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Protein

YTH domain-containing family protein 3

Gene

YTHDF3

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

Functioni

Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs and promotes RNA translation efficiency (PubMed:28106072, PubMed:28106076, PubMed:28281539). 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:22575960, PubMed:24284625, PubMed:28106072, PubMed:28106076, PubMed:28281539). Shares m6A-containing mRNAs targets with YTHDF1 and YTHDF2, and regulates different processes depending on the context (PubMed:28106072, PubMed:28106076). Facilitates the translation of targeted mRNAs in cooperation with YTHDF1 by binding to m6A-containing mRNAs and interacting with 40S and 60S ribosome subunits (PubMed:28106072, PubMed:28106076). Can also act as a regulator of mRNA stability in cooperation with YTHDF2 by binding to m6A-containing mRNA and promoting their degradation (PubMed:28106072). Recognizes and binds m6A-containing circular RNAs (circRNAs) and promotes their translation (PubMed:28281539). circRNAs are generated through back-splicing of pre-mRNAs, a non-canonical splicing process promoted by dsRNA structures across circularizing exons (PubMed:28281539).5 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei428N6-methyladenosineBy similarity1
Binding sitei468N6-methyladenosineBy similarity1
Binding sitei492N6-methyladenosineBy similarity1
Binding sitei497N6-methyladenosineBy similarity1

GO - Molecular functioni

GO - Biological processi

  • mRNA destabilization Source: UniProtKB
  • 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 3Curated
Gene namesi
Name:YTHDF3Imported
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 8

Organism-specific databases

EuPathDBiHostDB:ENSG00000185728.16
HGNCiHGNC:26465 YTHDF3
neXtProtiNX_Q7Z739

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

DisGeNETi253943
OpenTargetsiENSG00000185728
PharmGKBiPA134976395

Polymorphism and mutation databases

DMDMi74738853

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00002309912 – 585YTH domain-containing family protein 3Add BLAST584

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Modified residuei23PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ7Z739
MaxQBiQ7Z739
PeptideAtlasiQ7Z739
PRIDEiQ7Z739
ProteomicsDBi69483

PTM databases

GlyConnecti1905
iPTMnetiQ7Z739
PhosphoSitePlusiQ7Z739

Miscellaneous databases

PMAP-CutDBiQ7Z739

Expressioni

Inductioni

Following heat shock stress.1 Publication

Gene expression databases

BgeeiENSG00000185728 Expressed in 243 organ(s), highest expression level in endothelial cell
CleanExiHS_YTHDF3
ExpressionAtlasiQ7Z739 baseline and differential
GenevisibleiQ7Z739 HS

Organism-specific databases

HPAiHPA048703

Interactioni

Subunit structurei

Interacts with YTHDF1 (PubMed:28106072). Interacts with YTHDF2 (PubMed:28106072).1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
gagP045912EBI-2849837,EBI-6179727From Human immunodeficiency virus type 1 group M subtype B (isolate HXB2).

Protein-protein interaction databases

BioGridi128997, 25 interactors
IntActiQ7Z739, 24 interactors

Structurei

3D structure databases

ProteinModelPortaliQ7Z739
SMRiQ7Z739
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini416 – 550YTHPROSITE-ProRule annotationAdd BLAST135

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni422 – 424N6-methyladenosine bindingBy similarity3
Regioni438 – 439N6-methyladenosine bindingBy similarity2

Phylogenomic databases

GeneTreeiENSGT00390000017549
HOVERGENiHBG060315
InParanoidiQ7Z739
KOiK20102
PhylomeDBiQ7Z739

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

Sequence (1+)i

Sequence statusi: Complete.

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

This entry has 1 described isoform and 9 potential isoforms that are computationally mapped.Show allAlign All

Q7Z739-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSATSVDQRP KGQGNKVSVQ NGSIHQKDAV NDDDFEPYLS SQTNQSNSYP
60 70 80 90 100
PMSDPYMPSY YAPSIGFPYS LGEAAWSTAG DQPMPYLTTY GQMSNGEHHY
110 120 130 140 150
IPDGVFSQPG ALGNTPPFLG QHGFNFFPGN ADFSTWGTSG SQGQSTQSSA
160 170 180 190 200
YSSSYGYPPS SLGRAITDGQ AGFGNDTLSK VPGISSIEQG MTGLKIGGDL
210 220 230 240 250
TAAVTKTVGT ALSSSGMTSI ATNSVPPVSS AAPKPTSWAA IARKPAKPQP
260 270 280 290 300
KLKPKGNVGI GGSAVPPPPI KHNMNIGTWD EKGSVVKAPP TQPVLPPQTI
310 320 330 340 350
IQQPQPLIQP PPLVQSQLPQ QQPQPPQPQQ QQGPQPQAQP HQVQPQQQQL
360 370 380 390 400
QNRWVAPRNR GAGFNQNNGA GSENFGLGVV PVSASPSSVE VHPVLEKLKA
410 420 430 440 450
INNYNPKDFD WNLKNGRVFI IKSYSEDDIH RSIKYSIWCS TEHGNKRLDA
460 470 480 490 500
AYRSLNGKGP LYLLFSVNGS GHFCGVAEMK SVVDYNAYAG VWSQDKWKGK
510 520 530 540 550
FEVKWIFVKD VPNNQLRHIR LENNDNKPVT NSRDTQEVPL EKAKQVLKII
560 570 580
ATFKHTTSIF DDFAHYEKRQ EEEEAMRRER NRNKQ
Length:585
Mass (Da):63,861
Last modified:October 1, 2003 - v1
Checksum:iC7021FE48DEA441E
GO

