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IKAROS family zinc finger 1

IKAROS family zinc finger 1 (Ikaros)


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GeneName IKAROS family zinc finger 1
Aliases ENSDARG:ENSDARG00000013539; ikaros, znfn1a1
Description IKAROS family zinc finger 1 (Ikaros)
GenomicLocation chromosome 13 15911857-15948447 reverse strand
ExternalIDs Entrez:30177; EMBL:AF092175; UniGene:8122; ZFIN:ZDB-GENE-980526-304;
TranscriptID ENSDART:ENSDART00000016430; ENSDART:ENSDART00000042377; ENSDART:ENSDART00000046079; ENSDART:ENSDART00000050481; ENSDART:ENSDART00000079724
mRNA NCBI:NM_130986
GeneDescription Ikzf1 gene binds and activates the enhancer (delta-A element) of the CD3-delta gene. Functions in
the specification and the maturation of the T-lymphocyte. Also interacts with a critical control
element in the TDT (terminal deoxynucleotidyltransferase) promoter as well as with the promoters for other genes expressed during early stages of B- and T-cell development
GeneFunction Willett et al. (2001) found that Ikaros was found to be most highly expressed in the thymus and pronephros , which is consistent with the differentiation of T and B cells, respectively, in these organs (Willett et al., 1997b, 1999; Danilova et al.,(2000). During development in zebrafish, Ikaros expression begins in lateral mesoderm, and continues in the intermediate cell mass (ICM), which is derived from lateral mesoderm and has been shown to generate primitive hematopoietic precursors. Ikaros-expressing cells were also found in the pharyngeal region, near the forming thymus. Later, such cells were seen in the pronephros, the site of hematopoiesis in adult fish. The timing of appearance of Ikaros-expressing cells suggests that, similar to other vertebrates, lymphocytes in the thymus arise from hematopoietic tissue located near the dorsal aorta or in the ICM.

Lam et al. (2003) in this study, they have extended investigation on the maturation of the zebrafish immune system. The expression of immune-related genes of the zebrafish was monitored like ikaros, which encodes a transcription factor which is used as an early lymphoid marker, rag-1 etc to correlate the immune-related gene expression profiles,the in situ detection of cells expressing these genes in lymphoid tissues, and the detection of Ig and the on set of humoral immunity, and enable a better understanding of the different maturation state of theimmune system during zebrafish development.They found that Ikaros expression was first detected at 1 day post-fertilization (dpf) and thereafter increased gradually to more than two-fold between 28 and 42 dpf before decreasing to less than the initial 1 dpf expression level in adult fish (aged 105 dpf).

Murayama et al. (2006) by using an in situ photoactivatable cell tracer in the transparent zebrafish embryo, they demonstrated that definitive blood precursors appeared between the dorsal aorta and axial vein, validating the homology of this tissue with the AGM (aorta-gonadmesonephros) of amniotes. These cells first migrated through the blood to a previously undescribed caudal hematopoietic tissue (CHT), where they differentiated, expanded, and further migrated to seed the definitive hematopoietic organs, the thymus and kidney. Immigrants on the way to the thymus expressed c-myb and ikaros but not rag1; they were probably no longer HSCs, however, because they lacked scl and runx1 expression, unlike immigrants to the kidney.

Schorpp et al. (2006) examined the role of the transcription factor Ikaros in zebrafish lymphopoiesis. The phenotype of zebrafish homozygous for a recessive ikaros allele containing a nonsense mutation in the last coding exon was found to be similar to the situation of a loss-of-function mutation in the mouse. In fish larvae homozygous for an ikaros allele predicted to lack the C-terminal zinc fingers, T lymphopoiesis is absent; the presence of VHD_J_ rearrangements in adolescent fish is delayed in mutants. In adolescent mutant fish, T cells expressing tcrb and tcrd and B cells expressing igm are formed with low efficiency and display an oligoclonal Ag receptor repertoire.

GeneCloning This gene is contained in BAC clone CH211-57F7 (Vector:pTARBAC2.1)
GeneStructure This gene encodes 5 transcripts.

(ENSDART00000079724) is a novel transcript. It consists of 8 exons and is 1,915 bps in length. The protein product (ENSDARP00000074176) consists of 526 residues.

(ENSDART00000016430) consists of 9 exons and is 1,948 bps in length. The protein product (ENSDARP00000013960) consists of 537 residues.

(ENSDART00000042377) consists of 4 exons and is 1,219 bps in length. The protein product (ENSDARP00000042376) consists of 294 residues.

(ENSDART00000046079) consists of 6 exons and is 1,513 bps in length. The protein product (ENSDARP00000046078) consists of 392 residues.

(ENSDART00000050481) consists of 7 exons and is 1,639 bps in length. The protein product (ENSDARP00000050480) consists of 434 residues.

