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Conserved domains on  [gi|25148414|ref|NP_741601|]
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UPF3 domain-containing protein [Caenorhabditis elegans]

Protein Classification

RNA-binding protein( domain architecture ID 10506944)

RNA-binding protein such as Saccharomyces cerevisiae nonsense-mediated mRNA decay protein 3 (UPF3), which is involved in nonsense-mediated decay of mRNAs containing premature stop codons; contains an RNA recognition motif (RRM)

Gene Ontology:  GO:0003723
PubMed:  15853797|22278943|18515081
SCOP:  3000110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Smg4_UPF3 pfam03467
Smg-4/UPF3 family; This family contains proteins that are involved in nonsense mediated mRNA ...
 9-171 1.26e-45

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: 152.82  E-value: 1.26e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25148414     9 VKVVLRRLPKYMTEHEVLEQISPLPEEVIGTYFHPANFSFDRCAYATLTVNFSEYcDSMMEFERRFDGYIFVDSRGNDSA 88
Cdd:pfam03467   4 TKVVIRRLPPNLTEEEFLEQLSPLPGEVDWFYFVPGKKSLKPPAYSRAYINFKDP-EDLLQFADRFDGHVFVDSKGNEYP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25148414    89 AVVEAASNQNFAKcdRNRMKEDTRVGAILTDKYYLDFCKKLEEERAIPILTLEQQIRKLNQP---DDARTQIDKMETPLV 165
Cdd:pfam03467  83 AIVEFAPYQKVPK--KKDKKKDAREGTIDKDPEYKEFLESLEKPEEDPESALIQEELEEEEEekeKEEAKKEKKTTTPLI 160


                  ....*.
gi 25148414   166 KYFFEK 171
Cdd:pfam03467 161 EFLKEK 166
 
Name Accession Description Interval E-value
Smg4_UPF3 pfam03467
Smg-4/UPF3 family; This family contains proteins that are involved in nonsense mediated mRNA ...
 9-171 1.26e-45

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: 152.82  E-value: 1.26e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25148414     9 VKVVLRRLPKYMTEHEVLEQISPLPEEVIGTYFHPANFSFDRCAYATLTVNFSEYcDSMMEFERRFDGYIFVDSRGNDSA 88
Cdd:pfam03467   4 TKVVIRRLPPNLTEEEFLEQLSPLPGEVDWFYFVPGKKSLKPPAYSRAYINFKDP-EDLLQFADRFDGHVFVDSKGNEYP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25148414    89 AVVEAASNQNFAKcdRNRMKEDTRVGAILTDKYYLDFCKKLEEERAIPILTLEQQIRKLNQP---DDARTQIDKMETPLV 165
Cdd:pfam03467  83 AIVEFAPYQKVPK--KKDKKKDAREGTIDKDPEYKEFLESLEKPEEDPESALIQEELEEEEEekeKEEAKKEKKTTTPLI 160


                  ....*.
gi 25148414   166 KYFFEK 171
Cdd:pfam03467 161 EFLKEK 166
RRM_like_Smg4_UPF3 cd12455
RNA recognition motif (RRM)-like Smg4_UPF3 domain in yeast up-frameshift suppressor 3 (Upf3p), ...
 10-94 4.05e-25

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: 96.56  E-value: 4.05e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25148414  10 KVVLRRLPKYMTEHEVLEQISPL-PEEVIGTYFHPANFS--FDRCAYATLTVNFSEYcDSMMEFERRFDGYIFVDSRGND 86
Cdd:cd12455   1 KVVIRRLPPSLTEEEFLEQIAPLiKPTVDWFYFVGGKSSldFKPPTYSRAYINFKNP-EDLIEFRRKFDGYVFVDSKGNE 79


                ....*...
gi 25148414  87 SAAVVEAA 94
Cdd:cd12455  80 YPAIVEFA 87
 
Name Accession Description Interval E-value
Smg4_UPF3 pfam03467
Smg-4/UPF3 family; This family contains proteins that are involved in nonsense mediated mRNA ...
 9-171 1.26e-45

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: 152.82  E-value: 1.26e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25148414     9 VKVVLRRLPKYMTEHEVLEQISPLPEEVIGTYFHPANFSFDRCAYATLTVNFSEYcDSMMEFERRFDGYIFVDSRGNDSA 88
Cdd:pfam03467   4 TKVVIRRLPPNLTEEEFLEQLSPLPGEVDWFYFVPGKKSLKPPAYSRAYINFKDP-EDLLQFADRFDGHVFVDSKGNEYP 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25148414    89 AVVEAASNQNFAKcdRNRMKEDTRVGAILTDKYYLDFCKKLEEERAIPILTLEQQIRKLNQP---DDARTQIDKMETPLV 165
Cdd:pfam03467  83 AIVEFAPYQKVPK--KKDKKKDAREGTIDKDPEYKEFLESLEKPEEDPESALIQEELEEEEEekeKEEAKKEKKTTTPLI 160


                  ....*.
gi 25148414   166 KYFFEK 171
Cdd:pfam03467 161 EFLKEK 166
RRM_like_Smg4_UPF3 cd12455
RNA recognition motif (RRM)-like Smg4_UPF3 domain in yeast up-frameshift suppressor 3 (Upf3p), ...
 10-94 4.05e-25

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: 96.56  E-value: 4.05e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25148414  10 KVVLRRLPKYMTEHEVLEQISPL-PEEVIGTYFHPANFS--FDRCAYATLTVNFSEYcDSMMEFERRFDGYIFVDSRGND 86
Cdd:cd12455   1 KVVIRRLPPSLTEEEFLEQIAPLiKPTVDWFYFVGGKSSldFKPPTYSRAYINFKNP-EDLIEFRRKFDGYVFVDSKGNE 79


                ....*...
gi 25148414  87 SAAVVEAA 94
Cdd:cd12455  80 YPAIVEFA 87
RRM_like_Smg4_UPF3B cd12728
RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on ...
 10-97 4.88e-12

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: 61.08  E-value: 4.88e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25148414  10 KVVLRRLPKYMTEHEVLEQISPLPEEVIGTYFhPANFSFDRCAYATLTVNFSEYCDSMMeFERRFDGYIFVDSRGNDSAA 89
Cdd:cd12728   3 KVVIRRLPPSLTKEQLEEHLQPLPEHDYFEFF-SNDSSLYPHMFSRAYINFKNQEDIVL-FRDRFDGYVFIDNRGQEYPA 80


                ....*...
gi 25148414  90 VVEAASNQ 97
Cdd:cd12728  81 IVEFAPFQ 88
RRM_like_Smg4_UPF3A cd12727
RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A ...
 8-94 1.10e-11

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: 60.23  E-value: 1.10e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25148414   8 HVKVVLRRLPKYMTEHEVLEQISPLPEEVIGTYFhPANFSFDRCAYATLTVNFSEYCDSMMeFERRFDGYIFVDSRGNDS 87
Cdd:cd12727   2 LSKVVIRRLPPNLTKEQLEEQLRPLPAHDYFEFF-AADQSLYPHLFSRAYINFKNPEDILL-FRDRFDGYVFIDNKGQEY 79


                ....*..
gi 25148414  88 AAVVEAA 94
Cdd:cd12727  80 PAVVEFA 86
 
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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