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Q6DGG4 (Q6DGG4_RAT) Unreviewed, UniProtKB/TrEMBL

Last modified February 19, 2014. Version 79. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Interferon regulatory factor PIRNR PIRNR038196
Gene names
Name:Irf1 Ensembl ENSRNOP00000010968 EMBL AAH76382.1 RGD 2920
ORF Names:rCG_33161 EMBL EDM04397.1
OrganismRattus norvegicus (Rat) [Reference proteome] EMBL AAH76382.1
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length328 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Subcellular location

Nucleus By similarity PIRNR PIRNR038196.

Sequence similarities

Belongs to the IRF family. PIRNR PIRNR038196

Ontologies

Keywords
   Biological processTranscription
Transcription regulation PIRNR PIRNR038196
   Cellular componentNucleus PIRNR PIRNR038196
   LigandDNA-binding PIRNR PIRNR038196
   Molecular functionActivator PIRNR PIRNR038196
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processCD8-positive, alpha-beta T cell differentiation

Inferred from electronic annotation. Source: Ensembl

apoptotic process

Inferred from electronic annotation. Source: Ensembl

cell cycle arrest

Inferred from electronic annotation. Source: Ensembl

cellular response to interferon-beta

Inferred from electronic annotation. Source: Ensembl

cellular response to mechanical stimulus

Inferred from electronic annotation. Source: Ensembl

defense response to virus

Inferred from electronic annotation. Source: Ensembl

interferon-gamma-mediated signaling pathway

Inferred from electronic annotation. Source: Ensembl

negative regulation of regulatory T cell differentiation

Inferred from electronic annotation. Source: Ensembl

positive regulation of interferon-beta production

Inferred from electronic annotation. Source: Ensembl

positive regulation of interleukin-12 biosynthetic process

Inferred from electronic annotation. Source: Ensembl

positive regulation of transcription from RNA polymerase II promoter

Inferred from electronic annotation. Source: Ensembl

regulation of CD8-positive, alpha-beta T cell proliferation

Inferred from electronic annotation. Source: Ensembl

regulation of MyD88-dependent toll-like receptor signaling pathway

Inferred from electronic annotation. Source: Ensembl

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: Ensembl

nuclear chromatin

Inferred from electronic annotation. Source: Ensembl

   Molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding

Inferred from electronic annotation. Source: Ensembl

sequence-specific DNA binding transcription factor activity

Inferred from electronic annotation. Source: Ensembl

Complete GO annotation...

Sequences

Sequence LengthMass (Da)Tools
Q6DGG4 [UniParc].

Last modified August 16, 2004. Version 1.
Checksum: EC18398A92747D75

FASTA32837,080
        10         20         30         40         50         60 
MPITRMRMRP WLEMQINSNQ IPGLSWINKE EMIFQIPWKH AAKHGWDINK DACLFRSWAI 

        70         80         90        100        110        120 
HTGRYKAGEK EPDPKTWKAN FRCAMNSLPD IEEVKDQSRN KGSSAVRVYR MLPPLTKNQR 

       130        140        150        160        170        180 
KERKSKSSRD TKSKTKRKLC GDSSPDTLSD GLSSSTLPDD HSSYTAQGYL GQDLDMDRDI 

       190        200        210        220        230        240 
TPALSPCVVS SSLSEWHMQM DIMPDSTTDL YNLQVSPMPS TSEAATDEDE EGKLPEDIMK 

       250        260        270        280        290        300 
LFEQSEWQPT HVDGKGYLLN EPGAQLSTVY GDFSCKEEPE IDSPGGDIEI GIQRVFTEMK 