Protein ENSDARP00000013960 ENSDARP00000042376 ENSDARP00000046078 ENSDARP00000050480 ENSDARP00000074176
ProteinDomainandFamilies has domain InterPro:IPR013087; InterPro:IPR001412; InterPro:IPR015880; InterPro:IPR007087;
Motifs has motif Prosite:PS00028; Prosite:PS00178; PFAM:PF00096; PRINTS:PR00048;
Expression ArrayExpress:ENSDARG00000013539
GeneOntology GO:0005622; GO:0006418; GO:0006829; GO:0003676; GO:0005524; GO:0008270; GO:0004812; GO:0046872;
Orthologs Entrez:10320;
VariationAndRepeats RSID:rs40885506; RSID:rs40885506; RSID:rs40885506; RSID:rs40885506; RSID:rs40885506; RSID:rs41244902; RSID:rs41244902; RSID:rs41244902; RSID:rs41244902; RSID:rs41244902; RSID:rs41130272; RSID:rs41130272; RSID:rs41130272; RSID:rs41130272; RSID:rs41130272; RSID:rs41130907; RSID:rs41130907; RSID:rs41130907; RSID:rs41130907; RSID:rs41130907; RSID:rs40757200; RSID:rs40757200; RSID:rs40757200; RSID:rs40757200; RSID:rs40757200; RSID:rs41243819; RSID:rs41243819; RSID:rs41243819; RSID:rs41243819; RSID:rs41243819; RSID:rs40687973; RSID:rs40687973; RSID:rs40687973; RSID:rs40687973; RSID:rs40687973; RSID:rs40968736; RSID:rs40968736; RSID:rs40968736; RSID:rs40968736; RSID:rs40968736; RSID:rs40978066; RSID:rs40978066; RSID:rs40978066; RSID:rs40978066; RSID:rs40978066
DisordersAndMutations ZFINID:ZDB-GENO-070827-1; ZFINID:ZDB-GENO-061212-1; Ikaros is an ENU based mutant, affected allel is it24980.
RelatedPubMedArticles Hansen J. D.; Strassburger P.; Du Pasquier L.: Conservation of a master hematopoietic switch gene during vertebrate evolution: isolation and characterization of Ikaros from teleost and amphibian species. Eur J Immunol. 1997. 27(11):3049-58. PMID:9394836

Hansen J. D.; Zapata A. G.: Lymphocyte development in fish and amphibians. Immunol Rev. 1998. 166:199-220. Review. PMID:9914914

Haire R. N.; Miracle A. L.; Rast J. P.; Litman G. W.: Members of the Ikaros gene family are present in early representative vertebrates. J Immunol. 2000. 165(1):306-12. PMID:10861066

Abdullah J. M.; Li X.; Nachtman R. G.; Jurecic R.: FLRF, a novel evolutionarily conserved RING finger gene, is differentially expressed in mouse fetal and adult hematopoietic stem cells and progenitors. Blood Cells Mol Dis. 2001. 27(1):320-33. PMID:11358394

Boggs S. S.: The Hematopoietic Microenvironment: Phylogeny and Ontogeny of the Hematopoietic Microenvironment. Hematology. 1999;4(1):31-44. PMID:11399551

Willett C. E.; Kawasaki H.; Amemiya C. T.; Lin S.; Steiner L. A.: Ikaros expression as a marker for lymphoid progenitors during zebrafish development. Dev Dyn. 2001 222(4):694-8. PMID:11748838

Willett, C.E., Kawasaki, H., Amemiya, C.T., Lin, S., and Steiner, L.A. (2001) Ikaros expression as a marker for lymphoid progenitors during zebrafish development. Dev. Dyn. 222(4):694-698. PMID: 11748838

Lam S. H.; Chua H. L.; Gong Z.; Lam T. J.; Sin Y. M.: Development and maturation of the immune system in zebrafish.; Danio rerio: a gene expression profiling, in situ hybridization and immunological study. Dev Comp Immunol. 2004. 28(1):9-28. PMID:12962979

Katoh M.: Molecular evolution of Wnt2b orthologs. Int J Oncol. 2005 Apr;26(4):1135-9. PMID:15754012

Lam S. H.; Sin Y. M.; Gong Z.; Lam T. J.: Effects of thyroid hormone on the development of immune system in zebrafish. Gen Comp Endocrinol. 2005. 142(3):325-35. PMID:15935159

Schorpp M.; Bialecki M.; Diekhoff D.; Walderich B.; Odenthal J.; Maischein H. M.; Zapata A. G.; Boehm T.: Conserved functions of Ikaros in vertebrate lymphocyte development: genetic evidence for distinct larval and adult phases of T cell development and two lineages of B cells in zebrafish. J Immunol. 2006. 177(4):2463-76. PMID:16888008

Murayama E.; Kissa K.; Zapata A.; Mordelet E.; Briolat V.; Lin H. F.; Handin R. I.; Herbomel P.: Tracing hematopoietic precursor migration to successive hematopoietic organs during zebrafish development. Immunity. 2006. 25(6):963-75. PMID:17157041

Songhet P.; Adzic D.; Reibe S.; Rohr K. B.: fgf1 is required for normal differentiation of erythrocytes in zebrafish primitive hematopoiesis. Dev Dyn. 2007. 236(3):633-43. PMID:17219402

Villablanca E. J.; Pistocchi A.; Court F. A.; Cotelli F.; Bordignon C.; Allende M. L.; Traversari C.; Russo V.: Abrogation of prostaglandin E2/EP4 signaling impairs the development of rag1+ lymphoid precursors in the thymus of zebrafish embryos. J Immunol. 2007. 179(1):357-64. PMID:17579056

Paffett-Lugassy N.; Hsia N.; Fraenkel P. G.; Paw B.; Leshinsky I.; Barut B.; Bahary N.; Caro J.; Handin R.; Zon L. I.: Functional conservation of erythropoietin signaling in zebrafish. Blood. 2007. 110(7):2718-26. PMID:17579187
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: r6 - 2011-11-22 - RajivRana
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