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Orthodenticle homolog 2


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GeneName otx2
Aliases ENSDARG:ENSDARG00000011235; zOtx2; zotx-2; MGC136535; id:ibd2915; zgc:136535; otx2
Description Orthodenticle homolog 2
GenomicLocation chromosome 17 44291216-44296095 reverse strand
ExternalIDs Entrez:30501; EMBL:D26173; UniGene:334; ZFIN:ZDB-GENE-980526-406;
TranscriptID ENSDART:ENSDART00000126097; ENSDART:ENSDART00000008816
mRNA NCBI:NM_131251
GeneDescription Otx2 encodes for a transcription factor which is a member of the bicoid sub-family of homeodomain containing transcription factor.It plays an important role in brain and sensory organ development.
GeneFunction Scholpp et al. (2007) showed that before the formation of zona limitans intrathalamica (ZLI), the intervening boundary regions between prethalamus and thalamus, both otx1l and otx2 are expressed in spatially restricted domains. Formation of ZLI and the Irx-1b-positive thalamus requireotx1l/2; they further showed that embryos impaired in otx1l/2function fail to form these areas and instead the pretectum and the prethalamus expand into the mis-specified area. They further reported that conditional expression of Otx2in these morphant embryos rescues the formation of ZLI at its correctlocation.
GeneCloning The gene is conatined in a BAC clone DKEY-166F24 (Vector: pIndigoBAC-536).
GeneStructure It codes for two transcripts. ENSDART00000008816 consists of 3 exons and length of the transcript is 2,161 bp.The protein product ENSDARP00000020202 consists of 289 residues. the second transcript ENSDART00000126097 consists of 3 exons with the transcript length of 2,212 bps.The protein product ENSDARP00000111153 consists of 289 residues.
Protein ENSDARP00000111153 ENSDARP00000020202
ProteinDomainandFamilies has domain InterPro:IPR003022; InterPro:IPR013851; InterPro:IPR001356; InterPro:IPR012287; InterPro:IPR003025;
Motifs has motif Prosite:PS00027; PFAM:PF00046; PFAM:PF03529; PRINTS:PR00024; PRINTS:PR00028; PRINTS:PR00031; PRINTS:PR01255; PRINTS:PR01257; UniProt:OTX2_DANRE;
Expression ArrayExpress:ENSDARG00000011235;
GeneOntology GO:0005634; GO:0005634; GO:0007275; GO:0006355; GO:0045449; GO:0042221; GO:0030901; GO:0030902; GO:0030917; GO:0007275; GO:0006355; GO:0045449; GO:0042221; GO:0030901; GO:0030902; GO:0030917; GO:0003677; GO:0003700; GO:0043565; GO:0003677; GO:0003700; GO:0043565;
Orthologs Entrez:5015;
VariationAndRepeats RSID:rs40793604: RSID:rs40793604
DisordersAndMutations ZFINID:ZDB-GENO-100506-20;ZFINID:ZDB-GENO-100412-5;ZFINID:ZDB-GENO-100412-1;MO1-otx2 has been used against otx2 gene.
RelatedPubMedArticles Scholpp, S.; Foucher, I.; Staudt, N.; Peukert, D.; Lumsden, A.; Houart, C.: Otx1l, Otx2 and Irx1b establish and position the ZLI in the diencephalon. Development. 134: 3167-3176 ,2007. PMID:17670791 NCBI Resource Coordinators.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 41(Database issue):D8-D20. 2013. PMID:23193264
Kersey, P. J.; Allen, J. E.; Christensen, M.; et al.: Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res. 2013. PMID:24163254
Sigrist, C. J. A.; de, Castro, E; Cerutti, L; Cuche, B. A.; Hulo, N.; Bridge, A.; Bougueleret, L. Xenarios, I.: New and continuing developments at PROSITE. Nucleic Acids Res. doi: 10.1093/nar/gks1067. 2012. PMID:23161676
Punta, M.; Coggill, P. C.; Eberhardt, et al.: The Pfam protein families database. Nucleic Acids Res. 40(Database Issue):D290-D301. 2012. PMID:22127870
Hunter, S.; Jones P.; Mitchell A.; et al.: Interpro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. doi: 10.1093/nar/gkr948. 2011. PMID:22096229
Carbon, S.; Ireland, A.; Mungall, C. J.; Shu, S.; Marshall, B.; Lewis, S.; AMIGO Hub; Web Presence Working Group.: AMIGO: online access to ontology and annotation data. Bioinformatics. 25(2):288-9. 2009. PMID:19033274
Ashburner, M.; Ball, C. A.; Blake, J. A.; et al. The Gene Ontology Consortium.: Gene ontology: tool for the unification of biology. Nat. Genet. 25(1):25-9. 2000. PMID:10802651
Sherry, S. T.; Ward, M. H.; Kholodov, M.; Baker, J.; Phan, L.; Smigielski, E. M.; Sirotkin, K.: dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 1;29(1):308-11. 2001. PMID:11125122
Bradford, Y.; Conlin, T.; Dunn, N.; et al.: ZFIN: enhancements and updates to the zebrafish model organism database. Nucleic Acids Res. 39(suppl 1):D822-D829. 2011. PMID:21036866
Kapushesky, M.; Adamusiak, T.; Burdett, T.; et al.: Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Res. 40(Database isue):D1077-81. 2012. PMID:22064864

Web resources:
NCBI: http://www.ncbi.nlm.nih.gov/
PFAM: http://pfam.sanger.ac.uk/
PROSITE: http://prosite.expasy.org/
Interpro: http://www.ebi.ac.uk/interpro/
ZFIN: http://zfin.org/
Expression Atlas (EMBL): http://www.ebi.ac.uk/gxa/
Ensembl: http://asia.ensembl.org/Danio_rerio/
Database of Single Nucleotide Polymorphisms (dbSNP). Bethesda (MD): National Center for Biotechnology Information, National Library of Medicine.: http://www.ncbi.nlm.nih.gov/SNP/
PRINTS from Genomenet: http://www.genome.jp/
European Nucleotide Archive: http://www.ebi.ac.uk/ena/home
UNIGENE: http://www.ncbi.nlm.nih.gov/unigene/
AMIGO Gene Ontology: http://amigo.geneontology.org
Topic revision: r3 - 2013-07-07 - RamcharanAngom
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