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Conserved domains on  [gi|442619723|ref|NP_001014631|]
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couch potato, isoform T [Drosophila melanogaster]

Protein Classification

RNA-binding protein( domain architecture ID 10190560)

RNA-binding protein containing an RNA recognition motif (RRM) similar to Drosophila melanogaster couch potato that may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS)

CATH:  3.30.70.330
Gene Ontology:  GO:0003723
SCOP:  3000110

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM_cpo cd12684
RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein ...
441-524 9.24e-52

RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein and similar proteins; This subfamily corresponds to the RRM of Cpo, an RNA-binding protein encoded by Drosophila couch potato (cpo) gene. Cpo contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS).


:

Pssm-ID: 410085 [Multi-domain]  Cd Length: 83  Bit Score: 172.40  E-value: 9.24e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442619723 441 VRTLFVSGLPMDAKPRELYLLFRAYEGYEGSLLKVTSKNGKTASPVGFVTFHTRAGAEAAKQDLqQGVRFDPDMPQTIRL 520
Cdd:cd12684    1 VRTLFVSGLPMDAKPRELYLLFRAYKGYEGSLLKVTSKNGKTTSPVGFVTFLSRQAAEAAKQDL-QGVRFDPDLPQTLRL 79

                 ....
gi 442619723 521 EFAK 524
Cdd:cd12684   80 EFAK 83
 
Name Accession Description Interval E-value
RRM_cpo cd12684
RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein ...
441-524 9.24e-52

RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein and similar proteins; This subfamily corresponds to the RRM of Cpo, an RNA-binding protein encoded by Drosophila couch potato (cpo) gene. Cpo contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS).


Pssm-ID: 410085 [Multi-domain]  Cd Length: 83  Bit Score: 172.40  E-value: 9.24e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442619723 441 VRTLFVSGLPMDAKPRELYLLFRAYEGYEGSLLKVTSKNGKTASPVGFVTFHTRAGAEAAKQDLqQGVRFDPDMPQTIRL 520
Cdd:cd12684    1 VRTLFVSGLPMDAKPRELYLLFRAYKGYEGSLLKVTSKNGKTTSPVGFVTFLSRQAAEAAKQDL-QGVRFDPDLPQTLRL 79

                 ....
gi 442619723 521 EFAK 524
Cdd:cd12684   80 EFAK 83
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
444-505 3.94e-10

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: 56.09  E-value: 3.94e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 442619723  444 LFVSGLPMDAKPRELYLLFRAYEGYEGslLKVTSKNGKTASPVGFVTFHTRAGAEAAKQDLQ 505
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKS--IRLVRDETGRSKGFAFVEFEDEEDAEKAIEALN 60
RRM smart00360
RNA recognition motif;
443-511 1.53e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.05  E-value: 1.53e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 442619723   443 TLFVSGLPMDAKPRELYLLFRAYEGYEGSLLKVTSKNGKTAsPVGFVTFHTRAGAEAAKQDLqQGVRFD 511
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSK-GFAFVEFESEEDAEKALEAL-NGKELD 67
 
Name Accession Description Interval E-value
RRM_cpo cd12684
RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein ...
441-524 9.24e-52

RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein and similar proteins; This subfamily corresponds to the RRM of Cpo, an RNA-binding protein encoded by Drosophila couch potato (cpo) gene. Cpo contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS).


Pssm-ID: 410085 [Multi-domain]  Cd Length: 83  Bit Score: 172.40  E-value: 9.24e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442619723 441 VRTLFVSGLPMDAKPRELYLLFRAYEGYEGSLLKVTSKNGKTASPVGFVTFHTRAGAEAAKQDLqQGVRFDPDMPQTIRL 520
Cdd:cd12684    1 VRTLFVSGLPMDAKPRELYLLFRAYKGYEGSLLKVTSKNGKTTSPVGFVTFLSRQAAEAAKQDL-QGVRFDPDLPQTLRL 79

                 ....
gi 442619723 521 EFAK 524
Cdd:cd12684   80 EFAK 83
RRM_RBPMS_like cd12420
RNA recognition motif (RRM) found in RNA-binding protein with multiple splicing (RBP-MS)-like ...
442-521 9.79e-37

RNA recognition motif (RRM) found in RNA-binding protein with multiple splicing (RBP-MS)-like proteins; This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4.


Pssm-ID: 409854 [Multi-domain]  Cd Length: 76  Bit Score: 131.29  E-value: 9.79e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442619723 442 RTLFVSGLPMDAKPRELYLLFRAYEGYEGSLLKVTSKNgktASPVGFVTFHTRAGAEAAKQDLqQGVRFDPDMPQTIRLE 521
Cdd:cd12420    1 RTLFVSGLPLDVKERELYNLFRPLPGYEASQLKFTGKN---TQPVGFVTFESRAAAEAAKDAL-QGMRFDPDTPQVLRLE 76
RRM_RBPMS cd12682
RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing ...
441-522 3.54e-31

RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing (RBP-MS); This subfamily corresponds to the RRM of RBP-MS, also termed heart and RRM expressed sequence (hermes), an RNA-binding proteins found in various vertebrate species. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RBP-MS physically interacts with Smad2, Smad3 and Smad4 and plays a role in regulation of Smad-mediated transcriptional activity. In addition, RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development.


