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Protein

YTH domain-containing protein 1

Gene

Ythdc1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 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 (PubMed:25389274). Regulates alternative splice site selection (PubMed:10564280, PubMed:9473574).3 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei380 – 3801N6-methyladenosineBy similarity
Binding sitei431 – 4311N6-methyladenosineBy similarity

GO - Molecular functioni

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

GO - Biological processi

  • mRNA splice site selection Source: UniProtKB
  • mRNA splicing, via spliceosome Source: RGD
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
YTH domain-containing protein 1
Alternative name(s):
Putative splicing factor YT521
RA301-binding protein
Gene namesi
Name:Ythdc1
Synonyms:Yt521
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494 Componenti: Chromosome 14

Organism-specific databases

RGDi621706. Ythdc1.

Subcellular locationi

  • Nucleus 1 Publication

  • Note: Localizes to a novel subnuclear structure, the YT bodies.

GO - Cellular componenti

  • nuclear body Source: RGD
  • nucleoplasm Source: RGD
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 738738YTH domain-containing protein 1PRO_0000223077Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei146 – 1461PhosphoserineBy similarity
Modified residuei148 – 1481PhosphothreonineBy similarity
Modified residuei311 – 3111PhosphoserineBy similarity
Modified residuei318 – 3181PhosphoserineBy similarity
Modified residuei320 – 3201PhosphoserineBy similarity
Modified residuei321 – 3211PhosphoserineBy similarity
Modified residuei323 – 3231PhosphoserineBy similarity
Modified residuei427 – 4271PhosphoserineBy similarity
Modified residuei438 – 4381PhosphoserineBy similarity

Post-translational modificationi

Tyrosine phosphorylated.

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ9QY02.
PRIDEiQ9QY02.

PTM databases

PhosphoSiteiQ9QY02.

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

GenevisibleiQ9QY02. RN.

Interactioni

Subunit structurei

Interacts with EMD, KHDRBS1/SAM68, KHDRBS3, RBMX, TRA2B/SFRS10, SC35 and SF2.2 Publications

Protein-protein interaction databases

BioGridi251046. 1 interaction.
STRINGi10116.ENSRNOP00000002736.

Structurei

Secondary structure

1
738
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi349 – 3513Combined sources
Helixi352 – 3554Combined sources
Beta strandi359 – 3635Combined sources
Helixi368 – 37710Combined sources
Helixi384 – 39613Combined sources
Beta strandi400 – 4056Combined sources
Turni407 – 4093Combined sources
Beta strandi411 – 4188Combined sources
Helixi439 – 4413Combined sources
Beta strandi446 – 4527Combined sources
Helixi458 – 4603Combined sources
Turni467 – 4704Combined sources
Beta strandi481 – 4833Combined sources
Helixi485 – 49410Combined sources
Helixi499 – 5013Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2MTVNMR-A347-502[»]
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini358 – 495138YTHPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni364 – 3663N6-methyladenosine bindingBy similarity

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi172 – 26392Glu-richAdd
BLAST
Compositional biasi612 – 65443Pro-richAdd
BLAST
Compositional biasi658 – 73881Arg-richAdd
BLAST

Domaini

The YTH domain mediates RNA-binding.By similarity

Sequence similaritiesi

Contains 1 YTH domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiNOG311295.
GeneTreeiENSGT00690000102240.
HOGENOMiHOG000088650.
HOVERGENiHBG055528.
InParanoidiQ9QY02.
OMAiQPEKTCL.
OrthoDBiEOG7R2BMC.

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.

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

Isoform 1 (identifier: Q9QY02-1) [UniParc]FASTAAdd to basket

Also known as: YT521-B

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
MAADSREEKD GELNVLDDIL TEVPEQDDEL YNPESEQDKN EKKGSKRKSE
60 70 80 90 100
RMESIDTKRQ KPSIHSRQLI SKPLSSSVSN NKRIVSTKGK SVTEYKNEEY
110 120 130 140 150
QRSERNKRLD ADRKIRLSSS SSREPYKSQP EKPCLRKRDS ERRAKSPTPD
160 170 180 190 200
GSERIGLEVD RRASRSSQSS KEEGNSEEYG SDHETGSSAS SEQGNNTENE
210 220 230 240 250
EEGGEEDVEE DEEVDEDGDD DEEVDEDAEE EEDEEEDEEE EDEEEEEEEE
260 270 280 290 300
EEYEQDERDQ KEEGNDYDTR SEASDSGSES VSFTDGSVRS GSGTDGSDEK
310 320 330 340 350
KKERKRARGI SPIVFDRSGS SASESYAGSE KKHEKLSSSV RAVRKDQTSK
360 370 380 390 400
LKYVLQDARF FLIKSNNHEN VSLAKAKGVW STLPVNEKKL NLAFRSARSV
410 420 430 440 450
ILIFSVRESG KFQGFARLSS ESHHGGSPIH WVLPAGMSAK MLGGVFKIDW
460 470 480 490 500
ICRRELPFTK SAHLTNPWNE HKPVKIGRDG QEIELECGTQ LCLLFPPDES
510 520 530 540 550
IDLYQLIHKM RHKRRMHSQP RSRGRPSRRE PVRDVGRRRP EDYDIHNSRK
560 570 580 590 600
KPRIDYPPEF HQRPGYLKDP RYQEVDSFTN LIPNRRFSGV RRDVFLNGSY
610 620 630 640 650
NDYVREFHNM GPPPPWQGMP PYPGIEQPPH HPYYQHHAPP PQAHPPYSGH
660 670 680 690 700
HPVPHEARYR DKRVHDYDMR VDDFLRRTQA VVSGRRSRPR ERDRERERDR
710 720 730
PRDNRRDRER DRGRDRERER ERICDRDRDR GERGRYRR
Length:738
Mass (Da):85,902
Last modified:February 19, 2014 - v2
Checksum:i9FC68314E029FA98
GO
Isoform 2 (identifier: Q9QY02-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     328-345: Missing.
     577-584: Missing.

