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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
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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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