Pssm-ID: 410083 [Multi-domain]  Cd Length: 76  Bit Score: 115.91  E-value: 3.54e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442619723 441 VRTLFVSGLPMDAKPRELYLLFRAYEGYEGSLLKVTSKNgktasPVGFVTFHTRAGAEAAKQDLqQGVRFDPDMPQTIRL 520
Cdd:cd12682    1 VRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQ-----PVGFVSFDSRSEAEAAKNAL-NGIRFDPEIPQTLRL 74

                 ..
gi 442619723 521 EF 522
Cdd:cd12682   75 EF 76
RRM_RBPMS2 cd12683
RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing 2 ...
441-522 1.08e-30

RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing 2 (RBP-MS2); This subfamily corresponds to the RRM of RBP-MS2, encoded by RBPMS2 gene, a paralog of RNA-binding protein with multiple splicing (RBP-MS). The biological function of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410084 [Multi-domain]  Cd Length: 76  Bit Score: 114.75  E-value: 1.08e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442619723 441 VRTLFVSGLPMDAKPRELYLLFRAYEGYEGSLLKVTSKNgktasPVGFVTFHTRAGAEAAKQDLqQGVRFDPDMPQTIRL 520
Cdd:cd12683    1 VRTLFVSGLPVDIKPRELYLLFRPFKGYEGSLIKLTSKQ-----PVGFVTFDSRAGAEAAKNAL-NGIRFDPENPQTLRL 74

                 ..
gi 442619723 521 EF 522
Cdd:cd12683   75 EF 76
RRM_AtNSRA_like cd21618
RNA recognition motif (RRM) found in Arabidopsis thaliana nuclear speckle RNA-binding protein ...
442-524 7.43e-13

RNA recognition motif (RRM) found in Arabidopsis thaliana nuclear speckle RNA-binding protein A (AtNSRA) and similar protein; AtNSRA is an alternative splicing (AS) regulator that binds to specific mRNAs and modulates auxin effects on the transcriptome. It can be displaced from its targets upon binding to AS competitor long non-coding RNA (ASCO-RNA). Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410197 [Multi-domain]  Cd Length: 87  Bit Score: 64.21  E-value: 7.43e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442619723 442 RTLFVSGLPMDAKPRELYLLFRAYEGYEG-SLLKVTSKNGKTaSPVGFVTFHTRAGAEAAKQDLqQGVRFDPDMPQ--TI 518
Cdd:cd21618    4 STLYVEGLPLDATEREVAHIFRPFPGFKSvRLVPKEGKRGRK-LVLCFVDFADAQQAAAALETL-QGYRLDEDDSDskGL 81

                 ....*.
gi 442619723 519 RLEFAK 524
Cdd:cd21618   82 RISFAR 87
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
444-505 3.94e-10

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: 56.09  E-value: 3.94e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 442619723  444 LFVSGLPMDAKPRELYLLFRAYEGYEGslLKVTSKNGKTASPVGFVTFHTRAGAEAAKQDLQ 505
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKS--IRLVRDETGRSKGFAFVEFEDEEDAEKAIEALN 60
RRM smart00360
RNA recognition motif;
443-511 1.53e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.05  E-value: 1.53e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 442619723   443 TLFVSGLPMDAKPRELYLLFRAYEGYEGSLLKVTSKNGKTAsPVGFVTFHTRAGAEAAKQDLqQGVRFD 511
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSK-GFAFVEFESEEDAEKALEAL-NGKELD 67
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
444-505 1.33e-05

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: 43.43  E-value: 1.33e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 442619723 444 LFVSGLPMDAKPRELYLLFRAYegyeGSLLKVTSKNGKTASP--VGFVTFHTRAGAEAAKQDLQ 505
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKF----GEVVSVRIVRDRDGKSkgFAFVEFESPEDAEKALEALN 60
RRM_scw1_like cd12245
RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar ...
443-524 6.43e-05

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


Pssm-ID: 409691 [Multi-domain]  Cd Length: 79  Bit Score: 41.46  E-value: 6.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442619723 443 TLFVSGLPMDAKPRELYLLFRAYEGYEgsLLKVTSKNGktaSPVGFVTFHTRAGAEAAKQDLqQGVRFDPDMPQTIRLEF 522
Cdd:cd12245    4 TLFVANLGPNVSEQELRQLFSRQPGFR--RLRMHNKGG---GPVCFVEFEDVPFATQALNHL-QGAILSSSDRGGIRIEY 77