Show »
Length:712
Mass (Da):83,006
Checksum:iF1F56DDD71AE580F
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti353 – 3531Y → S in BAA23885 (PubMed:9473574).Curated
Sequence conflicti353 – 3531Y → S in AAD55973 (PubMed:10564280).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei328 – 34518Missing in isoform 2. 1 PublicationVSP_006819Add
BLAST
Alternative sequencei577 – 5848Missing in isoform 2. 1 PublicationVSP_006820

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D78303 mRNA. Translation: BAA23885.1.
AF144731 mRNA. Translation: AAD55973.1.
AABR06078005 Genomic DNA. No translation available.
CH473981 Genomic DNA. Translation: EDL89830.1.
RefSeqiNP_596914.1. NM_133423.1.
XP_006250870.1. XM_006250808.2. [Q9QY02-2]
UniGeneiRn.48752.

Genome annotation databases

EnsembliENSRNOT00000002736; ENSRNOP00000002736; ENSRNOG00000001996. [Q9QY02-1]
ENSRNOT00000002740; ENSRNOP00000002740; ENSRNOG00000001996. [Q9QY02-2]
GeneIDi170956.
KEGGirno:170956.
UCSCiRGD:621706. rat. [Q9QY02-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D78303 mRNA. Translation: BAA23885.1.
AF144731 mRNA. Translation: AAD55973.1.
AABR06078005 Genomic DNA. No translation available.
CH473981 Genomic DNA. Translation: EDL89830.1.
RefSeqiNP_596914.1. NM_133423.1.
XP_006250870.1. XM_006250808.2. [Q9QY02-2]
UniGeneiRn.48752.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2MTVNMR-A347-502[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi251046. 1 interaction.
STRINGi10116.ENSRNOP00000002736.

PTM databases

PhosphoSiteiQ9QY02.

Proteomic databases

PaxDbiQ9QY02.
PRIDEiQ9QY02.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000002736; ENSRNOP00000002736; ENSRNOG00000001996. [Q9QY02-1]
ENSRNOT00000002740; ENSRNOP00000002740; ENSRNOG00000001996. [Q9QY02-2]
GeneIDi170956.
KEGGirno:170956.
UCSCiRGD:621706. rat. [Q9QY02-1]

Organism-specific databases

CTDi91746.
RGDi621706. Ythdc1.

Phylogenomic databases

eggNOGiNOG311295.
GeneTreeiENSGT00690000102240.
HOGENOMiHOG000088650.
HOVERGENiHBG055528.
InParanoidiQ9QY02.
OMAiQPEKTCL.
OrthoDBiEOG7R2BMC.

Miscellaneous databases

NextBioi35583674.
PROiQ9QY02.

Gene expression databases

GenevisibleiQ9QY02. RN.

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. "Cloning of a gene, YT521, for a novel RNA splicing-related protein induced by hypoxia/reoxygenation."
    Imai Y., Matsuo N., Ogawa S., Tohyama M., Takagi T.
    Brain Res. Mol. Brain Res. 53:33-40(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION.
    Tissue: Brain.
  2. "The interaction and colocalization of Sam68 with the splicing-associated factor YT521-B in nuclear dots is regulated by the Src family kinase p59fyn."
    Hartmann A.M., Nayler O., Schwaiger F.W., Obermeier A., Stamm S.
    Mol. Biol. Cell 10:3909-3926(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION.
  3. "Genome sequence of the Brown Norway rat yields insights into mammalian evolution."
    Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G., Morgan M.
    , Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C., Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X., Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A., Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F.S.
    Nature 428:493-521(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Brown Norway.
  4. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The ER repeat protein YT521-B localizes to a novel subnuclear compartment."
    Nayler O., Hartmann A.M., Stamm S.
    J. Cell Biol. 150:949-962(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  6. "The STAR/GSG family protein rSLM-2 regulates the selection of alternative splice sites."
    Stoss O., Olbrich M., Hartmann A.M., Koenig H., Memmott J., Andreadis A., Stamm S.
    J. Biol. Chem. 276:8665-8673(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH KHDRBS3.
    Tissue: Brain.
  7. "Heterogeneous nuclear ribonucleoprotein G regulates splice site selection by binding to CC(A/C)-rich regions in pre-mRNA."
    Heinrich B., Zhang Z., Raitskin O., Hiller M., Benderska N., Hartmann A.M., Bracco L., Elliott D., Ben-Ari S., Soreq H., Sperling J., Sperling R., Stamm S.
    J. Biol. Chem. 284:14303-14315(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RBMX.
  8. "Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA."
    Theler D., Dominguez C., Blatter M., Boudet J., Allain F.H.
    Nucleic Acids Res. 42:13911-13919(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 347-502, FUNCTION, RNA-BINDING.

Entry informationi

Entry nameiYTDC1_RAT
AccessioniPrimary (citable) accession number: Q9QY02
Secondary accession number(s): G3V690, O54729
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 12, 2003
Last sequence update: February 19, 2014
Last modified: June 24, 2015
This is version 98 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.