdd:cd12353    37 TGKSKGYGFVSFVKKEDAENAIQGMNGQWLGGRNIRTN 74
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
7-51 2.61e-04

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


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 42.10  E-value: 2.61e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1063729863   7 GRSRGFGFITFADRRAMDESIREMHGRDFGD----RVISVNRAEPKLGR 51
Cdd:TIGR01628 216 GRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLakegKKLYVGRAQKRAER 264
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
5-46 3.77e-04

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


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 38.41  E-value: 3.77e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1063729863   5 DTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAE 46
Cdd:cd12381    37 EGGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPLYVALAQ 78
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
6-48 5.05e-04

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


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 38.21  E-value: 5.05e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1063729863   6 TGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEPK 48
Cdd:cd12674    38 TKKSRGYGFVSFSTHDDAEEALAKLKNRKLSGHILKLDFAKPR 80
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
5-51 5.68e-04

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


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 40.95  E-value: 5.68e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063729863   5 DTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEPKLGR 51
Cdd:TIGR01628 124 ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHER 170
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
3-42 6.20e-04

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


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 37.63  E-value: 6.20e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1063729863   3 ERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISV 42
Cdd:cd12311    33 DRYTRESRGFAFVRFYDKRDAEDAIDAMDGAELDGRELRV 72
RRM_RBM24_RBM38_like cd12384
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar ...
3-30 9.32e-04

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins; This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409818 [Multi-domain]  Cd Length: 76  Bit Score: 36.97  E-value: 9.32e-04
                          10        20
                  ....*....|....*....|....*...
gi 1063729863   3 ERDTGRSRGFGFITFADRRAMDESIREM 30
Cdd:cd12384    35 DRQTGKSRGYGFVTMADREAAERACKDP 62
RRM1_MSI2 cd12760
RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and ...
1-50 1.01e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins; This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 410153 [Multi-domain]  Cd Length: 93  Bit Score: 37.41  E-value: 1.01e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1063729863   1 MLERD--TGRSRGFGFITFADRRAMDESI----REMHGRDFGDRVISVNRAEPKLG 50
Cdd:cd12760    35 MVMRDptTKRSRGFGFVTFADPASVDKVLaqphHELDSKTIDPKVAFPRRAQPKMV 90
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
6-45 1.74e-03

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


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 36.43  E-value: 1.74e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1063729863   6 TGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12347    36 TEKHRGFAFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA 75
RRM2_U2AF65 cd12231
RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
4-45 2.04e-03

RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.


Pssm-ID: 409678 [Multi-domain]  Cd Length: 77  Bit Score: 36.09  E-value: 2.04e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1063729863   4 RDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12231    36 SATGLSKGYAFCEYVDDNVTDQAIAGLNGMQLGDKKLLVQRA 77
RRM1_MSI cd12576
RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, ...
1-24 2.23e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins; This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 409990 [Multi-domain]  Cd Length: 76  Bit Score: 36.27  E-value: 2.23e-03
                          10        20
                  ....*....|....*....|....*.
gi 1063729863   1 MLERD--TGRSRGFGFITFADRRAMD 24
Cdd:cd12576    30 MVMRDptTKRSRGFGFVTFSDPASVD 55
RRM2_hnRNPA_like cd12328
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; ...
1-27 2.58e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily; This subfamily corresponds to the RRM2 of 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. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). 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). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. 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.


Pssm-ID: 409766 [Multi-domain]  Cd Length: 73  Bit Score: 35.71  E-value: 2.58e-03
                          10        20
                  ....*....|....*....|....*..
gi 1063729863   1 MLERDTGRSRGFGFITFADRRAMDESI 27
Cdd:cd12328    32 VTDKETGKKRGFAFVTFDDHDSVDKIV 58
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
3-45 2.79e-03

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


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 35.87  E-value: 2.79e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1063729863   3 ERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12447    34 DRGSGRSKGYGYVDFATPEAAQKALAAMSGKEIDGRQINVDFS 76
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
6-42 3.00e-03

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 35.69  E-value: 3.00e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1063729863   6 TGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISV 42
Cdd:cd12417    37 TPGSRCYGYVTMASVEEADLCIKSLNKTELHGRVITV 73
RRM1_HuC cd12772
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup ...
2-47 3.02e-03

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. 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: 410165 [Multi-domain]  Cd Length: 85  Bit Score: 35.86  E-value: 3.02e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1063729863   2 LERD--TGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEP 47
Cdd:cd12772    36 LVRDkiTGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKVSYARP 83
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
10-47 3.03e-03

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


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 35.68  E-value: 3.03e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1063729863  10 RGFGFITFADRRAMDESIREMHGRDFGDRVISVNRAEP 47
Cdd:cd12251    35 KDYAFVHFEERDDAVKAMEEMNGKELEGSEIEVSLAKP 72
RRM2_hnRNPA0 cd12579
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) ...
3-48 3.62e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins; This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains 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.


