UniProtKB - Q9BYJ9 (YTHD1_HUMAN)
Protein
YTH domain-containing family protein 1
Gene
YTHDF1
Organism
Homo sapiens (Human)
Status
Functioni
Specifically recognizes and binds N6-methyladenosine (m6A)-containing mRNAs, and promotes mRNA translation efficiency (PubMed:24284625, PubMed:26046440, PubMed:26318451). M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability (PubMed:24284625). Acts as a regulator of mRNA translation efficiency: promotes ribosome loading to m6A-containing mRNAs and interacts with translation initiation factors eIF3 (EIF3A or EIF3B) to facilitate translation initiation (PubMed:26046440). Required to facilitate learning and memory formation in the hippocampus by enhancing protein synthesis upon neuronal stimulation: in response to neuronal stimulation, binds to m6A-containing neuronal mRNAs, promoting their translation, thereby contributing to learning and memory (By similarity). Acts as a regulator of axon guidance by binding to m6A-containing ROBO3 transcripts, thereby promoting their translation (By similarity). Acts as a negative regulator of antigen cross-presentation in myeloid dendritic cells (By similarity). Acts by binding and promoting translation of m6A-containing transcripts encoding proteins involved in lysosomal degradation and phagosome maturation, leading to increased antigen degradation 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).By similarity3 Publications
Caution
Promotes mRNA translation efficiency (PubMed:26046440). It is however unclear whether it plays a role in cap-independent mRNA translation following heat shock stress, since it has not been identified purified eIF3 preparations that promote cap-independent mRNA translation (PubMed:26593424).2 Publications
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 401 | N6-methyladenosineCombined sources1 Publication | 1 | |
Binding sitei | 441 | N6-methyladenosineBy similarity | 1 | |
Binding sitei | 465 | N6-methyladenosineCombined sources1 Publication | 1 | |
Binding sitei | 470 | N6-methyladenosineCombined sources1 Publication | 1 |
GO - Molecular functioni
- mRNA binding Source: GO_Central
- N6-methyladenosine-containing RNA binding Source: UniProtKB
- ribosome binding Source: UniProtKB
- RNA binding Source: UniProtKB
GO - Biological processi
- immune system process Source: UniProtKB-KW
- learning Source: UniProtKB
- memory Source: UniProtKB
- mRNA destabilization Source: GO_Central
- positive regulation of translation Source: UniProtKB
- positive regulation of translational initiation Source: UniProtKB
- regulation of antigen processing and presentation Source: UniProtKB
- regulation of axon guidance Source: UniProtKB
- regulation of long-term synaptic potentiation Source: UniProtKB
Keywordsi
Molecular function | RNA-binding |
Biological process | Immunity |
Enzyme and pathway databases
PathwayCommonsi | Q9BYJ9 |
Names & Taxonomyi
Protein namesi | Recommended name: YTH domain-containing family protein 1CuratedAlternative name(s): Dermatomyositis associated with cancer putative autoantigen 11 Publication Short name: DACA-11 Publication |
