Q9BYJ9 · YTHD1_HUMAN
- ProteinYTH domain-containing family protein 1
- GeneYTHDF1
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids559 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in mRNA stability and processing (PubMed:24284625, PubMed:32492408).
Acts as a regulator of mRNA stability by promoting degradation of m6A-containing mRNAs via interaction with the CCR4-NOT complex (PubMed:32492408).
The YTHDF paralogs (YTHDF1, YTHDF2 and YTHDF3) shares m6A-containing mRNAs targets and act redundantly to mediate mRNA degradation and cellular differentiation (PubMed:28106072, PubMed:32492408).
Required to facilitate learning and memory formation in the hippocampus by binding to m6A-containing neuronal mRNAs (By similarity).
Acts as a regulator of axon guidance by binding to m6A-containing ROBO3 transcripts (By similarity).
Acts as a negative regulator of antigen cross-presentation in myeloid dendritic cells (By similarity).
In the context of tumorigenesis, negative regulation of antigen cross-presentation limits the anti-tumor response by reducing efficiency of tumor-antigen cross-presentation (By similarity).
Promotes formation of phase-separated membraneless compartments, such as P-bodies or stress granules, by undergoing liquid-liquid phase separation upon binding to mRNAs containing multiple m6A-modified residues: polymethylated mRNAs act as a multivalent scaffold for the binding of YTHDF proteins, juxtaposing their disordered regions and thereby leading to phase separation (PubMed:31292544, PubMed:31388144, PubMed:32451507).
The resulting mRNA-YTHDF complexes then partition into different endogenous phase-separated membraneless compartments, such as P-bodies, stress granules or neuronal RNA granules (PubMed:31292544).
Features
Showing features for binding site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 395-397 | N6-methyladenosine 5'-phosphate residue (UniProtKB | ChEBI) of RNA (UniProtKB | ChEBI) | ||||
Sequence: KSY | ||||||
Binding site | 401 | N6-methyladenosine 5'-phosphate residue (UniProtKB | ChEBI) of RNA (UniProtKB | ChEBI) | ||||
Sequence: D | ||||||
Binding site | 411-412 | N6-methyladenosine 5'-phosphate residue (UniProtKB | ChEBI) of RNA (UniProtKB | ChEBI) | ||||
Sequence: WC | ||||||
Binding site | 441 | N6-methyladenosine 5'-phosphate residue (UniProtKB | ChEBI) of RNA (UniProtKB | ChEBI) | ||||
Sequence: N | ||||||
Binding site | 465 | N6-methyladenosine 5'-phosphate residue (UniProtKB | ChEBI) of RNA (UniProtKB | ChEBI) | ||||
Sequence: W | ||||||
Binding site | 470 | N6-methyladenosine 5'-phosphate residue (UniProtKB | ChEBI) of RNA (UniProtKB | ChEBI) | ||||
Sequence: W |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytoplasm | |
Cellular Component | cytoplasmic stress granule | |
Cellular Component | P-body | |
Molecular Function | mRNA binding | |
Molecular Function | N6-methyladenosine-containing RNA reader activity | |
Molecular Function | ribosome binding | |
Molecular Function | RNA binding | |
Biological Process | immune system process | |
Biological Process | learning | |
Biological Process | memory | |
Biological Process | mRNA destabilization | |
Biological Process | organelle assembly | |
Biological Process | positive regulation of translation | |
Biological Process | positive regulation of translational initiation | |
Biological Process | regulation of antigen processing and presentation | |
Biological Process | regulation of axon guidance | |
Biological Process | regulation of long-term synaptic potentiation | |
Biological Process | regulation of mRNA stability | |
Biological Process | stress granule assembly |
Keywords
- Molecular function
- Biological process
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameYTH domain-containing family protein 1
- Short namesDF1
- Alternative names
Gene names
Organism names
- Organism
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Homo
Accessions
- Primary accessionQ9BYJ9
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
Keywords
- Cellular component
Disease & Variants
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 397 | Strongly reduced binding to N6-methyladenosine (m6A)-containing RNAs. | ||||
Sequence: Y → A | ||||||
Mutagenesis | 401 | Increased binding to N6-methyladenosine (m6A)-containing RNAs. | ||||
Sequence: D → N | ||||||
Mutagenesis | 411 | Abolished binding to N6-methyladenosine (m6A)-containing RNAs. | ||||
Sequence: W → A | ||||||
Mutagenesis | 465 | Abolished binding to N6-methyladenosine (m6A)-containing RNAs. | ||||
Sequence: W → A | ||||||
Mutagenesis | 470 | Abolished binding to N6-methyladenosine (m6A)-containing RNAs. | ||||
Sequence: W → A | ||||||
Mutagenesis | 506 | Reduced binding to N6-methyladenosine (m6A)-containing RNAs. | ||||
Sequence: R → A |
Variants
We now provide the "Disease & Variants" viewer in its own tab.
