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Protein

YTH domain-containing family protein 1

Gene

YTHDF1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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).3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei401N6-methyladenosineCombined sources1 Publication1
Binding sitei441N6-methyladenosineBy similarity1
Binding sitei465N6-methyladenosineCombined sources1 Publication1
Binding sitei470N6-methyladenosineCombined sources1 Publication1

GO - Molecular functioni

  • N6-methyladenosine-containing RNA binding Source: UniProtKB
  • poly(A) RNA binding Source: UniProtKB
  • ribosome binding Source: UniProtKB

GO - Biological processi

  • positive regulation of translational initiation Source: UniProtKB
Complete GO annotation...

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
YTH domain-containing family protein 1Curated
Alternative name(s):
Dermatomyositis associated with cancer putative autoantigen 11 Publication
Short name:
DACA-11 Publication
Gene namesi
Name:YTHDF1Imported
Synonyms:C20orf21Imported
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:15867. YTHDF1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi397Y → A: Strongly reduced binding to N6-methyladenosine (m6A)-containing RNAs. 1 Publication1
Mutagenesisi401D → N: Increased binding to N6-methyladenosine (m6A)-containing RNAs. 1 Publication1
Mutagenesisi411W → A: Abolished binding to N6-methyladenosine (m6A)-containing RNAs. 1 Publication1
Mutagenesisi465W → A: Abolished binding to N6-methyladenosine (m6A)-containing RNAs. 1 Publication1
Mutagenesisi470W → A: Abolished binding to N6-methyladenosine (m6A)-containing RNAs. 1 Publication1
Mutagenesisi506R → A: Reduced binding to N6-methyladenosine (m6A)-containing RNAs. 1 Publication1

Organism-specific databases

OpenTargetsiENSG00000149658.
PharmGKBiPA25737.

Polymorphism and mutation databases

BioMutaiYTHDF1.
DMDMi28380041.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00002230732 – 559YTH domain-containing family protein 1Add BLAST558

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Modified residuei182PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9BYJ9.
MaxQBiQ9BYJ9.
PaxDbiQ9BYJ9.
PeptideAtlasiQ9BYJ9.
PRIDEiQ9BYJ9.

PTM databases

iPTMnetiQ9BYJ9.
PhosphoSitePlusiQ9BYJ9.

Miscellaneous databases

PMAP-CutDBQ9BYJ9.

Expressioni

Gene expression databases

BgeeiENSG00000149658.
CleanExiHS_YTHDF1.
ExpressionAtlasiQ9BYJ9. baseline and differential.
GenevisibleiQ9BYJ9. HS.

Interactioni

Subunit structurei

Interacts with ribosomes. Interacts with eIF3 (EIF3A or EIF3B).1 Publication

Protein-protein interaction databases

BioGridi120257. 60 interactors.
IntActiQ9BYJ9. 18 interactors.
MINTiMINT-7970439.
STRINGi9606.ENSP00000359364.

Structurei

Secondary structure

1559
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi366 – 374Combined sources9
Beta strandi390 – 397Combined sources8
Helixi399 – 408Combined sources10
Helixi415 – 428Combined sources14
Beta strandi434 – 440Combined sources7
Beta strandi443 – 452Combined sources10
Beta strandi457 – 459Combined sources3
Beta strandi465 – 467Combined sources3
Beta strandi473 – 485Combined sources13
Helixi486 – 488Combined sources3
Turni489 – 491Combined sources3
Helixi495 – 497Combined sources3
Helixi502 – 504Combined sources3
Helixi513 – 525Combined sources13
Helixi532 – 535Combined sources4
Helixi536 – 550Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4RCIX-ray1.97A/B/C/D361-559[»]
4RCJX-ray1.60A365-554[»]
ProteinModelPortaliQ9BYJ9.
SMRiQ9BYJ9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini389 – 523YTHPROSITE-ProRule annotationAdd BLAST135

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni395 – 397N6-methyladenosine bindingCombined sources1 Publication3
Regioni411 – 412N6-methyladenosine bindingCombined sources1 Publication2

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi241 – 331Gln/Pro-richAdd BLAST91

Sequence similaritiesi

Contains 1 YTH domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1901. Eukaryota.
ENOG410YABQ. LUCA.
GeneTreeiENSGT00390000017549.
HOVERGENiHBG060315.
InParanoidiQ9BYJ9.
KOiK20102.
OMAiGSKGPVY.
OrthoDBiEOG091G0D17.
PhylomeDBiQ9BYJ9.
TreeFamiTF323736.

Family and domain databases

InterProiIPR007275. YTH_domain.
[Graphical view]
PfamiPF04146. YTH. 1 hit.
[Graphical view]
PROSITEiPS50882. YTH. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9BYJ9-1) [UniParc]FASTAAdd to basket

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.

