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Q9QY02

- YTDC1_RAT

UniProt

Q9QY02 - YTDC1_RAT

Protein

YTH domain-containing protein 1

Gene

Ythdc1

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 90 (01 Oct 2014)
      Sequence version 2 (19 Feb 2014)
      Previous versions | rss
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    Functioni

    RNA-binding protein that regulates alternative splice site selection.2 Publications

    GO - Molecular functioni

    1. protein binding Source: RGD
    2. RNA binding Source: UniProtKB

    GO - Biological processi

    1. mRNA splice site selection Source: UniProtKB
    2. mRNA splicing, via spliceosome Source: RGD

    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: Unplaced

    Organism-specific databases

    RGDi621706. Ythdc1.

    Subcellular locationi

    Nucleus 1 Publication
    Note: Localizes to a novel subnuclear structure, the YT bodies.

    GO - Cellular componenti

    1. nuclear body Source: RGD
    2. nucleoplasm Source: RGD
    3. nucleus Source: UniProtKB

    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

    GenevestigatoriQ9QY02.

    Interactioni

    Subunit structurei

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

    Protein-protein interaction databases

    BioGridi251046. 1 interaction.

    Family & Domainsi

    Domains and Repeats

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

    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.
    OMAiREPYKSQ.

    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. Align

    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

    MAADSREEKD GELNVLDDIL TEVPEQDDEL YNPESEQDKN EKKGSKRKSE    50
    RMESIDTKRQ KPSIHSRQLI SKPLSSSVSN NKRIVSTKGK SVTEYKNEEY 100
    QRSERNKRLD ADRKIRLSSS SSREPYKSQP EKPCLRKRDS ERRAKSPTPD 150
    GSERIGLEVD RRASRSSQSS KEEGNSEEYG SDHETGSSAS SEQGNNTENE 200
    EEGGEEDVEE DEEVDEDGDD DEEVDEDAEE EEDEEEDEEE EDEEEEEEEE 250
    EEYEQDERDQ KEEGNDYDTR SEASDSGSES VSFTDGSVRS GSGTDGSDEK 300
    KKERKRARGI SPIVFDRSGS SASESYAGSE KKHEKLSSSV RAVRKDQTSK 350
    LKYVLQDARF FLIKSNNHEN VSLAKAKGVW STLPVNEKKL NLAFRSARSV 400
    ILIFSVRESG KFQGFARLSS ESHHGGSPIH WVLPAGMSAK MLGGVFKIDW 450
    ICRRELPFTK SAHLTNPWNE HKPVKIGRDG QEIELECGTQ LCLLFPPDES 500
    IDLYQLIHKM RHKRRMHSQP RSRGRPSRRE PVRDVGRRRP EDYDIHNSRK 550
    KPRIDYPPEF HQRPGYLKDP RYQEVDSFTN LIPNRRFSGV RRDVFLNGSY 600
    NDYVREFHNM GPPPPWQGMP PYPGIEQPPH HPYYQHHAPP PQAHPPYSGH 650
    HPVPHEARYR DKRVHDYDMR VDDFLRRTQA VVSGRRSRPR ERDRERERDR 700
    PRDNRRDRER DRGRDRERER ERICDRDRDR GERGRYRR 738
    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:
    EMBL
    GenBank
    DDBJ
    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_006250808.1. [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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D78303 mRNA. Translation: BAA23885.1 .
    AF144731 mRNA. Translation: AAD55973.1 .
    AABR06078005 Genomic DNA. No translation available.
    CH473981 Genomic DNA. Translation: EDL89830.1 .
    RefSeqi NP_596914.1. NM_133423.1.
    XP_006250870.1. XM_006250808.1. [Q9QY02-2 ]
    UniGenei Rn.48752.

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 251046. 1 interaction.

    PTM databases

    PhosphoSitei Q9QY02.

    Proteomic databases

    PaxDbi Q9QY02.
    PRIDEi Q9QY02.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSRNOT00000002736 ; ENSRNOP00000002736 ; ENSRNOG00000001996 . [Q9QY02-1 ]
    ENSRNOT00000002740 ; ENSRNOP00000002740 ; ENSRNOG00000001996 . [Q9QY02-2 ]
    GeneIDi 170956.
    KEGGi rno:170956.
    UCSCi RGD:621706. rat. [Q9QY02-1 ]

    Organism-specific databases

    CTDi 91746.
    RGDi 621706. Ythdc1.

    Phylogenomic databases

    eggNOGi NOG311295.
    GeneTreei ENSGT00690000102240.
    HOGENOMi HOG000088650.
    HOVERGENi HBG055528.
    InParanoidi Q9QY02.
    OMAi REPYKSQ.

    Miscellaneous databases

    NextBioi 35583674.
    PROi Q9QY02.

    Gene expression databases

    Genevestigatori Q9QY02.

    Family and domain databases

    InterProi IPR007275. YTH_domain.
    [Graphical view ]
    Pfami PF04146. YTH. 1 hit.
    [Graphical view ]
    PROSITEi PS50882. YTH. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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.

    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: October 1, 2014
    This is version 90 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

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3