Gene namesi | |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
EuPathDBi | HostDB:ENSG00000149658.17 |
HGNCi | HGNC:15867, YTHDF1 |
MIMi | 616529, gene |
neXtProti | NX_Q9BYJ9 |
Subcellular locationi
Keywords - Cellular componenti
CytoplasmPathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 397 | Y → A: Strongly reduced binding to N6-methyladenosine (m6A)-containing RNAs. 1 Publication | 1 | |
Mutagenesisi | 401 | D → N: Increased binding to N6-methyladenosine (m6A)-containing RNAs. 1 Publication | 1 | |
Mutagenesisi | 411 | W → A: Abolished binding to N6-methyladenosine (m6A)-containing RNAs. 1 Publication | 1 | |
Mutagenesisi | 465 | W → A: Abolished binding to N6-methyladenosine (m6A)-containing RNAs. 1 Publication | 1 | |
Mutagenesisi | 470 | W → A: Abolished binding to N6-methyladenosine (m6A)-containing RNAs. 1 Publication | 1 | |
Mutagenesisi | 506 | R → A: Reduced binding to N6-methyladenosine (m6A)-containing RNAs. 1 Publication | 1 |
Organism-specific databases
DisGeNETi | 54915 |
OpenTargetsi | ENSG00000149658 |
PharmGKBi | PA25737 |
Miscellaneous databases
Pharosi | Q9BYJ9, Tbio |
Polymorphism and mutation databases
BioMutai | YTHDF1 |
DMDMi | 28380041 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Initiator methioninei | RemovedCombined sources | |||
ChainiPRO_0000223073 | 2 – 559 | YTH domain-containing family protein 1Add BLAST | 558 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 2 | N-acetylserineCombined sources | 1 | |
Modified residuei | 182 | PhosphoserineCombined sources | 1 |
Keywords - PTMi
Acetylation, PhosphoproteinProteomic databases
EPDi | Q9BYJ9 |
jPOSTi | Q9BYJ9 |
MassIVEi | Q9BYJ9 |
MaxQBi | Q9BYJ9 |
PaxDbi | Q9BYJ9 |
PeptideAtlasi | Q9BYJ9 |
PRIDEi | Q9BYJ9 |
ProteomicsDBi | 79659 [Q9BYJ9-1] 79660 [Q9BYJ9-2] |
PTM databases
GlyConnecti | 2853, 1 O-Linked glycan (1 site) |
GlyGeni | Q9BYJ9, 5 sites, 1 O-linked glycan (5 sites) |
iPTMneti | Q9BYJ9 |
MetOSitei | Q9BYJ9 |
PhosphoSitePlusi | Q9BYJ9 |
Expressioni
Gene expression databases
Bgeei | ENSG00000149658, Expressed in female gonad and 245 other tissues |
ExpressionAtlasi | Q9BYJ9, baseline and differential |
Genevisiblei | Q9BYJ9, HS |
Organism-specific databases
HPAi | ENSG00000149658, Low tissue specificity |
Interactioni
Subunit structurei
Binary interactionsi
Hide detailsQ9BYJ9
Protein-protein interaction databases
BioGRIDi | 120257, 102 interactors |
IntActi | Q9BYJ9, 59 interactors |
MINTi | Q9BYJ9 |
STRINGi | 9606.ENSP00000359364 |
Miscellaneous databases
RNActi | Q9BYJ9, protein |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | Q9BYJ9 |
ModBasei | Search... |
PDBe-KBi | Search... |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 389 – 523 | YTHPROSITE-ProRule annotationAdd BLAST | 135 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 395 – 397 | N6-methyladenosine bindingCombined sources1 Publication | 3 | |
Regioni | 411 – 412 | N6-methyladenosine bindingCombined sources1 Publication | 2 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 241 – 331 | Gln/Pro-richAdd BLAST | 91 |
Phylogenomic databases
eggNOGi | KOG1901, Eukaryota |