The viewer provides 598 variants from UniProt as well as other sources including ClinVar and dbSNP.
Organism-specific databases
Miscellaneous
Chemistry
Genetic variation databases
PTM/Processing
Features
Showing features for initiator methionine, modified residue, chain, modified residue (large scale data).
Type | ID | Position(s) | Source | Description | |||
---|---|---|---|---|---|---|---|
Initiator methionine | 1 | UniProt | Removed | ||||
Sequence: M | |||||||
Modified residue | 2 | UniProt | N-acetylserine | ||||
Sequence: S | |||||||
Chain | PRO_0000223073 | 2-559 | UniProt | YTH domain-containing family protein 1 | |||
Sequence: SATSVDTQRTKGQDNKVQNGSLHQKDTVHDNDFEPYLTGQSNQSNSYPSMSDPYLSSYYPPSIGFPYSLNEAPWSTAGDPPIPYLTTYGQLSNGDHHFMHDAVFGQPGGLGNNIYQHRFNFFPENPAFSAWGTSGSQGQQTQSSAYGSSYTYPPSSLGGTVVDGQPGFHSDTLSKAPGMNSLEQGMVGLKIGDVSSSAVKTVGSVVSSVALTGVLSGNGGTNVNMPVSKPTSWAAIASKPAKPQPKMKTKSGPVMGGGLPPPPIKHNMDIGTWDNKGPVPKAPVPQQAPSPQAAPQPQQVAQPLPAQPPALAQPQYQSPQQPPQTRWVAPRNRNAAFGQSGGAGSDSNSPGNVQPNSAPSVESHPVLEKLKAAHSYNPKEFEWNLKSGRVFIIKSYSEDDIHRSIKYSIWCSTEHGNKRLDSAFRCMSSKGPVYLLFSVNGSGHFCGVAEMKSPVDYGTSAGVWSQDKWKGKFDVQWIFVKDVPNNQLRHIRLENNDNKPVTNSRDTQEVPLEKAKQVLKIISSYKHTTSIFDDFAHYEKRQEEEEVVRKERQSRNKQ | |||||||
Modified residue | 182 | UniProt | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 182 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 198 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 252 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 273 | PRIDE | Phosphothreonine | ||||
Sequence: T | |||||||
Modified residue (large scale data) | 341 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 346 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 348 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 350 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 398 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 531 | PRIDE | Phosphoserine | ||||
Sequence: S |
Keywords
- PTM
Proteomic databases
PTM databases
Expression
Interaction
Subunit
Interacts with ribosomes (PubMed:26046440).
Interacts with eIF3 (EIF3A or EIF3B) (PubMed:26046440).
Interacts with YTHDF3 (PubMed:28106072).
