zic3 zic family member 3 heterotaxy 1 (odd-paired homolog, Drosophila) [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: zic3provided by ZNC
Official Full Name: zic family member 3 heterotaxy 1 (odd-paired homolog, Drosophila)provided by ZNC
Primary source: ZFIN:ZDB-GENE-030708-2
See related: Ensembl:ENSDARG00000071497 AllianceGenome:ZFIN:ZDB-GENE-030708-2
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: cb807; id:ibd2176; wu:fj52a10; wu:fq33c12
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 anterior/posterior axis specification and determination of left/right symmetry. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; mesoderm; neural keel; neural plate; and presumptive structure. Used to study right atrial isomerism; spina bifida; and visceral heterotaxy. Human ortholog(s) of this gene implicated in X-linked VACTERL association; situs inversus; and visceral heterotaxy. Orthologous to human ZIC3 (Zic family member 3). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 14

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	14	NC_007125.7 (32012470..32016615, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	14	NC_007125.6 (31672156..31676301, complement)

Chromosome 14 - NC_007125.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

a genomic sequence that is conserved between humans and zebrafish acts as an enhancer that likely controls zic3 and zic6 expression.
Title: A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression.
This demonstrated that Zic3 regulation of developmental genes is achieved predominantly through long distance regulatory mechanism and revealed that developmental transitions could be accompanied by dramatic changes in regulatory landscape.
Title: Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish.
BMP, Wnt and FGF signaling are needed for expression of the neural plate border specifiers pax3a and zic3 in zebrafish
Title: BMP, Wnt and FGF signals are integrated through evolutionarily conserved enhancers to achieve robust expression of Pax3 and Zic genes at the zebrafish neural plate border.
results demonstrate a functional conservation of Zic3 in left-right patterning and uncover a previously unrecognized role for Zic3 in convergent extension morphogenesis during early vertebrate development
Title: An essential and highly conserved role for Zic3 in left-right patterning, gastrulation and convergent extension morphogenesis.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
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
acts_upstream_of_or_within anterior/posterior axis specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within anterior/posterior pattern specification	IEP Inferred from Expression Pattern more info	PubMed
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within determination of left/right symmetry	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

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: zinc finger protein ZIC 3

Names: zinc finger protein of the cerebellum 3

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_001001950.2 → NP_001001950.1 zinc finger protein ZIC 3

See identical proteins and their annotated locations for NP_001001950.1

Status: PROVISIONAL

Source sequence(s)

BC096991

UniProtKB/TrEMBL

Q1XD37, Q6PV84

Related

ENSDARP00000096539.3, ENSDART00000105761.4

Conserved Domains (3) summary

sd00017
Location:282 → 302

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:368 → 390

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:324 → 351

zf-H2C2_2; Zinc-finger double domain