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

Summary

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. 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, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 9

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	9	NC_007120.7 (25775803..25837752)
105	previous assembly	GRCz10 (GCF_000002035.5)	9	NC_007120.6 (25964948..26026883)

Chromosome 9 - NC_007120.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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

General gene information

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Markers

fj89b08.y1 (e-PCR)
- UniSTS:200236

Z7813 (e-PCR)
- UniSTS:6485

G44809 (e-PCR)
- UniSTS:105611

G39217 (e-PCR)
- UniSTS:57004

fc92g08.x1 (e-PCR)
- UniSTS:188395

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 anatomical structure 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 2; 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)

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

ENSDARP00000156250.1, ENSDART00000188547.1

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
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: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007120.7 Reference GRCz11 Primary Assembly

Range

25775803..25837752

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005167525.4 → XP_005167582.1 zinc finger E-box-binding homeobox 2 isoform X2

UniProtKB/TrEMBL

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
XM_021478582.1 → XP_021334257.1 zinc finger E-box-binding homeobox 2 isoform X2

UniProtKB/TrEMBL

A0A8M2BF09, B0LVE9, F1QY45

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
XM_005167523.4 → XP_005167580.4 zinc finger E-box-binding homeobox 2 isoform X1

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
XM_021478583.1 → XP_021334258.1 zinc finger E-box-binding homeobox 2 isoform X3

UniProtKB/TrEMBL

A0A8M9Q4G0, B0LVE9

Conserved Domains (4) summary

sd00017
Location:879 → 899

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:162 → 184

zf-C2H2; Zinc finger, C2H2 type

pfam05605
Location:89 → 143

zf-Di19; Drought induced 19 protein (Di19), zinc-binding

pfam13465
Location:176 → 199

zf-H2C2_2; Zinc-finger double domain