zic1 zic family member 1 (odd-paired homolog, Drosophila) [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: zic1provided by ZNC
Official Full Name: zic family member 1 (odd-paired homolog, Drosophila)provided by ZNC
Primary source: ZFIN:ZDB-GENE-000208-4
See related: Ensembl:ENSDARG00000015567 AllianceGenome:ZFIN:ZDB-GENE-000208-4
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: opl; wu:fj51c06; zgc:136736
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and zinc ion binding activity. Acts upstream of or within brain development and embryonic retina morphogenesis in camera-type eye. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; neural keel; neural plate; neural rod; and presumptive neural plate. Human ortholog(s) of this gene implicated in Dandy-Walker syndrome and craniosynostosis. Orthologous to human ZIC1 (Zic family member 1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 24

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	24	NC_007135.7 (4970580..4973732, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	24	NC_007135.6 (4938793..4941945, complement)

Chromosome 24 - NC_007135.7 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?

lmo4b has an essential role in forebrain development as a modulator of six3 and rx3 expression, and thus indirectly influences neural cell fate commitment, cell proliferation and tissue growth in the anterior CNS.
Title: A zebrafish LMO4 ortholog limits the size of the forebrain and eyes through negative regulation of six3b and rx3.
Zic1 knockdown leads to a strong midline defect including partial cyclopia due to attenuated Nodal and Hedgehog signaling in the anterior ventral diencephalon and Zic1 is also required for maintaining early forebrain expression of cyp26a1
Title: Zic-associated holoprosencephaly: zebrafish Zic1 controls midline formation and forebrain patterning by regulating Nodal, Hedgehog, and retinoic acid signaling.
Zic1 and Zic4 control zebrafish 4th ventricle morphogenesis by regulating multiple mechanisms including cell proliferation and fate specification in the dorsal hindbrain.
Title: Zic1 and Zic4 regulate zebrafish roof plate specification and hindbrain ventricle morphogenesis.

Submit: New GeneRIF Correction

General gene information

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Markers

fd09f09.y1 (e-PCR)
- UniSTS:195078

fj51c06.x1 (e-PCR)
- UniSTS:188645

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
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within brain development	IEP Inferred from Expression Pattern more info
acts_upstream_of_or_within cell proliferation in hindbrain	IGI Inferred from Genetic Interaction more info	PubMed
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within embryonic retina morphogenesis in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within forebrain morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fourth ventricle development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hindbrain development	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
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: zinc finger protein ZIC 1

Names: zinc finger protein of the cerebellum 1

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_130933.2 → NP_571008.1 zinc finger protein ZIC 1

See identical proteins and their annotated locations for NP_571008.1

Status: VALIDATED

Source sequence(s)

CR388127

UniProtKB/TrEMBL

O93311, Q1RLX0

Related

ENSDARP00000106790.2, ENSDART00000127597.3

Conserved Domains (3) summary

sd00017
Location:269 → 291

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:357 → 379

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:313 → 340

zf-H2C2_2; Zinc-finger double domain