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Conserved domains on  [gi|1622968454|ref|XP_028697487|]
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regulator of nonsense transcripts 3B isoform X3 [Macaca mulatta]

Protein Classification

RNA-binding protein( domain architecture ID 106745)

RNA-binding protein containing an RNA recognition motif (RRM)

CATH:  3.30.70.330
Gene Ontology:  GO:0003723
PubMed:  15853797
SCOP:  3000110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 50-132 1.05e-48

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


The actual alignment was detected with superfamily member cd12728:

Pssm-ID: 473069  Cd Length: 89  Bit Score: 160.85  E-value: 1.05e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622968454  50 LSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKDPEYRK 129
Cdd:cd12728     1 LSKVVIRRLPPSLTKEQLEEHLQPLPEHDYFEFFSNDSSLYPHMFSRAYINFKNQEDIVLFRDRFDGYVFIDNRGQEYPA 80


                  ...
gi 1622968454 130 FLE 132
Cdd:cd12728    81 IVE 83
 
Name Accession Description Interval E-value
RRM_like_Smg4_UPF3B cd12728
RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on ...
 50-132 1.05e-48

RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on chromosome X (Upf3B); This subgroup corresponds to the RRM-like Smg4_UPF3 domain in Upf3B, also termed regulator of nonsense transcripts 3B, or nonsense mRNA reducing factor 3B, a human ortholog of yeast Upf3p and Caenorhabditis elegans SMG-4. It derives from X-linked gene UPF3B and is required for nonsense-mediated mRNA decay (NMD) in human. Upf3B is a nucleocytoplasmic shuttling protein that associates selectively with spliced beta-globin mRNA in vivo. Like other Upf3 proteins, Upf3B contains nuclear import and export signals, and a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that it may be an RNA binding protein.


Pssm-ID: 410127  Cd Length: 89  Bit Score: 160.85  E-value: 1.05e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622968454  50 LSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKDPEYRK 129
Cdd:cd12728     1 LSKVVIRRLPPSLTKEQLEEHLQPLPEHDYFEFFSNDSSLYPHMFSRAYINFKNQEDIVLFRDRFDGYVFIDNRGQEYPA 80


                  ...
gi 1622968454 130 FLE 132
Cdd:cd12728    81 IVE 83
Smg4_UPF3 pfam03467
Smg-4/UPF3 family; This family contains proteins that are involved in nonsense mediated mRNA ...
 51-175 1.40e-35

Smg-4/UPF3 family; This family contains proteins that are involved in nonsense mediated mRNA decay. A process that is triggered by premature stop codons in mRNA. The family includes Smg-4 and UPF3.


Pssm-ID: 460932 [Multi-domain]  Cd Length: 168  Bit Score: 129.33  E-value: 1.40e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622968454  51 SKVVIRRLPPTLTKEQLQEHLQPMP-EHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNK------ 123
Cdd:pfam03467   4 TKVVIRRLPPNLTEEEFLEQLSPLPgEVDWFYFVPGKKSLKPPAYSRAYINFKDPEDLLQFADRFDGHVFVDSKgneypa 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622968454 124 ---------------------------DPEYRKFLESYATDNEKMTSTP--ETLLEEIEAKNRE---LIAKKTTPLLSFL 171
Cdd:pfam03467  84 ivefapyqkvpkkkdkkkdaregtidkDPEYKEFLESLEKPEEDPESALiqEELEEEEEEKEKEeakKEKKTTTPLIEFL 163


                  ....
gi 1622968454 172 KNKQ 175
Cdd:pfam03467 164 KEKK 167
 
Name Accession Description Interval E-value
RRM_like_Smg4_UPF3B cd12728
RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on ...
 50-132 1.05e-48

RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on chromosome X (Upf3B); This subgroup corresponds to the RRM-like Smg4_UPF3 domain in Upf3B, also termed regulator of nonsense transcripts 3B, or nonsense mRNA reducing factor 3B, a human ortholog of yeast Upf3p and Caenorhabditis elegans SMG-4. It derives from X-linked gene UPF3B and is required for nonsense-mediated mRNA decay (NMD) in human. Upf3B is a nucleocytoplasmic shuttling protein that associates selectively with spliced beta-globin mRNA in vivo. Like other Upf3 proteins, Upf3B contains nuclear import and export signals, and a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that it may be an RNA binding protein.


Pssm-ID: 410127  Cd Length: 89  Bit Score: 160.85  E-value: 1.05e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622968454  50 LSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKDPEYRK 129
Cdd:cd12728     1 LSKVVIRRLPPSLTKEQLEEHLQPLPEHDYFEFFSNDSSLYPHMFSRAYINFKNQEDIVLFRDRFDGYVFIDNRGQEYPA 80


                  ...
gi 1622968454 130 FLE 132
Cdd:cd12728    81 IVE 83
RRM_like_Smg4_UPF3A cd12727
RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A ...
 49-132 1.79e-43

RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A); This subgroup corresponds to the RRM-like Smg4_UPF3 domain in Upf3A, also termed regulator of nonsense transcripts 3A, or nonsense mRNA reducing factor 3A, a human ortholog of yeast Upf3p and Caenorhabditis elegans SMG-4. It derives from gene UPF3A and is required for nonsense-mediated mRNA decay (NMD) in human. Upf3A is a nucleocytoplasmic shuttling protein that associates selectively with spliced beta-globin mRNA in vivo. Like other Upf3 proteins, Upf3A contains nuclear import and export signals, and a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that it may be an RNA binding protein.


