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Conserved domains on  [gi|1622885061|ref|XP_028693236|]
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regulator of nonsense transcripts 3A isoform X4 [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
Smg4_UPF3 super family cl47815
Smg-4/UPF3 family; This family contains proteins that are involved in nonsense mediated mRNA ...
 10-95 2.47e-17

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.


The actual alignment was detected with superfamily member pfam03467:

Pssm-ID: 460932 [Multi-domain]  Cd Length: 168  Bit Score: 78.09  E-value: 2.47e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622885061  10 KGLEYPAVVEFAPFQKIAKKKLKKKDAKTGSIEDDPEYKKFLETYCVEEEKTSANPETLLGEMEAKTRELIARR-----T 84
Cdd:pfam03467  77 KGNEYPAIVEFAPYQKVPKKKDKKKDAREGTIDKDPEYKEFLESLEKPEEDPESALIQEELEEEEEEKEKEEAKkekktT 156

                          90
                  ....*....|.
gi 1622885061  85 TPLLEYIKNRK 95
Cdd:pfam03467 157 TPLIEFLKEKK 167
 
Name Accession Description Interval E-value
Smg4_UPF3 pfam03467
Smg-4/UPF3 family; This family contains proteins that are involved in nonsense mediated mRNA ...
 10-95 2.47e-17

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: 78.09  E-value: 2.47e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622885061  10 KGLEYPAVVEFAPFQKIAKKKLKKKDAKTGSIEDDPEYKKFLETYCVEEEKTSANPETLLGEMEAKTRELIARR-----T 84
Cdd:pfam03467  77 KGNEYPAIVEFAPYQKVPKKKDKKKDAREGTIDKDPEYKEFLESLEKPEEDPESALIQEELEEEEEEKEKEEAKkekktT 156

                          90
                  ....*....|.
gi 1622885061  85 TPLLEYIKNRK 95
Cdd:pfam03467 157 TPLIEFLKEKK 167
RRM_like_Smg4_UPF3B cd12728
RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on ...
 10-24 9.85e-03

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: 34.89  E-value: 9.85e-03
                          10
                  ....*....|....*
gi 1622885061  10 KGLEYPAVVEFAPFQ 24
Cdd:cd12728    74 RGQEYPAIVEFAPFQ 88
 
Name Accession Description Interval E-value
Smg4_UPF3 pfam03467
Smg-4/UPF3 family; This family contains proteins that are involved in nonsense mediated mRNA ...
 10-95 2.47e-17

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: 78.09  E-value: 2.47e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622885061  10 KGLEYPAVVEFAPFQKIAKKKLKKKDAKTGSIEDDPEYKKFLETYCVEEEKTSANPETLLGEMEAKTRELIARR-----T 84
Cdd:pfam03467  77 KGNEYPAIVEFAPYQKVPKKKDKKKDAREGTIDKDPEYKEFLESLEKPEEDPESALIQEELEEEEEEKEKEEAKkekktT 156

                          90
                  ....*....|.
gi 1622885061  85 TPLLEYIKNRK 95
Cdd:pfam03467 157 TPLIEFLKEKK 167
RRM_like_Smg4_UPF3B cd12728
RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on ...
 10-24 9.85e-03

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: 34.89  E-value: 9.85e-03
                          10
                  ....*....|....*
gi 1622885061  10 KGLEYPAVVEFAPFQ 24
Cdd:cd12728    74 RGQEYPAIVEFAPFQ 88
 
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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