Computationally mapped potential isoform sequencesi

There are 9 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A087WY31A0A087WY31_HUMAN
YTH domain-containing family protei...
YTHDF3
588Annotation score:
A0A024R7W5A0A024R7W5_HUMAN
YTH domain family, member 3, isofor...
YTHDF3 hCG_41077
534Annotation score:
A0A087X0Q1A0A087X0Q1_HUMAN
YTH domain-containing family protei...
YTHDF3
583Annotation score:
S4R373S4R373_HUMAN
YTH domain-containing family protei...
YTHDF3
52Annotation score:
A0A087X0U5A0A087X0U5_HUMAN
YTH domain-containing family protei...
YTHDF3
119Annotation score:
A0A087WU63A0A087WU63_HUMAN
YTH domain-containing family protei...
YTHDF3
102Annotation score:
A0A087WWB0A0A087WWB0_HUMAN
YTH domain-containing family protei...
YTHDF3
111Annotation score:
A0A087X0C3A0A087X0C3_HUMAN
YTH domain-containing family protei...
YTHDF3
41Annotation score:
A0A087WU40A0A087WU40_HUMAN
YTH domain-containing family protei...
YTHDF3
86Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti139S → R in CAH56224 (PubMed:17974005).Curated1
Sequence conflicti381P → S in CAH56224 (PubMed:17974005).Curated1
Sequence conflicti532S → P in CAH56480 (PubMed:17974005).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK127574 mRNA Translation: BAG54526.1
AL832005 mRNA Translation: CAH56224.1
BX537996 mRNA Translation: CAH56480.1
CH471068 Genomic DNA Translation: EAW86867.1
BC052970 mRNA Translation: AAH52970.1
CCDSiCCDS75747.1
RefSeqiNP_001264742.1, NM_001277813.1
NP_001264743.1, NM_001277814.1
NP_001264744.1, NM_001277815.1
NP_001264745.1, NM_001277816.1
NP_001264746.1, NM_001277817.1
NP_001264747.1, NM_001277818.1
NP_689971.4, NM_152758.5
UniGeneiHs.491861

Genome annotation databases

EnsembliENST00000539294; ENSP00000473496; ENSG00000185728
GeneIDi253943
KEGGihsa:253943
UCSCiuc033bnj.2 human

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK127574 mRNA Translation: BAG54526.1
AL832005 mRNA Translation: CAH56224.1
BX537996 mRNA Translation: CAH56480.1
CH471068 Genomic DNA Translation: EAW86867.1
BC052970 mRNA Translation: AAH52970.1
CCDSiCCDS75747.1
RefSeqiNP_001264742.1, NM_001277813.1
NP_001264743.1, NM_001277814.1
NP_001264744.1, NM_001277815.1
NP_001264745.1, NM_001277816.1
NP_001264746.1, NM_001277817.1
NP_001264747.1, NM_001277818.1
NP_689971.4, NM_152758.5
UniGeneiHs.491861

3D structure databases

ProteinModelPortaliQ7Z739
SMRiQ7Z739
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi128997, 25 interactors
IntActiQ7Z739, 24 interactors

PTM databases

GlyConnecti1905
iPTMnetiQ7Z739
PhosphoSitePlusiQ7Z739

Polymorphism and mutation databases

DMDMi74738853

Proteomic databases

EPDiQ7Z739
MaxQBiQ7Z739
PeptideAtlasiQ7Z739
PRIDEiQ7Z739
ProteomicsDBi69483

Protocols and materials databases

DNASUi253943
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000539294; ENSP00000473496; ENSG00000185728
GeneIDi253943
KEGGihsa:253943
UCSCiuc033bnj.2 human

Organism-specific databases

CTDi253943
DisGeNETi253943
EuPathDBiHostDB:ENSG00000185728.16
GeneCardsiYTHDF3
HGNCiHGNC:26465 YTHDF3
HPAiHPA048703
neXtProtiNX_Q7Z739
OpenTargetsiENSG00000185728
PharmGKBiPA134976395
GenAtlasiSearch...

Phylogenomic databases

GeneTreeiENSGT00390000017549
HOVERGENiHBG060315
InParanoidiQ7Z739
KOiK20102
PhylomeDBiQ7Z739

Miscellaneous databases

ChiTaRSiYTHDF3 human
GeneWikiiYTHDF3
GenomeRNAii253943
PMAP-CutDBiQ7Z739
PROiPR:Q7Z739

Gene expression databases

BgeeiENSG00000185728 Expressed in 243 organ(s), highest expression level in endothelial cell
CleanExiHS_YTHDF3
ExpressionAtlasiQ7Z739 baseline and differential
GenevisibleiQ7Z739 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 nameiYTHD3_HUMAN
AccessioniPrimary (citable) accession number: Q7Z739
Secondary accession number(s): B3KXL4, Q63Z37, Q659A3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: October 1, 2003
Last modified: November 7, 2018
This is version 129 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

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 8
    Human chromosome 8: entries, gene names and cross-references to MIM
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