F1RCY6 · RENT1_DANRE
- ProteinRegulator of nonsense transcripts 1
- Geneupf1
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids1100 (go to sequence)
- Protein existenceEvidence at transcript level
- Annotation score5/5
Function
function
RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. The formation of an upf1-upf2-upf3 surveillance complex is believed to activate NMD.
Features
Showing features for binding site.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Binding site | 102 | Zn2+ 1 (UniProtKB | ChEBI) | |||
Binding site | 105 | Zn2+ 1 (UniProtKB | ChEBI) | |||
Binding site | 116 | Zn2+ 2 (UniProtKB | ChEBI) | |||
Binding site | 119 | Zn2+ 2 (UniProtKB | ChEBI) | |||
Binding site | 124 | Zn2+ 1 (UniProtKB | ChEBI) | |||
Binding site | 134 | Zn2+ 1 (UniProtKB | ChEBI) | |||
Binding site | 138 | Zn2+ 2 (UniProtKB | ChEBI) | |||
Binding site | 144 | Zn2+ 2 (UniProtKB | ChEBI) | |||
Binding site | 162 | Zn2+ 3 (UniProtKB | ChEBI) | |||
Binding site | 165 | Zn2+ 3 (UniProtKB | ChEBI) | |||
Binding site | 188 | Zn2+ 3 (UniProtKB | ChEBI) | |||
Binding site | 192 | Zn2+ 3 (UniProtKB | ChEBI) | |||
Binding site | 455 | ATP (UniProtKB | ChEBI) | |||
Binding site | 475-479 | ATP (UniProtKB | ChEBI) | |||
Binding site | 645 | ATP (UniProtKB | ChEBI) | |||
Binding site | 682 | ATP (UniProtKB | ChEBI) | |||
Binding site | 813 | ATP (UniProtKB | ChEBI) | |||
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytoplasm | |
Cellular Component | nucleus | |
Cellular Component | P-body | |
Cellular Component | perinuclear region of cytoplasm | |
Molecular Function | ATP binding | |
Molecular Function | DNA binding | |
Molecular Function | hydrolase activity | |
Molecular Function | RNA binding | |
Molecular Function | RNA helicase activity | |
Molecular Function | zinc ion binding | |
Biological Process | chordate embryonic development | |
Biological Process | nuclear-transcribed mRNA catabolic process | |
Biological Process | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | |
Biological Process | positive regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | |
Biological Process | regulation of gene expression | |
Biological Process | T cell differentiation in thymus |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameRegulator of nonsense transcripts 1
- EC number
- Alternative names
Gene names
Organism names
- Strains
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Actinopterygii > Neopterygii > Teleostei > Ostariophysi > Cypriniformes > Danionidae > Danioninae > Danio
Accessions
- Primary accessionF1RCY6
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
UniProt Annotation
GO Annotation
Keywords
- Cellular component
Phenotypes & Variants
Disruption phenotype
Morpholino knockdown leads to both intermediate and severe phenotypes of abnormal embryonic development (PubMed:19414594, PubMed:21227923).
Intermediate phenotypes show developmental delay, including aberrant formation of the head, tail, eye placodes and somites (PubMed:19414594, PubMed:21227923).
Severe phenotypes show severe developmental arrest, including yolk extension defects, and lack of recognizable morphological development (PubMed:19414594, PubMed:21227923).
High mortality rates of 80% to 85% at 5 days post-fertilization (PubMed:19414594).
Increase in premature stop codon containing slc24a5 mRNA transcript levels in melanocytes (PubMed:19414594, PubMed:21227923).
Intermediate phenotypes show developmental delay, including aberrant formation of the head, tail, eye placodes and somites (PubMed:19414594, PubMed:21227923).
Severe phenotypes show severe developmental arrest, including yolk extension defects, and lack of recognizable morphological development (PubMed:19414594, PubMed:21227923).
High mortality rates of 80% to 85% at 5 days post-fertilization (PubMed:19414594).
Increase in premature stop codon containing slc24a5 mRNA transcript levels in melanocytes (PubMed:19414594, PubMed:21227923).
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Chain | PRO_0000454185 | 1-1100 | Regulator of nonsense transcripts 1 | ||
Keywords
- PTM
Proteomic databases
Expression
Developmental stage
Expressed during early cleavage, gastrulation and at 1 day post-fertilization.
Gene expression databases
Interaction
Protein-protein interaction databases
Structure
Family & Domains
Features
Showing features for compositional bias, region, domain.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Compositional bias | 42-60 | Polar residues | |||
Region | 42-67 | Disordered | |||
Domain | 94-251 | Upf1 CH-rich | |||
Region | 102-134 | C3H | |||
Region | 116-144 | CC/SHH/C | |||
Region | 162-192 | C4 | |||
Region | 978-1065 | Disordered | |||
Compositional bias | 1005-1065 | Polar residues | |||
Sequence similarities
Belongs to the DNA2/NAM7 helicase family.
Keywords
- Domain
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length1,100
- Mass (Da)122,079
- Last updated2011-05-03 v1
- Checksum4DEA014222AA8F59
Computationally mapped potential isoform sequences
There is 1 potential isoform mapped to this entry
Entry | Entry name | Gene name | Length | ||
---|---|---|---|---|---|
A0A8M2BAV2 | A0A8M2BAV2_DANRE | upf1 | 1099 |
Features
Showing features for compositional bias, sequence conflict.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Compositional bias | 42-60 | Polar residues | |||
Sequence conflict | 96 | in Ref. 1; CAX18770 and 3; AAH45353 | |||
Compositional bias | 1005-1065 | Polar residues | |||
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
FM986817 EMBL· GenBank· DDBJ | CAX18770.1 EMBL· GenBank· DDBJ | mRNA | ||
CR931779 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. | |
CU693375 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. | |
BC045353 EMBL· GenBank· DDBJ | AAH45353.1 EMBL· GenBank· DDBJ | mRNA |