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Protein

YTH domain-containing family protein 1

Gene

YTHDF1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

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 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

GO - Biological processi

  • positive regulation of translation Source: UniProtKB
  • positive regulation of translational initiation Source: UniProtKB

Keywordsi

Molecular functionRNA-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

EuPathDBiHostDB:ENSG00000149658.17
HGNCiHGNC:15867 YTHDF1
MIMi616529 gene
neXtProtiNX_Q9BYJ9

Subcellular locationi

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
ProteomicsDBi79659
79660 [Q9BYJ9-2]

PTM databases

GlyConnecti1904
iPTMnetiQ9BYJ9
PhosphoSitePlusiQ9BYJ9

Miscellaneous databases

PMAP-CutDBiQ9BYJ9

Expressioni

Gene expression databases

BgeeiENSG00000149658 Expressed in 234 organ(s), highest expression level in female gonad
CleanExiHS_YTHDF1
ExpressionAtlasiQ9BYJ9 baseline and differential
GenevisibleiQ9BYJ9 HS

Interactioni

Subunit structurei

Interacts with ribosomes (PubMed:26046440). Interacts with eIF3 (EIF3A or EIF3B) (PubMed:26046440). Interacts with YTHDF3 (PubMed:28106072).2 Publications

Protein-protein interaction databases

BioGridi120257, 74 interactors
IntActiQ9BYJ9, 35 interactors
MINTiQ9BYJ9
STRINGi9606.ENSP00000359364

Structurei

Secondary structure

1559
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Phylogenomic databases

eggNOGiKOG1901 Eukaryota
ENOG410YABQ LUCA
GeneTreeiENSGT00390000017549
HOVERGENiHBG060315
InParanoidiQ9BYJ9
KOiK20102
OMAiQPKMKAK
OrthoDBiEOG091G0D17
PhylomeDBiQ9BYJ9
TreeFamiTF323736

Family and domain databases

InterProiView protein in InterPro
IPR007275 YTH_domain
PfamiView protein in Pfam
PF04146 YTH, 1 hit
PROSITEiView protein in PROSITE
PS50882 YTH, 1 hit

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

This 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 '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

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q5JXC6Q5JXC6_HUMAN
YTH domain-containing family protei...
YTHDF1
52Annotation score:

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 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
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

Similar 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
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, 74 interactors
IntActiQ9BYJ9, 35 interactors
MINTiQ9BYJ9
STRINGi9606.ENSP00000359364

PTM databases

GlyConnecti1904
iPTMnetiQ9BYJ9
PhosphoSitePlusiQ9BYJ9

Polymorphism and mutation databases

BioMutaiYTHDF1
DMDMi28380041

Proteomic databases

EPDiQ9BYJ9
MaxQBiQ9BYJ9
PaxDbiQ9BYJ9
PeptideAtlasiQ9BYJ9
PRIDEiQ9BYJ9
ProteomicsDBi79659
79660 [Q9BYJ9-2]

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
EuPathDBiHostDB:ENSG00000149658.17
GeneCardsiYTHDF1
HGNCiHGNC:15867 YTHDF1
MIMi616529 gene
neXtProtiNX_Q9BYJ9
OpenTargetsiENSG00000149658
PharmGKBiPA25737
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1901 Eukaryota
ENOG410YABQ LUCA
GeneTreeiENSGT00390000017549
HOVERGENiHBG060315
InParanoidiQ9BYJ9
KOiK20102
OMAiQPKMKAK
OrthoDBiEOG091G0D17
PhylomeDBiQ9BYJ9
TreeFamiTF323736

Miscellaneous databases

ChiTaRSiYTHDF1 human
GenomeRNAii54915
PMAP-CutDBiQ9BYJ9
PROiPR:Q9BYJ9
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000149658 Expressed in 234 organ(s), highest expression level in female gonad
CleanExiHS_YTHDF1
ExpressionAtlasiQ9BYJ9 baseline and differential
GenevisibleiQ9BYJ9 HS

Family and domain databases

InterProiView protein in InterPro
IPR007275 YTH_domain
PfamiView protein in Pfam
PF04146 YTH, 1 hit
PROSITEiView protein in PROSITE
PS50882 YTH, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiYTHD1_HUMAN
AccessioniPrimary (citable) accession number: Q9BYJ9
Secondary accession number(s): Q8N3G5
, Q8TBT1, Q96AN4, Q96S57, Q9BTI7, Q9NX79
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 12, 2003
Last sequence update: June 1, 2001
Last modified: October 10, 2018
This is version 149 of the entry and version 1 of the sequence. See 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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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