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Q9TQA6 (Q9TQA6_RAT) Unreviewed, UniProtKB/TrEMBL

Last modified July 9, 2014. Version 106. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry infoCustomize order

Names and origin

Protein names

MHC class II antigen EMBL AAV40636.1

RCG60985, isoform CRA_a EMBL EDL96798.1

RT1 class II, D beta 1 EMBL CAE83947.1

RT1-Db1 EMBL AGV39047.1

Rano class II histocompatibility antigen, D-1 beta chain Ensembl ENSRNOP00000000522
Gene names
Name:RT1-Db1 EMBL CAE83947.1 Ensembl ENSRNOP00000000522 RGD 1593282
Synonyms:Arrb2-ps RGD 1303212, Db1 EMBL AGV39047.1, Hla-dma RGD 735053, Hla-dmb RGD 735096, Psmb9 RGD 3427, RT1-Ba RGD 1595867, RT1-Bb RGD 3469, RT1-Da RGD 1593283, RT1-Db EMBL AAV40636.1, RT1-Db2 RGD 1595922, RT1-DOb RGD 1595814, RT1.D(n) EMBL AAD39083.1, Tap1 RGD 3817, Tap2 RGD 3818, Tesb RGD 1597063
ORF Names:rCG_60985 EMBL EDL96798.1
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length264 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at transcript level

General annotation (Comments)

Sequence similarities

Contains Ig-like C1-type (immunoglobulin-like) domain. SAAS SAAS014745

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2626 Potential EMBL AAD39083.1
Chain27 – 264238Class II MHC RT1.D(n) beta chain EMBL AAD39083.1
PRO_5000055051

Sequences

Sequence LengthMass (Da)Tools
Q9TQA6 [UniParc].

Last modified May 1, 2000. Version 1.
Checksum: C57FCD5C5CBF0FB3

FASTA26430,202
        10         20         30         40         50         60 
MVWLARDSCV AAVILLLTVL SPPVALVRDP TPRFLEQYKS ECYFYNGTQR VRLLVRYIYN 

        70         80         90        100        110        120 
REEYTRFDSD VGEFRAVTEL GRRDTEYYNK QKEYIERERA AVDTICRHNY EISDRFLVPR 

       130        140        150        160        170        180 
TVEPKVTVYP SKTQPLKHHN LLVCSVSDFY PGSVEVRWFR NGEEEKDGLV STGLIPNGDW 

       190        200        210        220        230        240 
TFQLLVMLEM VPQGGEVYTC QVEHPSLTSP VRVEWKAQST SAQNKKMSGV GGIVLGLLFL 