Pssm-ID: 410126  Cd Length: 87  Bit Score: 147.29  E-value: 1.79e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622968454  49 ALSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKDPEYR 128
Cdd:cd12727     1 TLSKVVIRRLPPNLTKEQLEEQLRPLPAHDYFEFFAADQSLYPHLFSRAYINFKNPEDILLFRDRFDGYVFIDNKGQEYP 80


                  ....
gi 1622968454 129 KFLE 132
Cdd:cd12727    81 AVVE 84
Smg4_UPF3 pfam03467
Smg-4/UPF3 family; This family contains proteins that are involved in nonsense mediated mRNA ...
 51-175 1.40e-35

Smg-4/UPF3 family; This family contains proteins that are involved in nonsense mediated mRNA decay. A process that is triggered by premature stop codons in mRNA. The family includes Smg-4 and UPF3.


Pssm-ID: 460932 [Multi-domain]  Cd Length: 168  Bit Score: 129.33  E-value: 1.40e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622968454  51 SKVVIRRLPPTLTKEQLQEHLQPMP-EHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNK------ 123
Cdd:pfam03467   4 TKVVIRRLPPNLTEEEFLEQLSPLPgEVDWFYFVPGKKSLKPPAYSRAYINFKDPEDLLQFADRFDGHVFVDSKgneypa 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622968454 124 ---------------------------DPEYRKFLESYATDNEKMTSTP--ETLLEEIEAKNRE---LIAKKTTPLLSFL 171
Cdd:pfam03467  84 ivefapyqkvpkkkdkkkdaregtidkDPEYKEFLESLEKPEEDPESALiqEELEEEEEEKEKEeakKEKKTTTPLIEFL 163


                  ....
gi 1622968454 172 KNKQ 175
Cdd:pfam03467 164 KEKK 167
RRM_like_Smg4_UPF3 cd12455
RNA recognition motif (RRM)-like Smg4_UPF3 domain in yeast up-frameshift suppressor 3 (Upf3p), ...
 52-132 5.14e-30

RNA recognition motif (RRM)-like Smg4_UPF3 domain in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins; This subfamily corresponds to the RRM-like Smg4_UPF3 domain found in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins. Upf3p, also termed nonsense-mediated mRNA decay protein 3, or Sua6p, a surveillance factor encoded by UPF3 gene from Saccharomyces cerevisiae. It is required for nonsense-mediated mRNA decay (NMD) in yeast. Upf3p is primarily cytoplasmic but accumulates inside the nucleus. Its nuclear import is mediated by the Srp1p (importin-alpha)/beta heterodimer while its nuclear export is mediated by a leucine-rich nuclear export sequence (NES-A), but not the Crm1p exportin. C. elegans SMG-4 is a nuclear shuttling protein that shuttles between the cytoplasm and nucleus through nuclear import and export signals similar to that of the yeast Upf3p. It is regulated by phosphorylation. Human orthologs of yeast Upf3p and C. elegans SMG-4 include Upf3A and Upf3B, which derive from two genes, UPF3A and X-linked UPF3B, respectively. Both, Upf3A (Up-frameshift suppressor 3 homolog A, also termed regulator of nonsense transcripts 3A, or nonsense mRNA reducing factor 3A) and Upf3B (Up-frameshift suppressor 3 homolog B on chromosome X, also termed regulator of nonsense transcripts 3B, or nonsense mRNA reducing factor 3B), are nucleocytoplasmic shuttling proteins. They associate selectively with spliced beta-globin mRNA in vivo, and tethering of any human Upf protein to the 3'UTR of beta-globin mRNA prevents NMD. The function of the Upf proteins in identifying and targeting nonsense mRNAs for rapid decay is conserved among eukaryotes. Besides, all Upf proteins in this family contain a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that they may be RNA binding proteins.


Pssm-ID: 409889  Cd Length: 88  Bit Score: 111.58  E-value: 5.14e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622968454  52 KVVIRRLPPTLTKEQLQEHLQPM--PEHDYFEFFSNDTSL--YPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKDPEY 127
Cdd:cd12455     1 KVVIRRLPPSLTEEEFLEQIAPLikPTVDWFYFVGGKSSLdfKPPTYSRAYINFKNPEDLIEFRRKFDGYVFVDSKGNEY 80


                  ....*
gi 1622968454 128 RKFLE 132
Cdd:cd12455    81 PAIVE 85
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 53-123 3.76e-04

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


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 38.80  E-value: 3.76e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622968454  53 VVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTslyPHMYARAYINFKNQEDIILFRDRFDGYVFLDNK 123
Cdd:cd00590     1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRD---GKSKGFAFVEFESPEDAEKALEALNGTELGGRP 68
RRM3_MEI2_EAR1_like cd12277
RNA recognition motif 3 (RRM3) found in Mei2-like proteins and terminal EAR1-like proteins; ...
 53-117 5.88e-04

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


Pssm-ID: 409719 [Multi-domain]  Cd Length: 86  Bit Score: 38.76  E-value: 5.88e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622968454  53 VVIRRLPPTLTKEQLQEHLQPM---PEHDYFEFFSNDTSLYPHMYAraYINFKNQEDIILFRDRFDGY 117
Cdd:cd12277     1 VMLRNIPNKYTQEMLLQEIDEHgkgGAYDFFYLPLDFKTKCNVGYA--FINFINPEAAERFYKAFNGK 66
 
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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