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arntl1b

aryl hydrocarbon receptor nuclear translocator-like 1b

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GeneInformationForm
GeneName arntl1b
Aliases ENSDARG:ENSDARG00000035732; zfBMAL3, bmal1b
Description aryl hydrocarbon receptor nuclear translocator-like 1b
GenomicLocation chromosome 7 67945182-68002908 reverse strand
ExternalIDs Entrez:352935; EMBL:BC134895; UniGene:40654; ZFIN:ZDB-GENE-030408-1;
TranscriptID ENSDART:ENSDART00000104523; ENSDART:ENSDART00000098259; ENSDART:ENSDART00000051823; ENSDART:ENSDART00000139227; ENSDART:ENSDART00000133011; ENSDART:ENSDART00000147837
mRNA NCBI:NM_178300
GeneDescription BMAL is a PAS domain-containing transcription factors, one of the key genes involved in circadian rhythms. Circadian rhythm consist of positive and negative elements, the positive ones being two basic helix-loop-helix, PAS domain-containing transcription factors, CLOCK and BMAL.
GeneFunction Ishikawa et al. (2002) isolated one novel Bmal and two novel Clock genes (zfBmal3,zfClock2 and zfClock3 ) from zebrafish eye mRNA by reverse transcriptase-based polymerase chain reaction (RT-PCR). They showed that zCRY1a, which represses zfCLOCK2-zfBMAL3-mediated transcription, interacts with zfCLOCK2 and zfBMAL3, whereas zCRY4, which does not repress zfCLOCK2-zfBMAL3-mediated transcription, does not. zCRY1a neither disrupts the physical and functional interactions between zfCLOCK2 and zfBMAL3 nor dissociates the zfCLOCK2-zfBMAL3 heterodimer from E-box containing DNA; instead, it binds to the zfCLOCK2-zfBMAL3-E-box DNA complex. These results indicate that the functional difference between the two types of CRY, repressor and non repressor, is due to the ability of each type to interact with CLOCK and BMAL protein and suggests that the former represses CLOCK-BMAL-mediated transcription by directly binding to the heterodimer–DNA complex.Hirayama et al. (2003) found that zCRY1a and zPER2 functions as regulators of the sub-cellular localizations of zCLOCK, zBMAL and/or the zCLOCK: zBMAL heterodimer and that, they also control cellular localization of the heterodimer in opposite directions. In addition, unlike in mammals, the co-expression of zCRY1a and zPER2 causes cytoplasmic retention of the zCRY:zPER2 heterodimer. Thesefindings suggest that functions for CRY and PER2 exist that are unique to the zebrafish circadian system.Abe et al. (2006) showed that zDec1 and zDec2 are involved in the circadian clock mechanism in photosensitive zebrafish peripheral cells by suppressing CLOCK/BMAL-induced gene expression and that the feedback loops of zDEC1 and zDEC2 may be interlocked with the PER/CRY core circadian feedback loops.
GeneCloning This gene is contained in BAC Clones DKEY-288C23 (Vector : pIndigoBAC-536) and CH211-276D1 (Vector : pTARBAC2.1)
GeneStructure The gene encodes for two transcripts.(ENSDART00000051823) consist of 18 exons and is 1,872 bps in length. The protein product (ENSDARP00000051822) consist of 623 residues.(ENSDART00000098259) consist of 91 exons and is 2,352 bps in length. The protein product (ENSDART00000098259) consist of 629 residues.
Protein ENSDARP00000095296 ENSDARP00000089031 ENSDARP00000051822 ENSDARP00000114569
ProteinDomainandFamilies has domain InterPro:IPR001067; InterPro:IPR011598; InterPro:IPR001092; InterPro:IPR013655; InterPro:IPR000014; InterPro:IPR013767; InterPro:IPR001610;
Motifs has motif PFAM:PF00010; PFAM:PF00989; PFAM:PF08447; PRINTS:PR00785;
Expression ArrayExpress:ENSDARG00000035732
GeneOntology GO:0005634; GO:0005667; GO:0006355; GO:0007165; GO:0045449; GO:0009648; GO:0003700; GO:0004871; GO:0030528; GO:0003677;
Orthologs Entrez:406;
VariationAndRepeats RSID:rs40696904; RSID:rs40861964; RSID:rs40684489; RSID:rs41191733; RSID:rs41076634; RSID:rs40920738; RSID:rs40874897; RSID:rs41023548; RSID:rs41026723;
DisordersAndMutations Ishikawa et al. (2002) they isolated one novel Bmal and two novel Clock genes (zfBmal3,zfClock2 and zfClock3 )from zebrafish eye mRNA by reverse transcriptase-based polymerase chain reaction (RT-PCR). They have also showed that zCRY1a, which represses zfCLOCK2-zfBMAL3-mediated transcription, interacts with zfCLOCK2 and zfBMAL3, whereas zCRY4, which does not repress zfCLOCK2-zfBMAL3-mediated transcription, does not. zCRY1a neither disrupts the physical and functional interactions between zfCLOCK2 and zfBMAL3 nor dissociates the zfCLOCK2-zfBMAL3 heterodimer from E-box containing DNA; instead, it binds to the zfCLOCK2-zfBMAL3-E-box DNA complex. These results indicate that the functional difference between the two types of CRY, repressor and non repressor, is due to the ability of each type to interact with CLOCK and BMAL protein and suggests that the former represses CLOCK-BMAL-mediated transcriptionby directly binding to the heterodimer–DNA complex.Hirayama et al. (2003) found that found that zCRY1a and zPER2 function as regulators of the sub-cellular localizations of zCLOCK, zBMAL and/or the zCLOCK: zBMAl heterodimer and that they control cellular localization of the heterodimer in opposite directions. In addition, unlike in mammals, the co-expression of zCRY1a and zPER2 causes cytoplasmic retention of the zCRY:zPER2 heterodimer. Thesefindings suggest that functions for CRY and PER2 exist that are unique to the zebra®sh circadian system.Abe et al. (2006) results indicate that zDec1 and zDec2 are involved in the circadian clock mechanism in photosensitive zebrafish peripheral cells by suppressing CLOCK/BMAL-induced gene expression and that the feedback loops of zDEC1 and zDEC2 may be interlocked with the PER/CRY core circadian feedback loops
RelatedPubMedArticles Ishikawa, T.; Hirayama, J.; Kobayashi, Y.; Todo, T.: Zebrafish CRY represses transcription mediated by CLOCK-BMAL heterodimer without inhibiting its binding to DNA. Genes Cells;7(10):1073-86, 2002. PMID:12354100 Hirayama, J.; Nakamura, H.; Ishikawa, T.; Kobayashi, Y.; Todo, T.: Functional and structural analyses of cryptochrome. Vertebrate CRY regions responsible for interaction with the CLOCK:BMAL1 heterodimer and its nuclear localization. J Biol Chem. ;278(37):35620-8, 2003. PMID:12832412 Tamai, T.K.; Young, L.C.; Whitmore, D.:Light signaling to the zebrafish circadian clock by Cryptochrome 1a.Proc Natl Acad Sci U S A.;104(37):14712-7.2007. PMID:17785416 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 - 2013-07-06 - DivyaJagga
 
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