« Hide

        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
Length:559
Mass (Da):60,874
Last modified:June 1, 2001 - v1
Checksum:iDB8AA15636130E18
GO
Isoform 2 (identifier: Q9BYJ9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-190: Missing.
     191-260: KIGDVSSSAV...KSGPVMGGGL → MLFLGSLGAW...QAFTATPSAR
     383-559: Missing.

Note: No experimental confirmation available.
Show »
Length:197
Mass (Da):20,833
Checksum:iDD50829544FE6119
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti123 – 124FP → AR in BAB62751 (Ref. 4) Curated2
Sequence conflicti283 – 284AP → PH in CAD39029 (PubMed:17974005).Curated2

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0068151 – 190Missing in isoform 2. 1 PublicationAdd BLAST190
Alternative sequenceiVSP_006816191 – 260KIGDV…MGGGL → MLFLGSLGAWGTTSISTGSI FSLKTLRSQHGGQVGLKVSR PRAPRMGAATPTPRAPWVAR WLMGSQAFTATPSAR in isoform 2. 1 PublicationAdd BLAST70
Alternative sequenceiVSP_006817383 – 559Missing in isoform 2. 1 PublicationAdd BLAST177

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK000398 mRNA. Translation: BAA91138.1.
AL096828 Genomic DNA. Translation: CAC09391.3.
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.
CCDSiCCDS13511.1. [Q9BYJ9-1]
RefSeqiNP_060268.2. NM_017798.3. [Q9BYJ9-1]
UniGeneiHs.744852.

Genome annotation databases

EnsembliENST00000370339; ENSP00000359364; ENSG00000149658. [Q9BYJ9-1]
GeneIDi54915.
KEGGihsa:54915.
UCSCiuc002yeh.4. human. [Q9BYJ9-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK000398 mRNA. Translation: BAA91138.1.
AL096828 Genomic DNA. Translation: CAC09391.3.
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.
CCDSiCCDS13511.1. [Q9BYJ9-1]
RefSeqiNP_060268.2. NM_017798.3. [Q9BYJ9-1]
UniGeneiHs.744852.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4RCIX-ray1.97A/B/C/D361-559[»]
4RCJX-ray1.60A365-554[»]
ProteinModelPortaliQ9BYJ9.
SMRiQ9BYJ9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120257. 60 interactors.
IntActiQ9BYJ9. 18 interactors.
MINTiMINT-7970439.
STRINGi9606.ENSP00000359364.

PTM databases

iPTMnetiQ9BYJ9.
PhosphoSitePlusiQ9BYJ9.

Polymorphism and mutation databases

BioMutaiYTHDF1.
DMDMi28380041.

Proteomic databases

EPDiQ9BYJ9.
MaxQBiQ9BYJ9.
PaxDbiQ9BYJ9.
PeptideAtlasiQ9BYJ9.
PRIDEiQ9BYJ9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000370339; ENSP00000359364; ENSG00000149658. [Q9BYJ9-1]
GeneIDi54915.
KEGGihsa:54915.
UCSCiuc002yeh.4. human. [Q9BYJ9-1]

Organism-specific databases

CTDi54915.
GeneCardsiYTHDF1.
HGNCiHGNC:15867. YTHDF1.
MIMi616529. gene.
neXtProtiNX_Q9BYJ9.
OpenTargetsiENSG00000149658.
PharmGKBiPA25737.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1901. Eukaryota.
ENOG410YABQ. LUCA.
GeneTreeiENSGT00390000017549.
HOVERGENiHBG060315.
InParanoidiQ9BYJ9.
KOiK20102.
OMAiGSKGPVY.
OrthoDBiEOG091G0D17.
PhylomeDBiQ9BYJ9.
TreeFamiTF323736.

Miscellaneous databases

ChiTaRSiYTHDF1. human.
GenomeRNAii54915.
PMAP-CutDBQ9BYJ9.
PROiQ9BYJ9.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000149658.
CleanExiHS_YTHDF1.
ExpressionAtlasiQ9BYJ9. baseline and differential.
GenevisibleiQ9BYJ9. HS.

Family and domain databases

InterProiIPR007275. YTH_domain.
[Graphical view]
PfamiPF04146. YTH. 1 hit.
[Graphical view]
PROSITEiPS50882. YTH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYTHD1_HUMAN
AccessioniPrimary (citable) accession number: Q9BYJ9
Secondary accession number(s): Q8N3G5
, Q8TBT1, Q96AN4, Q96S57, Q9BTI7, Q9NX79
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 12, 2003
Last sequence update: June 1, 2001
Last modified: November 30, 2016
This is version 133 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.