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Protein

YTH domain-containing family protein 3

Gene

Ythdf3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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

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

Keywordsi

Molecular functionRNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
YTH domain-containing family protein 3
Gene namesi
Name:Ythdf3
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 3

Organism-specific databases

MGIiMGI:1918850 Ythdf3

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00002309922 – 585YTH domain-containing family protein 3Add BLAST584

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineBy similarity1
Modified residuei23PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiQ8BYK6
PeptideAtlasiQ8BYK6
PRIDEiQ8BYK6

PTM databases

iPTMnetiQ8BYK6
PhosphoSitePlusiQ8BYK6

Expressioni

Gene expression databases

BgeeiENSMUSG00000047213 Expressed in 283 organ(s), highest expression level in mammary gland
CleanExiMM_YTHDF3
GenevisibleiQ8BYK6 MM

Interactioni

Subunit structurei

Interacts with YTHDF1. Interacts with YTHDF2.By similarity

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000103983

Structurei

3D structure databases

ProteinModelPortaliQ8BYK6
SMRiQ8BYK6
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

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi226 – 340Pro-richAdd BLAST115
Compositional biasi292 – 351Gln-richAdd BLAST60
Compositional biasi571 – 574Poly-Glu4

Phylogenomic databases

eggNOGiKOG1901 Eukaryota
ENOG410YABQ LUCA
GeneTreeiENSGT00390000017549
HOGENOMiHOG000232058
HOVERGENiHBG060315
InParanoidiQ8BYK6
KOiK20102
OMAiTWDDKGS
OrthoDBiEOG091G0D17
PhylomeDBiQ8BYK6
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 (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: Q8BYK6-1) [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
MSATSVDQRP KGQGNKVSVQ NGSIHQKDAV NDDDFEPYLS SQTNQNNSYP
60 70 80 90 100
PMSDPYMPSY YAPSIGFPYS LGEAAWSTAG DQPMPYLTTY GQMSNGEHHY
110 120 130 140 150
IPDGVFSQPG ALGNTPPFLG QHGFNFFPGN ADFSTWGTSG SQGQSTQNSA
160 170 180 190 200
YSSSYGYPPS SLGRAITDGQ AGFGNDTLSK VPGISSIEQG MTGLKIGGDL
210 220 230 240 250
TAAVTKTVGT ALSSSGMTSI ATNNVPPVSS AAPKPTSWAA IARKPAKPQP
260 270 280 290 300
KLKPKGNVGI GGSAVPPPPI KHNMNIGTWD EKGSVVKAPP TQPVLPPQTI
310 320 330 340 350
IQQPQPLIQP PPLVQSQLPQ QQPQPPQPQQ QQGPQPQAQP HQVQSQQPQL
360 370 380 390 400
QNRWVAPRNR GTGFNQNNGT 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):63,961
Last modified:April 4, 2006 - v2
Checksum:iE6A12F76A3781770
GO
Isoform 2 (identifier: Q8BYK6-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-17: MSATSVDQRPKGQGNKV → MFYLDLTLLHRATEETGEESF

Show »
Length:589
Mass (Da):64,661
Checksum:i7242DF6698B82294
GO
Isoform 3 (identifier: Q8BYK6-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     45-45: Q → QKYRRAKQLFHC

Show »
Length:596
Mass (Da):65,393
Checksum:iB965B13120C6218D
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti231A → P in AAH67042 (PubMed:15489334).Curated1
Sequence conflicti502E → G in BAC30267 (PubMed:16141072).Curated1
Sequence conflicti531N → D in BAE23284 (PubMed:16141072).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0178331 – 17MSATS…QGNKV → MFYLDLTLLHRATEETGEES F in isoform 2. 2 PublicationsAdd BLAST17
Alternative sequenceiVSP_01783445Q → QKYRRAKQLFHC in isoform 3. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK137245 mRNA Translation: BAE23284.1
AK039176 mRNA Translation: BAC30267.1
AK053736 mRNA Translation: BAC35498.1
BC057158 mRNA Translation: AAH57158.1
BC067040 mRNA Translation: AAH67040.1
BC067042 mRNA Translation: AAH67042.1
CCDSiCCDS38396.1 [Q8BYK6-3]
CCDS50869.1 [Q8BYK6-1]
RefSeqiNP_001139391.1, NM_001145919.1 [Q8BYK6-1]
NP_766265.3, NM_172677.3 [Q8BYK6-3]
UniGeneiMm.23834

Genome annotation databases

EnsembliENSMUST00000108345; ENSMUSP00000103982; ENSMUSG00000047213 [Q8BYK6-1]
ENSMUST00000108346; ENSMUSP00000103983; ENSMUSG00000047213 [Q8BYK6-3]
ENSMUST00000191774; ENSMUSP00000141610; ENSMUSG00000047213 [Q8BYK6-2]
GeneIDi229096
KEGGimmu:229096
UCSCiuc008org.3 mouse [Q8BYK6-3]
uc008orh.3 mouse [Q8BYK6-2]
uc008ori.3 mouse [Q8BYK6-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK137245 mRNA Translation: BAE23284.1
AK039176 mRNA Translation: BAC30267.1
AK053736 mRNA Translation: BAC35498.1
BC057158 mRNA Translation: AAH57158.1
BC067040 mRNA Translation: AAH67040.1
BC067042 mRNA Translation: AAH67042.1
CCDSiCCDS38396.1 [Q8BYK6-3]
CCDS50869.1 [Q8BYK6-1]
RefSeqiNP_001139391.1, NM_001145919.1 [Q8BYK6-1]
NP_766265.3, NM_172677.3 [Q8BYK6-3]
UniGeneiMm.23834

3D structure databases

ProteinModelPortaliQ8BYK6
SMRiQ8BYK6
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000103983

PTM databases

iPTMnetiQ8BYK6
PhosphoSitePlusiQ8BYK6

Proteomic databases

PaxDbiQ8BYK6
PeptideAtlasiQ8BYK6
PRIDEiQ8BYK6

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000108345; ENSMUSP00000103982; ENSMUSG00000047213 [Q8BYK6-1]
ENSMUST00000108346; ENSMUSP00000103983; ENSMUSG00000047213 [Q8BYK6-3]
ENSMUST00000191774; ENSMUSP00000141610; ENSMUSG00000047213 [Q8BYK6-2]
GeneIDi229096
KEGGimmu:229096
UCSCiuc008org.3 mouse [Q8BYK6-3]
uc008orh.3 mouse [Q8BYK6-2]
uc008ori.3 mouse [Q8BYK6-1]

Organism-specific databases

CTDi253943
MGIiMGI:1918850 Ythdf3

Phylogenomic databases

eggNOGiKOG1901 Eukaryota
ENOG410YABQ LUCA
GeneTreeiENSGT00390000017549
HOGENOMiHOG000232058
HOVERGENiHBG060315
InParanoidiQ8BYK6
KOiK20102
OMAiTWDDKGS
OrthoDBiEOG091G0D17
PhylomeDBiQ8BYK6
TreeFamiTF323736

Miscellaneous databases

ChiTaRSiYthdf3 mouse
PROiPR:Q8BYK6
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000047213 Expressed in 283 organ(s), highest expression level in mammary gland
CleanExiMM_YTHDF3
GenevisibleiQ8BYK6 MM

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_MOUSE
AccessioniPrimary (citable) accession number: Q8BYK6
Secondary accession number(s): Q3UVI5
, Q6NXJ6, Q6NXJ8, Q8BKB6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: April 4, 2006
Last modified: November 7, 2018
This is version 99 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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