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Protein

YTH domain-containing family protein 3

Gene

YTHDF3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs. 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.2 Publications

GO - Molecular functioni

  1. N6-methyladenosine-containing RNA binding Source: UniProtKB
  2. poly(A) RNA binding Source: UniProtKB
Complete GO annotation...

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
YTH domain-containing family protein 3
Gene namesi
Name:YTHDF3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 8

Organism-specific databases

HGNCiHGNC:26465. YTHDF3.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134976395.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed2 Publications
Chaini2 – 585584YTH domain-containing family protein 3PRO_0000230991Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserine2 Publications
Modified residuei23 – 231Phosphoserine1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ7Z739.
PaxDbiQ7Z739.
PRIDEiQ7Z739.

PTM databases

PhosphoSiteiQ7Z739.

Miscellaneous databases

PMAP-CutDBQ7Z739.

Expressioni

Gene expression databases

CleanExiHS_YTHDF3.
ExpressionAtlasiQ7Z739. baseline and differential.
GenevestigatoriQ7Z739.

Organism-specific databases

HPAiHPA048703.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
gagP045912EBI-2849837,EBI-6179727From a different organism.

Protein-protein interaction databases

BioGridi128997. 10 interactions.
IntActiQ7Z739. 3 interactions.
MINTiMINT-5005374.
STRINGi9606.ENSP00000398476.

Structurei

3D structure databases

ProteinModelPortaliQ7Z739.
SMRiQ7Z739. Positions 392-570.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini416 – 550135YTHPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 YTH domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiNOG276347.
GeneTreeiENSGT00390000017549.
HOVERGENiHBG060315.
InParanoidiQ7Z739.
PhylomeDBiQ7Z739.

Family and domain databases

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

Sequencei

Sequence statusi: Complete.

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

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

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti139 – 1391S → R in CAH56224 (PubMed:17974005).Curated
Sequence conflicti381 – 3811P → S in CAH56224 (PubMed:17974005).Curated
Sequence conflicti532 – 5321S → P in CAH56480 (PubMed:17974005).Curated

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.
UCSCiuc003xuy.4. human.

Polymorphism databases

DMDMi74738853.

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. Positions 392-570.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi128997. 10 interactions.
IntActiQ7Z739. 3 interactions.
MINTiMINT-5005374.
STRINGi9606.ENSP00000398476.

PTM databases

PhosphoSiteiQ7Z739.

Polymorphism databases

DMDMi74738853.

Proteomic databases

MaxQBiQ7Z739.
PaxDbiQ7Z739.
PRIDEiQ7Z739.

Protocols and materials databases

DNASUi253943.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000539294; ENSP00000473496; ENSG00000185728.
GeneIDi253943.
KEGGihsa:253943.
UCSCiuc003xuy.4. human.

Organism-specific databases

CTDi253943.
GeneCardsiGC08P064081.
HGNCiHGNC:26465. YTHDF3.
HPAiHPA048703.
neXtProtiNX_Q7Z739.
PharmGKBiPA134976395.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG276347.
GeneTreeiENSGT00390000017549.
HOVERGENiHBG060315.
InParanoidiQ7Z739.
PhylomeDBiQ7Z739.

Miscellaneous databases

ChiTaRSiYTHDF3. human.
GeneWikiiYTHDF3.
GenomeRNAii253943.
NextBioi92198.
PMAP-CutDBQ7Z739.
PROiQ7Z739.

Gene expression databases

CleanExiHS_YTHDF3.
ExpressionAtlasiQ7Z739. baseline and differential.
GenevestigatoriQ7Z739.

Family and domain databases

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

Publicationsi

« Hide 'large scale' publications
  1. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Tongue.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Skeletal muscle and Spinal cord.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Testis.
  5. Bienvenut W.V., Vousden K.H., Lukashchuk N.
    Submitted (MAR-2008) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 256-271; 408-414 AND 534-542, IDENTIFICATION BY MASS SPECTROMETRY.
    Tissue: Lung carcinoma.
  6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  7. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
  8. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-23, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  9. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. Cited for: RNA-BINDING, FUNCTION.
  11. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
  12. "N-methyladenosine-dependent regulation of messenger RNA stability."
    Wang X., Lu Z., Gomez A., Hon G.C., Yue Y., Han D., Fu Y., Parisien M., Dai Q., Jia G., Ren B., Pan T., He C.
    Nature 505:117-120(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: RNA-BINDING, FUNCTION.

Entry informationi

Entry nameiYTHD3_HUMAN
AccessioniPrimary (citable) accession number: Q7Z739
Secondary accession number(s): B3KXL4, Q63Z37, Q659A3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: October 1, 2003
Last modified: March 4, 2015
This is version 97 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

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
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.