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Q9QY02 (YTDC1_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 78. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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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 lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

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

General annotation (Comments)

Function

May be part of a signal transduction pathway that influences splice site selection.

Subunit structure

Interacts with EMD, KHDRBS1/SAM68, KHDRBS3, RBMX, TRA2B/SFRS10, SC35 and SF2. Ref.4 Ref.5

Subcellular location

Nucleus. Note: Localizes to a novel subnuclear structure, the YT bodies. Ref.3

Tissue specificity

Ubiquitous.

Post-translational modification

Tyrosine phosphorylated.

Sequence similarities

Contains 1 YTH domain.

Ontologies

Keywords
   Biological processmRNA processing
mRNA splicing
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processmRNA splicing, via spliceosome

Inferred from direct assay Ref.2. Source: RGD

   Cellular_componentnuclear body

Inferred from direct assay Ref.2. Source: RGD

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
Modified residue5181Phosphoserine By similarity

Natural variations

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

Sequences

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

Last modified May 1, 2000. Version 1.
Checksum: 220D0CD8A22A77FD

FASTA73885,825
        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 LKSVLQDARF 

       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: 9E9442B991ACFA09
Show »

FASTA71282,930

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).
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).
[3]"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.
[4]"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.
[5]"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.
IPIIPI00196301.
IPI00213467.
RefSeqNP_596914.1. NM_133423.1.
UniGeneRn.48752.

3D structure databases

ProteinModelPortalQ9QY02.
SMRQ9QY02. Positions 337-512.
ModBaseSearch...

PTM databases

PhosphoSiteQ9QY02.

Proteomic databases

PaxDbQ9QY02.
PRIDEQ9QY02.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID170956.
KEGGrno:170956.
UCSCRGD:621706. rat.

Organism-specific databases

CTD91746.
RGD621706. Ythdc1.

Phylogenomic databases

eggNOGNOG311295.
HOGENOMHOG000088650.
HOVERGENHBG055528.
InParanoidQ9QY02.
OrthoDBEOG4ZW5BC.

Gene expression databases

ArrayExpressQ9QY02.
GenevestigatorQ9QY02.
GermOnlineENSRNOG00000001996. Rattus norvegicus.

Family and domain databases

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

Other

NextBio621483.

Entry information

Entry nameYTDC1_RAT
AccessionPrimary (citable) accession number: Q9QY02
Secondary accession number(s): O54729
Entry history
Integrated into UniProtKB/Swiss-Prot: February 12, 2003
Last sequence update: May 1, 2000
Last modified: April 3, 2013
This is version 78 of the entry and version 1 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

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