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Q9QY02 (YTDC1_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 86. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
YTH domain-containing protein 1
Alternative name(s):
Putative splicing factor YT521
RA301-binding protein
Gene names
Name:Ythdc1
Synonyms:Yt521
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length738 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

RNA-binding protein that regulates alternative splice site selection. Ref.1 Ref.2

Subunit structure

Interacts with EMD, KHDRBS1/SAM68, KHDRBS3, RBMX, TRA2B/SFRS10, SC35 and SF2. Ref.6 Ref.7

Subcellular location

Nucleus. Note: Localizes to a novel subnuclear structure, the YT bodies. Ref.5

Tissue specificity

Ubiquitous.

Domain

The YTH domain mediates RNA-binding By similarity.

Post-translational modification

Tyrosine phosphorylated.

Sequence similarities

Contains 1 YTH domain.

Ontologies

Keywords
   Biological processmRNA processing
mRNA splicing
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   LigandRNA-binding
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processmRNA splice site selection

Inferred from sequence or structural similarity. Source: UniProtKB

mRNA splicing, via spliceosome

Inferred from direct assay Ref.2. Source: RGD

   Cellular_componentnuclear body

Inferred from direct assay Ref.2. Source: RGD

nucleoplasm

Inferred from direct assay Ref.2. Source: RGD

nucleus

Inferred from sequence or structural similarity. Source: UniProtKB

   Molecular_functionRNA binding

Inferred from sequence or structural similarity. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9QY02-1)

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.
Isoform 2 (identifier: Q9QY02-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 738738YTH domain-containing protein 1
PRO_0000223077

Regions

Domain358 – 495138YTH
Compositional bias172 – 26392Glu-rich
Compositional bias612 – 65443Pro-rich
Compositional bias658 – 73881Arg-rich

Amino acid modifications

Modified residue1461Phosphoserine By similarity
Modified residue1481Phosphothreonine By similarity
Modified residue3111Phosphoserine By similarity
Modified residue3181Phosphoserine By similarity
Modified residue3201Phosphoserine By similarity
Modified residue3211Phosphoserine By similarity
Modified residue3231Phosphoserine By similarity
Modified residue4271Phosphoserine By similarity
Modified residue4381Phosphoserine By similarity

Natural variations

Alternative sequence328 – 34518Missing in isoform 2.
VSP_006819
Alternative sequence577 – 5848Missing in isoform 2.
VSP_006820

Experimental info

Sequence conflict3531Y → S in BAA23885. Ref.1
Sequence conflict3531Y → S in AAD55973. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (YT521-B) [UniParc].

Last modified February 19, 2014. Version 2.
Checksum: 9FC68314E029FA98

FASTA73885,902
        10         20         30         40         50         60 
MAADSREEKD GELNVLDDIL TEVPEQDDEL YNPESEQDKN EKKGSKRKSE RMESIDTKRQ 

        70         80         90        100        110        120 
KPSIHSRQLI SKPLSSSVSN NKRIVSTKGK SVTEYKNEEY QRSERNKRLD ADRKIRLSSS 

       130        140        150        160        170        180 
SSREPYKSQP EKPCLRKRDS ERRAKSPTPD GSERIGLEVD RRASRSSQSS KEEGNSEEYG 

       190        200        210        220        230        240 
SDHETGSSAS SEQGNNTENE EEGGEEDVEE DEEVDEDGDD DEEVDEDAEE EEDEEEDEEE 

       250        260        270        280        290        300 
EDEEEEEEEE EEYEQDERDQ KEEGNDYDTR SEASDSGSES VSFTDGSVRS GSGTDGSDEK 

       310        320        330        340        350        360 
KKERKRARGI SPIVFDRSGS SASESYAGSE KKHEKLSSSV RAVRKDQTSK LKYVLQDARF 

       370        380        390        400        410        420 
FLIKSNNHEN VSLAKAKGVW STLPVNEKKL NLAFRSARSV ILIFSVRESG KFQGFARLSS 

       430        440        450        460        470        480 
ESHHGGSPIH WVLPAGMSAK MLGGVFKIDW ICRRELPFTK SAHLTNPWNE HKPVKIGRDG 

       490        500        510        520        530        540 
QEIELECGTQ LCLLFPPDES IDLYQLIHKM RHKRRMHSQP RSRGRPSRRE PVRDVGRRRP 

       550        560        570        580        590        600 
EDYDIHNSRK KPRIDYPPEF HQRPGYLKDP RYQEVDSFTN LIPNRRFSGV RRDVFLNGSY 

       610        620        630        640        650        660 
NDYVREFHNM GPPPPWQGMP PYPGIEQPPH HPYYQHHAPP PQAHPPYSGH HPVPHEARYR 

       670        680        690        700        710        720 
DKRVHDYDMR VDDFLRRTQA VVSGRRSRPR ERDRERERDR PRDNRRDRER DRGRDRERER 

       730 
ERICDRDRDR GERGRYRR 

« Hide

Isoform 2 [UniParc].

Checksum: F1F56DDD71AE580F
Show »

FASTA71283,006

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
D78303 mRNA. Translation: BAA23885.1.
AF144731 mRNA. Translation: AAD55973.1.
AABR06078005 Genomic DNA. No translation available.
CH473981 Genomic DNA. Translation: EDL89830.1.
RefSeqNP_596914.1. NM_133423.1.
XP_006250870.1. XM_006250808.1.
UniGeneRn.48752.

3D structure databases

ProteinModelPortalQ9QY02.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid251046. 1 interaction.

PTM databases

PhosphoSiteQ9QY02.

Proteomic databases

PaxDbQ9QY02.
PRIDEQ9QY02.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000002736; ENSRNOP00000002736; ENSRNOG00000001996. [Q9QY02-1]
ENSRNOT00000002740; ENSRNOP00000002740; ENSRNOG00000001996. [Q9QY02-2]
GeneID170956.
KEGGrno:170956.
UCSCRGD:621706. rat. [Q9QY02-1]

Organism-specific databases

CTD91746.
RGD621706. Ythdc1.

Phylogenomic databases

eggNOGNOG311295.
GeneTreeENSGT00690000102240.
HOGENOMHOG000088650.
HOVERGENHBG055528.
InParanoidQ9QY02.
PhylomeDBQ9QY02.

Gene expression databases

GenevestigatorQ9QY02.

Family and domain databases

InterProIPR007275. YTH_domain.
[Graphical view]
PfamPF04146. YTH. 1 hit.
[Graphical view]
PROSITEPS50882. YTH. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio35583674.
PROQ9QY02.

Entry information

Entry nameYTDC1_RAT
AccessionPrimary (citable) accession number: Q9QY02
Secondary accession number(s): G3V690, O54729
Entry history
Integrated into UniProtKB/Swiss-Prot: February 12, 2003
Last sequence update: February 19, 2014
Last modified: April 16, 2014
This is version 86 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families