       310        320 
NMDPVMWMDT LLGNSTRPPS IQAIPCAP 

« Hide

References

« Hide 'large scale' references
[1]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Gerhard D.S., Wagner L., Feingold E.A., Shenmen C.M., Grouse L.H., Schuler G., Klein S.L., Old S., Rasooly R., Good P., Guyer M., Peck A.M., Derge J.G., Lipman D., Collins F.S., Jang W., Sherry S., Feolo M. expand/collapse author list , Misquitta L., Lee E., Rotmistrovsky K., Greenhut S.F., Schaefer C.F., Buetow K., Bonner T.I., Haussler D., Kent J., Kiekhaus M., Furey T., Brent M., Prange C., Schreiber K., Shapiro N., Bhat N.K., Hopkins R.F., Hsie F., Driscoll T., Soares M.B., Casavant T.L., Scheetz T.E., Brown-stein M.J., Usdin T.B., Toshiyuki S., Carninci P., Piao Y., Dudekula D.B., Ko M.S., Kawakami K., Suzuki Y., Sugano S., Gruber C.E., Smith M.R., Simmons B., Moore T., Waterman R., Johnson S.L., Ruan Y., Wei C.L., Mathavan S., Gunaratne P.H., Wu J., Garcia A.M., Hulyk S.W., Fuh E., Yuan Y., Sneed A., Kowis C., Hodgson A., Muzny D.M., McPherson J., Gibbs R.A., Fahey J., Helton E., Ketteman M., Madan A., Rodrigues S., Sanchez A., Whiting M., Madari A., Young A.C., Wetherby K.D., Granite S.J., Kwong P.N., Brinkley C.P., Pearson R.L., Bouffard G.G., Blakesly R.W., Green E.D., Dickson M.C., Rodriguez A.C., Grimwood J., Schmutz J., Myers R.M., Butterfield Y.S., Griffith M., Griffith O.L., Krzywinski M.I., Liao N., Morin R., Morrin R., Palmquist D., Petrescu A.S., Skalska U., Smailus D.E., Stott J.M., Schnerch A., Schein J.E., Jones S.J., Holt R.A., Baross A., Marra M.A., Clifton S., Makowski K.A., Bosak S., Malek J.
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Lung EMBL AAH76382.1.
[2]"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 ENSRNOP00000010968.
[3]"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 EDM04397.1.
[4]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 EDM04397.1.
[5]Ensembl
Submitted (JUL-2011) to UniProtKB
Cited for: IDENTIFICATION.
Strain: Brown Norway Ensembl ENSRNOP00000010968.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AABR06063819 Genomic DNA. No translation available.
BC076382 mRNA. Translation: AAH76382.1.
CH473948 Genomic DNA. Translation: EDM04397.1.
CH473948 Genomic DNA. Translation: EDM04399.1.
CH473948 Genomic DNA. Translation: EDM04401.1.
UniGeneRn.6396.

3D structure databases

ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000010968; ENSRNOP00000010968; ENSRNOG00000008144.

Organism-specific databases

RGD2920. Irf1.

Phylogenomic databases

GeneTreeENSGT00740000114956.
HOVERGENHBG003455.
InParanoidQ6DGG4.
OMACKEEPEV.
OrthoDBEOG72ZCFD.
TreeFamTF328512.

Gene expression databases

GenevestigatorQ6DGG4.

Family and domain databases

Gene3D1.10.10.10. 1 hit.
InterProIPR017431. Interferon_reg_fac-1/2.
IPR019817. Interferon_reg_fac_CS.
IPR001346. Interferon_reg_fact_DNA-bd_dom.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamPF00605. IRF. 1 hit.
[Graphical view]
PIRSFPIRSF038196. IFN_RF1/2. 1 hit.
PRINTSPR00267. INTFRNREGFCT.
SMARTSM00348. IRF. 1 hit.
[Graphical view]
PROSITEPS00601. IRF_1. 1 hit.
PS51507. IRF_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROQ6DGG4.

Entry information

Entry nameQ6DGG4_RAT
AccessionPrimary (citable) accession number: Q6DGG4
Entry history
Integrated into UniProtKB/TrEMBL: August 16, 2004
Last sequence update: August 16, 2004
Last modified: February 19, 2014
This is version 79 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)