Pssm-ID: 409993 [Multi-domain]  Cd Length: 80  Bit Score: 35.58  E-value: 3.62e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1063729863   3 ERDTGRSRGFGFITFADRRAMDES-IREMHGRDfGDRViSVNRAEPK 48
Cdd:cd12579    34 DKDTGKKRGFGFVYFEDHDSADKAaVVKFHSIN-GHRV-EVKKAVPK 78
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
9-45 4.29e-03

RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 35.45  E-value: 4.29e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1063729863   9 SRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12407    39 SKGFGFVTFANSADADRAREKLNGTVVEGRKIEVNNA 75
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
3-48 4.80e-03

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins; This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation.


Pssm-ID: 409836 [Multi-domain]  Cd Length: 81  Bit Score: 35.27  E-value: 4.80e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1063729863   3 ERDTGRSRGFGFITFADRRAMDESIrEMHGRDFGDRVISVNRAEPK 48
Cdd:cd12402    36 ENGPGRLRGFGYVEFEDRESLIQAL-SLNEESLKNRRIRVDVAGQA 80
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
7-45 5.31e-03

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


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 34.97  E-value: 5.31e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1063729863   7 GRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12355    41 GQPRGYCFVTFETKEEAEKAIECLNGKLALGKKLVVRWA 79
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
3-45 5.45e-03

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.


Pssm-ID: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 35.18  E-value: 5.45e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1063729863   3 ERDTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNRA 45
Cdd:cd12671    41 DRETGKPKGYGFCEYQDQETALSAMRNLNGYELNGRALRVDNA 83
RRM1_HRB1_GBP2 cd21605
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, ...
7-42 5.51e-03

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410184 [Multi-domain]  Cd Length: 77  Bit Score: 34.96  E-value: 5.51e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1063729863   7 GRSRGFGFITFADRRAMDESIREMHGRDFGDRVISV 42
Cdd:cd21605    38 GRHRGMGTVEFTNKEDVDRAISKFDHTMFMGREIFV 73
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
10-44 5.54e-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: 34.93  E-value: 5.54e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1063729863  10 RGFGFITFADRRAMDESIrEMHGRDFGDRVISVNR 44
Cdd:cd12298    45 NGFAFVTFEDADSAESAL-QLNGTLLDNRKISVSL 78
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
132-218 6.75e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 37.57  E-value: 6.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063729863 132 DRYADRDRY-VDRERYIDDRYDGAARYGARDRFDSREAYIPRDRYASDRYAAPADRFAGGDRYSRGSDRYPPGSYDKARS 210
Cdd:TIGR01642  32 SRFRDRHRRsRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKR 111

                  ....*...
gi 1063729863 211 FERDIAPS 218
Cdd:TIGR01642 112 SLWDIKPP 119
RRM2_TIA1 cd12618
RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar ...
6-43 8.39e-03

RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins; This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs.


Pssm-ID: 410030 [Multi-domain]  Cd Length: 78  Bit Score: 34.60  E-value: 8.39e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1063729863   6 TGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVN 43
Cdd:cd12618    40 TGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN 77
RRM1_TDP43 cd12321
RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar ...
1-19 8.88e-03

RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.


Pssm-ID: 409760 [Multi-domain]  Cd Length: 74  Bit Score: 34.30  E-value: 8.88e-03
                          10
                  ....*....|....*....
gi 1063729863   1 MLERDTGRSRGFGFITFAD 19
Cdd:cd12321    32 KKDPKTGRSKGFGFVRFAS 50
RRM2_I_PABPs cd12379
RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This ...
5-44 9.41e-03

RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409813 [Multi-domain]  Cd Length: 77  Bit Score: 34.47  E-value: 9.41e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1063729863   5 DTGRSRGFGFITFADRRAMDESIREMHGRDFGDRVISVNR 44
Cdd:cd12379    38 ENGGSKGYGFVHFETEEAAERAIEKVNGMLLNGKKVFVGR 77
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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