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cdh6

cadherin 6

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GeneInformationForm
GeneName cdh6
Aliases ENSDARG:ENSDARG00000014522; zgc:103673, cadherin 6
Description cadherin 6
GenomicLocation chromosome 2 28216925-28270171 reverse strand
ExternalIDs Entrez:541393; EMBL:AB193290; UniGene:132516; ZFIN:ZDB-GENE-050320-92;
TranscriptID ENSDART:ENSDART00000131506; ENSDART:ENSDART00000013638
mRNA NCBI:NM_001013520
GeneDescription Cdh6 helps in maintenance of orderly structure such as epithelium. Strong transcriptional expression of this gene has been observed in hepatocellular and renal carcinoma cell lines.
GeneFunction Kubota et al.(2007) used cdh6 antisense Morpholino oligonucleotide and in situ analysis they came to know about Cdh6 role in nephrogenesis. They have cloned Cdh6 homolog which shows 60-63 % identity and 76-78% similarity to human, mouse, chicken and xenopus. In situ analysis showed Cdh6 expression in pronephric ducts and nephron primorida at 14 hpf, which increases at 24 hpf. On injecting Cdh6 MOs they found some defects in zebrafish embryos ie short yolk extension and short bent tail, small head by 30hpf. Some defect becomes prominent with time but embyo died on 5 day post fertilization. Histological studies showed abnormally fused glomerulus primordial, abnormally bent pronephric tubule anlagen etc. In summary, Cdh6 is proves to play important role in pronephrons in zebrafish embryos. Liu Q et al.(2008) usedCdh6 antisense morphino oligonucleotides and analysed differentiation of retinal ganglion cells, amacrine cells. They analysed Cdh6 knockdown embyos using multiple markers and found that factors important for retinal development was greatly reduced expression of Notch- Delta genes and proneural gene ath5 . In summary, they found that differentiation of retinal ganglion cells, amacrine cells and photoreceptors was disrupted in Cdh6 morphant. This suggested cdh6 role in normal formation of zebrafish retina.
GeneCloning

GeneStructure Cdh6 encodes for two transcripts. ENSDART00000013638) consists of 12 exons and is 3,242 bps in length. The protein product (ENSDARP00000025811) consist of 794 residues. ENSDART00000131506) consists of 11 exons and is 4,217 bps in length. The protein product (ENSDARP00000117877) consist of 794 residues.
Protein ENSDARP00000117877 ENSDARP00000025811
ProteinDomainandFamilies has domain InterPro:IPR000233; InterPro:IPR002126;
Motifs has motif Prosite:PS00232;Prosite:PS50268; PFAM:PF00028; PFAM:PF01049; PRINTS:PR00205;
Expression ArrayExpress:ENSDARG00000014522
GeneOntology GO:0016020; GO:0016021; GO:0007156; GO:0048793; GO:0006816; GO:0005509; GO:0019855; GO:0005262;
Orthologs

VariationAndRepeats RSID:rs180044796; RSID:rs180044797; RSID:rs180044797; RSID:rs40729351; RSID:rs40729351; RSID:rs180044798; RSID:rs180044798; RSID:rs180044799; RSID:rs180044799; RSID:rs41015405; RSID:rs41015405; RSID:rs180044800; RSID:rs180044800; RSID:rs180044801; RSID:rs180044801; RSID:rs180044802; RSID:rs180044802; RSID:rs180044803; RSID:rs180044803; RSID:rs180044804; RSID:rs180044804; RSID:rs180044805; RSID:rs180044805; RSID:rs179475105; RSID:rs179475105; RSID:rs180044806; RSID:rs180044806; RSID:rs180044807; RSID:rs180044807; RSID:rs40912896; RSID:rs40912896; RSID:rs179475094; RSID:rs179475094; RSID:rs180044808; RSID:rs180044808; RSID:rs180044809; RSID:rs180044809; RSID:rs180044810
DisordersAndMutations Kubota et al., 2007 They have purchased the Fluorescein-labeled antisense Morpholino oligonucleotides (MOs) from Gene Tools (Philomath, OR, USA). These MOs were designed complementary to the 5 sequence near the translational initiation site of cdh6 (cdh6MOs) with the sequences: cdh6MO-1, 5- AAGAAGTACAATCCAAGTCCTCATC-3 (targets 5 sequence spanning the start codon, italicized); and cdh6MO-2,5-ATCCTATCTGCCAAAGTTACAGAGC-3 (directed against the sequence 5 of the UTR to the start codon).
RelatedPubMedArticles Kubota, F.; Murakami, T.; Mogi, K.; Yorifuji, H.:Cadherin-6 is required for zebrafish nephrogenesis during early development. Int. J. Dev. Biol 51: 123-12,2007. PMID:17294363 Liu, Q.; Londraville, R.; Marrs, J.A.; Wilson, A.L.; Mbimba, T.; Murakami, T.; Kubota, F.; Zheng, W.; Fatkins, D.G.: Cadherin-6 Function in Zebrafish Retinal Development. Dev Neurobiol.68(8): 11071122,2008 . PMID:18506771 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: r2 - 2013-07-26 - ParasSehgal
 
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