GeneTreei | ENSGT00940000156911 |
HOGENOMi | CLU_022715_0_0_1 |
InParanoidi | Q9BYJ9 |
OMAi | QNRWIAP |
OrthoDBi | 1523251at2759 |
PhylomeDBi | Q9BYJ9 |
TreeFami | TF323736 |
Family and domain databases
InterProi | View protein in InterPro IPR007275, YTH_domain |
Pfami | View protein in Pfam PF04146, YTH, 1 hit |
PROSITEi | View protein in PROSITE PS50882, YTH, 1 hit |
s (2+)i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
This entry describes 2 produced by isoformsialternative splicing. AlignAdd to basketThis entry has 2 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All
Isoform 1 (identifier: Q9BYJ9-1) [UniParc]FASTAAdd to basket
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
10 20 30 40 50
MSATSVDTQR TKGQDNKVQN GSLHQKDTVH DNDFEPYLTG QSNQSNSYPS
60 70 80 90 100
MSDPYLSSYY PPSIGFPYSL NEAPWSTAGD PPIPYLTTYG QLSNGDHHFM
110 120 130 140 150
HDAVFGQPGG LGNNIYQHRF NFFPENPAFS AWGTSGSQGQ QTQSSAYGSS
160 170 180 190 200
YTYPPSSLGG TVVDGQPGFH SDTLSKAPGM NSLEQGMVGL KIGDVSSSAV
210 220 230 240 250
KTVGSVVSSV ALTGVLSGNG GTNVNMPVSK PTSWAAIASK PAKPQPKMKT
260 270 280 290 300
KSGPVMGGGL PPPPIKHNMD IGTWDNKGPV PKAPVPQQAP SPQAAPQPQQ
310 320 330 340 350
VAQPLPAQPP ALAQPQYQSP QQPPQTRWVA PRNRNAAFGQ SGGAGSDSNS
360 370 380 390 400
PGNVQPNSAP SVESHPVLEK LKAAHSYNPK EFEWNLKSGR VFIIKSYSED
410 420 430 440 450
DIHRSIKYSI WCSTEHGNKR LDSAFRCMSS KGPVYLLFSV NGSGHFCGVA
460 470 480 490 500
EMKSPVDYGT SAGVWSQDKW KGKFDVQWIF VKDVPNNQLR HIRLENNDNK
510 520 530 540 550
PVTNSRDTQE VPLEKAKQVL KIISSYKHTT SIFDDFAHYE KRQEEEEVVR
KERQSRNKQ
Computationally mapped potential isoform sequencesi
There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basketQ5JXC6 | Q5JXC6_HUMAN | YTH domain-containing family protei... | YTHDF1 | 52 | Annotation score: |
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 123 – 124 | FP → AR in BAB62751 (Ref. 4) Curated | 2 | |
Sequence conflicti | 283 – 284 | AP → PH in CAD39029 (PubMed:17974005).Curated | 2 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_006815 | 1 – 190 | Missing in isoform 2. 1 PublicationAdd BLAST | 190 | |
Alternative sequenceiVSP_006816 | 191 – 260 | KIGDV…MGGGL → MLFLGSLGAWGTTSISTGSI FSLKTLRSQHGGQVGLKVSR PRAPRMGAATPTPRAPWVAR WLMGSQAFTATPSAR in isoform 2. 1 PublicationAdd BLAST | 70 | |
Alternative sequenceiVSP_006817 | 383 – 559 | Missing in isoform 2. 1 PublicationAdd BLAST | 177 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AK000398 mRNA Translation: BAA91138.1 AL096828 Genomic DNA No translation available. BC003681 mRNA Translation: AAH03681.1 BC016920 mRNA Translation: AAH16920.2 BC025264 mRNA Translation: AAH25264.1 BC050284 mRNA Translation: AAH50284.1 AB055518 mRNA Translation: BAB62751.1 AL834366 mRNA Translation: CAD39029.1 |
CCDSi | CCDS13511.1 [Q9BYJ9-1] |
RefSeqi | NP_060268.2, NM_017798.3 [Q9BYJ9-1] |
Genome annotation databases
Ensembli | ENST00000370339; ENSP00000359364; ENSG00000149658 [Q9BYJ9-1] |
GeneIDi | 54915 |
KEGGi | hsa:54915 |
UCSCi | uc002yeh.4, human [Q9BYJ9-1] |
Keywords - Coding sequence diversityi
