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NK2 transcription factor related 2a


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GeneName nkx2.2a
Aliases ENSDARG:ENSDARG00000053298; nkx2-2, wu:fc83b01, nk2.2, nkx2.2, id:ibd5090, zgc:136536
Description NK2 transcription factor related 2a
GenomicLocation chromosome 17 42929655-42937363 forward strand
ExternalIDs Entrez:30697; EMBL:X85977; ZFIN:ZDB-GENE-980526-403; UniGene:75083
TranscriptID ENSDART:ENSDART00000081396; ENSDART:ENSDART00000140549
mRNA NCBI:NM_131422
GeneDescription nkx2.2b is a homeobox gene that is strongly expressed in the trunk LFP of zebrafish and represents a unique marker for the characterization of LFP formation. nkx2.2b and its paralog nkx2.2a arose by gene duplication in zebrafish.
GeneFunction Pauls S et al., 2007 studied the role of nkx2.2a and Nkx2.2 during the development of the endocrine pancreas. zebrafish nkx2.2a is also expressed in the anterior pancreatic bud and, later, in the differentiated pancreatic ducts. Based on this they concluded that nkx2.2a has a novel role in development of pancreatic ducts.Schafer M et al.,2006 stated that different levels of HH and Nkx2.2 activities are responsible for the alternating appearance of LFP and p3 neuronal progenitor cells in the zebrafish ventral neural tube. They showed that the zebrafish LFP and p3 neuronal progenitor cell populations are dependent on Delta-Notch signaling, but are differently regulated by Hedgehog (HH) and Nkx2.2 activities.Barth KA et al.,1995 isolated zebrafish nk2.2. They observed a band of cells expressing nkx2.2 located within a few cell diameters of cells expressing the signalling molecule sonic hedgehog/vertebrate hedgehog-1 (shh/vhh-1). On the basis of evidences they suggested a requirement of shh/vhh-1 protein for the spatial regulation of nk2.2 expression.
GeneCloning The gene is contained in a BAC clone DKEY-89L19 (Vector: pIndigoBAC-536).
GeneStructure The gene encodes three transcripts. The first transcript has 4 exons, the length being 738 bps and generates a protein prouct 245 residues long. The second transcript has 2 exon, the length being 1,730 bps and its protein product being 269 residues long. The third tanscript has 3 exons, the length being 1,555 bps and the protein product being 273 residues long.
Protein ENSDARP00000075838 ENSDARP00000117693
ProteinDomainandFamilies has domain InterPro:IPR001356; InterPro:IPR012287;
Motifs has motif Prosite:PS00027; PFAM:PF00046; PRINTS:PR00024; PRINTS:PR00028; UniProt:NX22A_DANRE;
Expression ArrayExpress:ENSDARG00000053298;
GeneOntology GO:0005634; GO:0005634; GO:0045449; GO:0006355; GO:0031018; GO:0021508; GO:0045449; GO:0006355; GO:0031018; GO:0021508; GO:0003700; GO:0043565; GO:0003677; GO:0003700; GO:0043565; GO:0003677;
Orthologs Entrez:4821;
VariationAndRepeats RSID:rs40817812
DisordersAndMutations The morpholino antisense oligonucleotide targeted against the upstream regions of nkx2.2a has the following sequences – 5’ TCTTTAGGGACATTTTCCAAACCAG-3’ Two other nkx2.2a morpholinos has also been employed MOnk-SPLI, 5′-AGGCCGTGTACTGGTAAAACAAAGG; MOnk-5UTR, 5′-TGGAGCATTTGATGCAGTCAAGTTG.MOnk-SPLI is directed against the junction between the second intron and the third exon and MOnk-5UTR against a part of the 5′UTR common to both nkx2.2a mRNA variants and upstream of the start codon .
RelatedPubMedArticles Barth, K.A. and Wilson, S.W. Expression of zebrafish nk2.2 is influenced by sonic hedgehog/vertebrate hedgehog-1 and demarcates a zone of neuronal differentiation in the embryonic forebrain. Development 121: 1755-1768, 1995, PMID:7600991 . Schafer, M., Kinzel, D., and Winkler, C. Discontinuous organization and specification of the lateral floor plate in zebrafish. Dev. Biol. 301(1): 117-129, 2006, PMID:17045256 . Pauls S, Zecchin E, Tiso N, Bortolussi M, Argenton F. Function and regulation of zebrafish nkx2.2a during development of pancreatic islet and ducts. Dev Biol. 2007 Apr 15;304(2):875-90. Epub 2007 Jan 20, PMID:17335795 .Schäfer M, Kinzel D, Winkler C. Discontinuous organization and specification of the lateral floor plate in zebrafish. Dev Biol. 2007 Jan 1;301(1):117-29. Epub 2006 Sep 16, PMID:17045256 .Schäfer M, Kinzel D, Neuner C, Schartl M, Volff JN, Winkler C. Hedgehog and retinoid signalling confines nkx2.2b expression to the lateral floor plate of the zebrafish trunk. Mech Dev. 2005 Jan;122(1):43-56, PMID:15582776 . 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 - 2013-07-06 - RamcharanAngom
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