       250        260 
GAGLFVYFRN QKGQSGLQPT GLLN 

« Hide

References

« Hide 'large scale' references
[1]"Nucleotide sequences of three distinct complementary DNA clones encoding rat class II major histocompatibility complex RT1.D beta-chain proteins."
Tian L., Wang M., Yu J., Kahan B.D., Stepkowski S.M.
Immunogenetics 49:735-737(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE.
Strain: Brown Norway EMBL AAD39083.1.
[2]Boehm S., Borzym K., Gelling S., Gimmel V., Heitmann K., Kosiura A., Lang N., Lehrack S., Thiel J., Sontag M., Hurt P., Himmelbauer H., Sudbrak R., Reinhardt R.
Submitted (DEC-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE.
Strain: Brown Norway EMBL CAE83947.1.
[3]"The genomic sequence and comparative analysis of the rat major histocompatibility complex."
Hurt P., Walter L., Sudbrak R., Klages S., Mueller I., Shiina T., Inoko H., Lehrach H., Guenther E., Reinhardt R., Himmelbauer H.
Genome Res. 14:631-639(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE.
Strain: Brown Norway EMBL CAE83947.1.
[4]"Open reading frame sequencing and structure-based alignment of polypeptides encoded by RT1-Bb, RT1-Ba, RT1-Db, and RT1-Da alleles."
Ettinger R.A., Moustakas A.K., Lobaton S.D.
Immunogenetics 56:585-596(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE.
Strain: BN/CrlBR EMBL AAV40636.1.
Tissue: Thymus EMBL AAV40636.1.
[5]"Genome sequence of the Brown Norway rat yields insights into mammalian evolution."
Rat Genome Sequencing Project Consortium
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 Ensembl ENSRNOP00000000522.
[6]"Gene and alternative splicing annotation with AIR."
Florea L., Di Francesco V., Miller J., Turner R., Yao A., Harris M., Walenz B., Mobarry C., Merkulov G.V., Charlab R., Dew I., Deng Z., Istrail S., Li P., Sutton G.
Genome Res. 15:54-66(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE.
Strain: BN EMBL EDL96798.1.
[7]Mural R.J., Li P.W., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S.H., Dew I., Evans C.A., Ferriera S., Flanigan M., Fosler C., Glodek A., Gu Z., Holt R.A., Jennings D., Kraft C.L., Lu F. expand/collapse author list , Nguyen T., Nusskern D.R., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Wang Z., Woodage T., Zheng X.H., Zhong F.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE.
Strain: BN EMBL EDL96798.1.
[8]Ensembl
Submitted (FEB-2012) to UniProtKB
Cited for: IDENTIFICATION.
Strain: Brown Norway Ensembl ENSRNOP00000000522.
[9]"Natural polymorphisms in Tap2 influence negative selection and CD4?CD8 lineage commitment in the rat."
EURATRANS
Tuncel J., Haag S., Yau A.C.Y., Norin U., Baud A., Lonnblom E., Maratou K., Ytterberg A.J., Ekman D., Thordardottir S., Johannesson M., Gillett A., Stridh P., Jagodic M., Olsson T., Fernandez-Teruel A., Zubarev R.A., Mott R. expand/collapse author list , Aitman T.J., Flint J., Holmdahl R.
PLoS Genet. 10:e1004151-e1004151(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE.
Strain: DA.1H EMBL AGV39047.1.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AABR06099861 Genomic DNA. No translation available.
AF084933 mRNA. Translation: AAD39083.1.
AY626207 mRNA. Translation: AAV40636.1.
KC222950 mRNA. Translation: AGV39047.1.
BX883043 Genomic DNA. Translation: CAE83947.1.
CH473988 Genomic DNA. Translation: EDL96798.1.
RefSeqNP_001008884.1. NM_001008884.2.
UniGeneRn.33311.

3D structure databases

ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000000522; ENSRNOP00000000522; ENSRNOG00000033215.
GeneID294270.
KEGGrno:294270.

Organism-specific databases

CTD294270.
RGD1593282. RT1-Db1.

Phylogenomic databases

GeneTreeENSGT00560000076676.
HOVERGENHBG012730.
InParanoidQ9TQA6.
KOK06752.
OMANGMERVR.
OrthoDBEOG7PS1GV.
TreeFamTF336626.

Gene expression databases

GenevestigatorQ9TQA6.

Family and domain databases

Gene3D2.60.40.10. 1 hit.
3.10.320.10. 1 hit.
InterProIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003006. Ig/MHC_CS.
IPR003597. Ig_C1-set.
IPR011162. MHC_I/II-like_Ag-recog.
IPR014745. MHC_II_a/b_N.
IPR000353. MHC_II_b_N.
[Graphical view]
PfamPF07654. C1-set. 1 hit.
PF00969. MHC_II_beta. 1 hit.
[Graphical view]
ProDomPD000328. MHC_II_b_N. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTSM00407. IGc1. 1 hit.
SM00921. MHC_II_beta. 1 hit.
[Graphical view]
SUPFAMSSF54452. SSF54452. 1 hit.
PROSITEPS50835. IG_LIKE. 1 hit.
PS00290. IG_MHC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio637862.

Entry information

Entry nameQ9TQA6_RAT
AccessionPrimary (citable) accession number: Q9TQA6
Entry history
Integrated into UniProtKB/TrEMBL: May 1, 2000
Last sequence update: May 1, 2000
Last modified: July 9, 2014
This is version 106 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)