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    zeb2a zinc finger E-box binding homeobox 2a [ Danio rerio (zebrafish) ]

    Gene ID: 100003889, updated on 2-Nov-2024

    Summary

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    Official Symbol
    zeb2aprovided by ZNC
    Official Full Name
    zinc finger E-box binding homeobox 2aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-070912-553
    See related
    Ensembl:ENSDARG00000062338 AllianceGenome:ZFIN:ZDB-GENE-070912-553
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    sip1a; sb:eu412; wu:fc92g08; si:dkey-52o2.2
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within several processes, including chordate embryonic development; convergent extension; and negative regulation of fibroblast growth factor receptor signaling pathway. Predicted to be located in nucleus. Is expressed in several structures, including head; nervous system; neural plate; neuroectoderm; and tail bud. Human ortholog(s) of this gene implicated in Hirschsprung's disease and Mowat-Wilson syndrome. Orthologous to human ZEB2 (zinc finger E-box binding homeobox 2). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    all
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    Genomic context

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    See zeb2a in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (25775813..25837752)
    105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (25964948..26026883)

    Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene enhancer of polycomb homolog 2 (Drosophila) Neighboring gene activin A receptor type 2Aa Neighboring gene glycosyltransferase-like domain containing 1 Neighboring gene Rho GTPase activating protein 15 Neighboring gene uncharacterized LOC137496474

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Interplay of Zeb2a, Id2a and Batf3 regulates microglia and dendritic cell development in the zebrafish brain. Nguyen LTM, et al. Development, 2024 Feb 1. PMID 38240311
    2. Zebrafish sip1a and sip1b are essential for normal axial and neural patterning. Delalande JM, et al. Dev Dyn, 2008 Apr. PMID 18351671, Free PMC Article
    3. Zebrafish churchill regulates developmental gene expression and cell migration. Taibi A, et al. Dev Dyn, 2013 Jun. PMID 23443939, Free PMC Article
    4. Churchill and Sip1a repress fibroblast growth factor signaling during zebrafish somitogenesis. Kok FO, et al. Dev Dyn, 2010 Feb. PMID 20034103, Free PMC Article
    5. Localized EMT reprograms glial progenitors to promote spinal cord repair. Klatt Shaw D, et al. Dev Cell, 2021 Mar 8. PMID 33609461, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Interplay of Zeb2a, Id2a and Batf3 regulates microglia and dendritic cell development in the zebrafish brain.
      Title: Interplay of Zeb2a, Id2a and Batf3 regulates microglia and dendritic cell development in the zebrafish brain.
    2. Data show that zebrafish sip1a and sip1b are essential for normal axial and neural patterning.
      Title: Zebrafish sip1a and sip1b are essential for normal axial and neural patterning.
    3. Knockdown of ChCh or Sip1a results in misshapen somites that are short and narrow.
      Title: Churchill and Sip1a repress fibroblast growth factor signaling during zebrafish somitogenesis.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Clone Names

    • MGC175265

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in central nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within convergent extension involved in axis elongation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within dorsal convergence IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within dorsal convergence IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within dorsal/ventral pattern formation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within dorsal/ventral pattern formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within fibroblast growth factor receptor signaling pathway involved in somitogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within negative regulation of fibroblast growth factor receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within neural crest formation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within neural crest formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within somitogenesis IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within somitogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger E-box-binding homeobox 2a
    Names
    Smad-interacting protein-1a
    transcription factor SIP1a
    zeb2

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001114551.2 → NP_001108023.2  zinc finger E-box-binding homeobox 2a isoform 1

      Status: VALIDATED

      Source sequence(s)
      CR405716
      UniProtKB/TrEMBL
      A0A8M2BF09, B0LVE9, F1QY45
      Related
      ENSDARP00000105699.2, ENSDART00000127834.4
      Conserved Domains (4) summary
      sd00017
      Location:1002 → 1022
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:285 → 307
      zf-C2H2; Zinc finger, C2H2 type
      pfam05605
      Location:212 → 266
      zf-Di19; Drought induced 19 protein (Di19), zinc-binding
      pfam13465
      Location:299 → 322
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001135104.2 → NP_001128576.2  zinc finger E-box-binding homeobox 2a isoform 2

      Status: VALIDATED

      Source sequence(s)
      CR405716
      UniProtKB/TrEMBL
      A0A8M2BFJ5, B0LVE9
      Related
      ENSDARP00000152334.1, ENSDART00000189994.1
      Conserved Domains (4) summary
      sd00017
      Location:246 → 266
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:285 → 307
      zf-C2H2; Zinc finger, C2H2 type
      pfam05605
      Location:212 → 266
      zf-Di19; Drought induced 19 protein (Di19), zinc-binding
      pfam13465
      Location:299 → 322
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007120.7 Reference GRCz11 Primary Assembly

      Range
      25775813..25837752
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068223261.1 → XP_068079362.1  zinc finger E-box-binding homeobox 2a isoform X1

      Related
      ENSDARP00000156250.1, ENSDART00000188547.1

    2. XM_005167523.5 → XP_005167580.4  zinc finger E-box-binding homeobox 2a isoform X2

      UniProtKB/TrEMBL
      A0A8M2BFJ5, B0LVE9
      Conserved Domains (4) summary
      sd00017
      Location:246 → 266
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:285 → 307
      zf-C2H2; Zinc finger, C2H2 type
      pfam05605
      Location:212 → 266
      zf-Di19; Drought induced 19 protein (Di19), zinc-binding
      pfam13465
      Location:299 → 322
      zf-H2C2_2; Zinc-finger double domain

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394754.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      223920..285859
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCz11 ALT_DRER_TU_2

    Genomic

    1. NW_018395281.1 Reference GRCz11 ALT_DRER_TU_2

      Range
      242993..304729
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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