Alternative splicingSimilar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AK000398 mRNA Translation: BAA91138.1 AL096828 Genomic DNA No translation available. BC003681 mRNA Translation: AAH03681.1 BC016920 mRNA Translation: AAH16920.2 BC025264 mRNA Translation: AAH25264.1 BC050284 mRNA Translation: AAH50284.1 AB055518 mRNA Translation: BAB62751.1 AL834366 mRNA Translation: CAD39029.1 |
CCDSi | CCDS13511.1 [Q9BYJ9-1] |
RefSeqi | NP_060268.2, NM_017798.3 [Q9BYJ9-1] |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
4RCI | X-ray | 1.97 | A/B/C/D | 361-559 | [»] | |
4RCJ | X-ray | 1.60 | A | 365-554 | [»] | |
SMRi | Q9BYJ9 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 120257, 102 interactors |
IntActi | Q9BYJ9, 59 interactors |
MINTi | Q9BYJ9 |
STRINGi | 9606.ENSP00000359364 |
PTM databases
GlyConnecti | 2853, 1 O-Linked glycan (1 site) |
GlyGeni | Q9BYJ9, 5 sites, 1 O-linked glycan (5 sites) |
iPTMneti | Q9BYJ9 |
MetOSitei | Q9BYJ9 |
PhosphoSitePlusi | Q9BYJ9 |
Polymorphism and mutation databases
BioMutai | YTHDF1 |
DMDMi | 28380041 |
Proteomic databases
EPDi | Q9BYJ9 |
jPOSTi | Q9BYJ9 |
MassIVEi | Q9BYJ9 |
MaxQBi | Q9BYJ9 |
PaxDbi | Q9BYJ9 |
PeptideAtlasi | Q9BYJ9 |
PRIDEi | Q9BYJ9 |
ProteomicsDBi | 79659 [Q9BYJ9-1] 79660 [Q9BYJ9-2] |
Protocols and materials databases
Antibodypediai | 44459, 126 antibodies |
Genome annotation databases
Ensembli | ENST00000370339; ENSP00000359364; ENSG00000149658 [Q9BYJ9-1] |
GeneIDi | 54915 |
KEGGi | hsa:54915 |
UCSCi | uc002yeh.4, human [Q9BYJ9-1] |
Organism-specific databases
CTDi | 54915 |
DisGeNETi | 54915 |
EuPathDBi | HostDB:ENSG00000149658.17 |
GeneCardsi | YTHDF1 |
HGNCi | HGNC:15867, YTHDF1 |
HPAi | ENSG00000149658, Low tissue specificity |
MIMi | 616529, gene |
neXtProti | NX_Q9BYJ9 |
OpenTargetsi | ENSG00000149658 |
PharmGKBi | PA25737 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG1901, Eukaryota |
GeneTreei | ENSGT00940000156911 |
HOGENOMi | CLU_022715_0_0_1 |
InParanoidi | Q9BYJ9 |
OMAi | QNRWIAP |
OrthoDBi | 1523251at2759 |
PhylomeDBi | Q9BYJ9 |
TreeFami | TF323736 |
Enzyme and pathway databases
PathwayCommonsi | Q9BYJ9 |
Miscellaneous databases
BioGRID-ORCSi | 54915, 3 hits in 839 CRISPR screens |
ChiTaRSi | YTHDF1, human |
GenomeRNAii | 54915 |
Pharosi | Q9BYJ9, Tbio |
PROi | PR:Q9BYJ9 |
RNActi | Q9BYJ9, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000149658, Expressed in female gonad and 245 other tissues |
ExpressionAtlasi | Q9BYJ9, baseline and differential |
Genevisiblei | Q9BYJ9, HS |
Family and domain databases
InterProi | View protein in InterPro IPR007275, YTH_domain |
Pfami | View protein in Pfam PF04146, YTH, 1 hit |
PROSITEi | View protein in PROSITE PS50882, YTH, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | YTHD1_HUMAN | |
Accessioni | Q9BYJ9Primary (citable) accession number: Q9BYJ9 Secondary accession number(s): Q8N3G5 Q9NX79 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | February 12, 2003 |
Last sequence update: | June 1, 2001 | |
Last modified: | December 2, 2020 | |
This is version 165 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - Human chromosome 20
Human chromosome 20: entries, gene names and cross-references to MIM