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rx3

retinal homeobox gene 3

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GeneInformationForm
GeneName rx3
Aliases ENSDARG:ENSDARG00000052893; eym, chk, chokh, eyes missing
Description retinal homeobox gene 3
GenomicLocation chromosome 21 9291473-9294542 forward strand
ExternalIDs EMBL:AF001909; Entrez:30474; UniGene:540; ZFIN:ZDB-GENE-990415-238;
TranscriptID ENSDART:ENSDART00000074833
mRNA NCBI:NM_131227
GeneDescription

GeneFunction McCollum et al.(2007) had identified that zebrafish lmo4b is a negative regulator of the fore brain growth that acted through the restriction of rx3 and six3 expression during early segmentation stages. They further demonstrated that morpholino knockdown of lmo4b resulted in expansion of the post gastrula expression damins of rx3 and six3. They showed that overexpression of lmo4b by mRNA injection caused a dosage-sensitive reduction in rx3 expression. Stigloher et al.(2006) demonstrated that at late gastrulation rx3 biases cell specification choices towards the retinal fate. They showed it by using the direct cell tracing techniques that retinal precursors acquired a telecephalic fate in the embryos that are homozygous for the ex3 null allele. This led to the enlargement of the telecephalon and lack of eyes. Rojas-Munoz et al.(2005) identified two mutant alleles for the zebrafish chokh gene which displayed a reduction or the absence of retinal pigment epithelium (RPE). They further revealed that chokh gene encodes rx3 using the genetic mapping and molecular characterization techniques. Kennedy et al.(2004) identified two alleles of an eyeless mutant, chokh in the zebrafish F(3) mutagenesis screens.They found that sequence analysis of the chk alleles revealed a nonsense or missense mutations in the rx3 gene.
GeneCloning rx3 Contained in [BAC] CH211-233A1
GeneStructure rx3 encodes a single transcript.The transcript ENSDART00000074833 consists of 3 exons and is 1,411 bps in length. The protein product ENSDARP00000069319 consist of 292 residues.
Protein ENSDARP:ENSDARP00000069319;
ProteinDomainandFamilies InterPro:IPR001356; InterPro:IPR003654; InterPro:IPR009057; InterPro:IPR017970;
Motifs Prosite:PS00027; Prosite:PS50071; Prosite:PS50803; PFAM:PF00046; PFAM:PF03826;
Expression ArrayExpress:ENSDARG00000052893;
GeneOntology GO:0005634; GO:0045449; GO:0006355; GO:0007275; GO:0048596; GO:0001708; GO:0006350; GO:0006353; GO:0031564; GO:0001654; GO:0030900; GO:0003677; GO:0003700; GO:0043565;
Orthologs Entrez:30062;
VariationAndRepeats RSID:rs40867435
DisordersAndMutations ZFINID:ZDB-GENO-040611-1;ZFINID:ZDB-GENO-060822-1;ZFINID:ZDB-GENO-020514-2;ZFINID:ZDB-GENO-081016-1;ZFINID:ZDB-GENO-081016-2;ZFINID:ZDB-GENO-051229-2;ZFINID:ZDB-GENO-051229-1;ZFINID:ZDB-GENO-080128-2;ZFINID:ZDB-GENO-050209-13;ZFINID:ZDB-GENO-080606-48;ZFINID:ZDB-GENO-040513-1;Rx3 gene is disrupted in the zebrafish mutant called chokh (chk)..
RelatedPubMedArticles Kennedy, B.N.; Stearns, G.W.; Smyth, V.A.; Ramamurthy, V.; van Eeden, F.; Ankoudinova, I.; Raible, D.; Hurley, J.B.; Brockerhoff, S.E.: Zebrafish rx3 and mab21l2 are required during eye morphogenesis.Dev Biol. 270(2):336-49, 2004. PMID:15183718 Rojas-Muñoz, A.; Dahm, R.; Nüsslein-Volhard, C.: chokh/rx3 specifies the retinal pigment epithelium fate independently of eye morphogenesis.Dev Biol. 288(2):348-62,2005 . PMID:16300752 Stigloher, C.; Ninkovic, J; Laplante, M.; Geling, A.; Tannhäuser, B.; Topp, S.; Kikuta, H.; Becker, T.S.; Houart, C.; Bally-Cuif, L.: Segregation of telencephalic and eye-field identities inside the zebrafish forebrain territory is controlled by Rx3.Development. 133(15):2925-35,2006 . PMID:16818451 McCollum, C.W.; Amin, S.R.; Pauerstein, P.; Lane, M.E.: A zebrafish LMO4 ortholog limits the size of the forebrain and eyes through negative regulation of six3b and rx3.Dev Biol. 309(2):373-85,2007. PMID:17692837 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: r4 - 2013-09-03 - SubburajK
 
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