Binary interactions
Protein-protein interaction databases
Chemistry
Miscellaneous
Structure
Family & Domains
Features
Showing features for compositional bias, region, domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 1-23 | Polar residues | ||||
Sequence: MSATSVDTQRTKGQDNKVQNGSL | ||||||
Region | 1-50 | Disordered | ||||
Sequence: MSATSVDTQRTKGQDNKVQNGSLHQKDTVHDNDFEPYLTGQSNQSNSYPS | ||||||
Compositional bias | 35-50 | Polar residues | ||||
Sequence: EPYLTGQSNQSNSYPS | ||||||
Region | 238-363 | Disordered | ||||
Sequence: ASKPAKPQPKMKTKSGPVMGGGLPPPPIKHNMDIGTWDNKGPVPKAPVPQQAPSPQAAPQPQQVAQPLPAQPPALAQPQYQSPQQPPQTRWVAPRNRNAAFGQSGGAGSDSNSPGNVQPNSAPSVE | ||||||
Compositional bias | 283-317 | Pro residues | ||||
Sequence: APVPQQAPSPQAAPQPQQVAQPLPAQPPALAQPQY | ||||||
Compositional bias | 339-362 | Polar residues | ||||
Sequence: GQSGGAGSDSNSPGNVQPNSAPSV | ||||||
Domain | 389-523 | YTH | ||||
Sequence: GRVFIIKSYSEDDIHRSIKYSIWCSTEHGNKRLDSAFRCMSSKGPVYLLFSVNGSGHFCGVAEMKSPVDYGTSAGVWSQDKWKGKFDVQWIFVKDVPNNQLRHIRLENNDNKPVTNSRDTQEVPLEKAKQVLKII |
Domain
This leads to the partition of m6A-containing mRNAs into membraneless compartments, where mRNAs may be stored, degraded or used to transport mRNAs to dendritic arbors in neurons (PubMed:31292544).
Sequence similarities
Phylogenomic databases
Family and domain databases
Sequence & Isoform
- Sequence statusComplete
This entry describes 2 isoforms produced by Alternative splicing.
Q9BYJ9-1
This isoform has been chosen as the canonical sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
- Name1
- Length559
- Mass (Da)60,874
- Last updated2001-06-01 v1
- ChecksumDB8AA15636130E18
Q9BYJ9-2
- Name2
Computationally mapped potential isoform sequences
There is 1 potential isoform mapped to this entry
Entry | Entry name | Gene name | Length | ||
---|---|---|---|---|---|
Q5JXC6 | Q5JXC6_HUMAN | YTHDF1 | 52 |
Features
Showing features for compositional bias, alternative sequence, sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 1-23 | Polar residues | ||||
Sequence: MSATSVDTQRTKGQDNKVQNGSL | ||||||
Alternative sequence | VSP_006815 | 1-190 | in isoform 2 | |||
Sequence: Missing | ||||||
Compositional bias | 35-50 | Polar residues | ||||
Sequence: EPYLTGQSNQSNSYPS | ||||||
Sequence conflict | 123-124 | in Ref. 4; BAB62751 | ||||
Sequence: FP → AR | ||||||
Alternative sequence | VSP_006816 | 191-260 | in isoform 2 | |||
Sequence: KIGDVSSSAVKTVGSVVSSVALTGVLSGNGGTNVNMPVSKPTSWAAIASKPAKPQPKMKTKSGPVMGGGL → MLFLGSLGAWGTTSISTGSIFSLKTLRSQHGGQVGLKVSRPRAPRMGAATPTPRAPWVARWLMGSQAFTATPSAR | ||||||
Sequence conflict | 283-284 | in Ref. 5; CAD39029 | ||||
Sequence: AP → PH | ||||||
Compositional bias | 283-317 | Pro residues | ||||
Sequence: APVPQQAPSPQAAPQPQQVAQPLPAQPPALAQPQY | ||||||
Compositional bias | 339-362 | Polar residues | ||||
Sequence: GQSGGAGSDSNSPGNVQPNSAPSV | ||||||
Alternative sequence | VSP_006817 | 383-559 | in isoform 2 | |||
Sequence: Missing |
Keywords
- Coding sequence diversity
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AK000398 EMBL· GenBank· DDBJ | BAA91138.1 EMBL· GenBank· DDBJ | mRNA | ||
AL096828 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. | |
BC003681 EMBL· GenBank· DDBJ | AAH03681.1 EMBL· GenBank· DDBJ | mRNA | ||
BC016920 EMBL· GenBank· DDBJ | AAH16920.2 EMBL· GenBank· DDBJ | mRNA | ||
BC025264 EMBL· GenBank· DDBJ | AAH25264.1 EMBL· GenBank· DDBJ | mRNA | ||
BC050284 EMBL· GenBank· DDBJ | AAH50284.1 EMBL· GenBank· DDBJ | mRNA | ||
AB055518 EMBL· GenBank· DDBJ | BAB62751.1 EMBL· GenBank· DDBJ | mRNA | ||
AL834366 EMBL· GenBank· DDBJ | CAD39029.1 EMBL· GenBank· DDBJ | mRNA |