                 ..
gi 442619723 523 AK 524
Cdd:cd12245   78 AK 79
RRM2_U1A_like cd12247
RNA recognition motif 2 (RRM2) found in the U1A/U2B"/SNF protein family; This subfamily ...
442-506 1.22e-04

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


Pssm-ID: 409693 [Multi-domain]  Cd Length: 72  Bit Score: 40.62  E-value: 1.22e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 442619723 442 RTLFVSGLPMDAKPRELYLLFRAYEGYEGslLKVTSKNGktaspVGFVTFHTRAGAEAAKQDLQQ 506
Cdd:cd12247    3 KILFLQNLPEETTKEMLEMLFNQFPGFKE--VRLVPRRG-----IAFVEFETEEQATVALQALQG 60
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
443-511 3.32e-04

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: 39.41  E-value: 3.32e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 442619723 443 TLFVSGLPMDAKPRELYLLFRAYegyeGSLLKVT-SKNGKTASPVGF--VTFHTRAGAEAAKQDLqQGVRFD 511
Cdd:cd12408    1 TIRVTNLSEDATEEDLRELFRPF----GPISRVYlAKDKETGQSKGFafVTFETREDAERAIEKL-NGFGYD 67
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
443-524 4.34e-04

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


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 39.05  E-value: 4.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442619723 443 TLFVSGLPMDAKPRE----LYLLFRAYegyeGSLLKVTSknGKTASPVG--FVTFHTRAGAEAAKQDLQQGVRFDPDMpq 516
Cdd:cd12246    1 TLYINNLNEKIKKDElkrsLYALFSQF----GPVLDIVA--SKSLKMRGqaFVVFKDVESATNALRALQGFPFYGKPM-- 72

                 ....*...
gi 442619723 517 tiRLEFAK 524
Cdd:cd12246   73 --RIQYAK 78
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
444-510 5.50e-04

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409769 [Multi-domain]  Cd Length: 71  Bit Score: 38.82  E-value: 5.50e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 442619723 444 LFVSGLPMDAKPRELYLLFRAYegyeGSLLKVTSKNGKTaspVGFVTFHTRAGAEAAKQDL----QQG----VRF 510
Cdd:cd12332    4 LFVGNLPNDITEEEFKELFQKY----GEVSEVFLNKGKG---FGFIRLDTRANAEAAKAELdgtpRKGrqlrVRF 71
RRM2_Hu cd12652
RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to ...
444-504 7.98e-04

RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410055 [Multi-domain]  Cd Length: 79  Bit Score: 38.46  E-value: 7.98e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 442619723 444 LFVSGLPMDAKPRELYLLFRAYegyeGSLlkVTSK-----NGKTASPVGFVTFHTRAGAEAAKQDL 504
Cdd:cd12652    3 LYVSGLPKTMTQKELEQLFSQF----GRI--ITSRilcdnVTGLSRGVGFIRFDKRVEAERAIKAL 62
RRM1_SRSF1_like cd12338
RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and ...
443-522 1.25e-03

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


Pssm-ID: 409775 [Multi-domain]  Cd Length: 72  Bit Score: 37.73  E-value: 1.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442619723 443 TLFVSGLPMDAKPRELYLLFRAYegyeGSLLKVTSKNGKTASPVGFVTFHTRAGAEAAKQDlQQGVRFDpdmPQTIRLEF 522
Cdd:cd12338    1 RIYVGNLPGDIRERDIEDLFYKY----GPILAIDLKNRRRGPPFAFVEFEDPRDAEDAIRG-RDGYDFD---GYRLRVEF 72
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
443-505 1.49e-03

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


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 37.69  E-value: 1.49e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 442619723 443 TLFVSGLPMDAKPRELYLLFRAYegyeGSLLKVTSKNGKTAspvGFVTFHTRAGAEAAKQDLQ 505
Cdd:cd12346    3 TVFVGGLDPNVTEEDLRVLFGPF----GEIVYVKIPPGKGC---GFVQFVNRASAEAAIQKLQ 58
RRM1_SECp43_like cd12344
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
443-526 2.90e-03

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


Pssm-ID: 409780 [Multi-domain]  Cd Length: 82  Bit Score: 36.90  E-value: 2.90e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 442619723 443 TLFVSGLPMDAKPRELYLLFrAYEGYEGSLLKV--TSKNGKTASpVGFVTFHTRAGAEAAKQDLqQGVRFdPDMPQTIRL 520
Cdd:cd12344    1 TLWMGDLEPWMDEAYISSCF-AKTGEEVVSVKIirNKQTGKSAG-YCFVEFATQEAAEQALEHL-NGKPI-PNTQQRFRL 76

                 ....*.
gi 442619723 521 EFAKSN 526
Cdd:cd12344   77 NWASFS 82
 
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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