Zic1 zinc finger protein of the cerebellum 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Zic1provided by MGI
Official Full Name: zinc finger protein of the cerebellum 1provided by MGI
Primary source: MGI:MGI:106683
See related: Ensembl:ENSMUSG00000032368 AllianceGenome:MGI:106683
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: ZIC; ZNF201
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including central nervous system development; positive regulation of protein import into nucleus; and positive regulation of transcription by RNA polymerase II. Acts upstream of or within adult walking behavior and central nervous system development. Located in cytoplasm and nucleus. Is expressed in several structures, including central nervous system; embryo mesenchyme; future brain; metanephros; and visual system. Used to study Dandy-Walker syndrome and Joubert syndrome. 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, Nov 2024]
Expression: Biased expression in cerebellum adult (RPKM 92.7), whole brain E14.5 (RPKM 45.5) and 4 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9 E3.2; 9 48.26 cM

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (91240111..91250136, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (91358058..91365768, complement)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

In an ongoing expression screen, this study identified that Tfap2b, Casq2, Penk, Zic1, and Zic3 are expressed in unique cell types in and around the developing eye.
Title: Localization of Tfap2β, Casq2, Penk, Zic1, and Zic3 Expression in the Developing Retina, Muscle, and Sclera of the Embryonic Mouse Eye.
Documented a significant increase in Zic1 mRNA in inguinal subcutaneous fat from acutely cold-exposed mice, which was paralleled by an increase in UCP1-positive adipocytes and in parenchymal noradrenergic innervation. This transient, depot-specific molecular signature was associated not to Zic1 promoter demethylation, but to chromatin remodeling through an H3K9me3 histone modification.
Title: Zic1 mRNA is transiently upregulated in subcutaneous fat of acutely cold-exposed mice.
Geminin and Zic1 could cooperatively activate the expression of several shared targets encoding transcription factors that control neurogenesis, neural plate patterning, and neuronal differentiation.
Title: Gene regulatory networks in neural cell fate acquisition from genome-wide chromatin association of Geminin and Zic1.
Zic1 and Zic2 proteins are essential to control the balance between two defined neuron types in the postnatal forebrain.
Title: Zic-Proteins Are Repressors of Dopaminergic Forebrain Fate in Mice and C. elegans.
Brn2-Zic1 axis is essential to specify neural fate in retinoic-acid-treated embryonic stem cells.
Title: A Brn2-Zic1 axis specifies the neuronal fate of retinoic-acid-treated embryonic stem cells.
Zic1 and Zic2 are required for coordinating mature neuronal gene expression patterns.
Title: Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.
Association with DNA-bound Pax3 strengthens the ability of both Zic1 and Gli2 to transactivate Myf5 in the epaxial somite.
Title: Pax3 synergizes with Gli2 and Zic1 in transactivating the Myf5 epaxial somite enhancer.
Zic1 and Zic4 have both Shh-dependent and -independent roles during cerebellar development and multiple developmental disruptions underlie Zic1/4-related Dandy-walker malformation.
Title: Multiple developmental programs are altered by loss of Zic1 and Zic4 to cause Dandy-Walker malformation cerebellar pathogenesis.
Myf5 activation in newly forming somites is delayed in Zic2 mutant embryos until the time of Zic1 activation, and both Zic2 and Myf5 require noggin for their activation
Title: A role for Zic1 and Zic2 in Myf5 regulation and somite myogenesis.
Zic1, a neural developmental transcription factor, plays an important role in shear flow mechanotransduction in osteocytes.
Title: Zic1 transcription factor in bone: neural developmental protein regulates mechanotransduction in osteocytes.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D9Mit110 (e-PCR), detects polymorphism
- UniSTS:116778

NoName (e-PCR)
- UniSTS:548439

PMC304100P7 (e-PCR)
- UniSTS:272532

D32167 (e-PCR)
- UniSTS:159904

UniSTS:466091 (e-PCR)
- UniSTS:466091

Zic1 (e-PCR), detects polymorphism
- UniSTS:466091

Zic1 (e-PCR), detects polymorphism
- UniSTS:144839

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
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 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within adult walking behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in brain development	IDA Inferred from Direct Assay more info	PubMed
involved_in brain development	ISO Inferred from Sequence Orthology more info
involved_in cell cycle	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within central nervous system development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within central nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in forebrain development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in hippocampus development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in inner ear morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in maintenance of cell number	IGI Inferred from Genetic Interaction more info	PubMed
involved_in olfactory bulb development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in pattern specification process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein import into nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of smoothened signaling pathway	IPI Inferred from Physical Interaction more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal system development	NAS Non-traceable Author Statement more info	PubMed
involved_in spinal cord development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: zinc finger protein ZIC 1

Names: Zic family member 1 (odd-paired homolog, Drosophila); odd-paired homolog

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_001376941.1 → NP_001363870.1 zinc finger protein ZIC 1

Status: VALIDATED

Description

Transcript Variant: Variants 1 and 2 encode the same protein.

Source sequence(s)

AC116582, AK141431, BC060247, CD741655

UniProtKB/Swiss-Prot

P46684, Q6PAK5, Q80Y18

UniProtKB/TrEMBL

Q3TWA9

Related

ENSMUSP00000068858.4, ENSMUST00000065360.5

Conserved Domains (3) summary

COG5189
Location:298 → 382

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

sd00017
Location:276 → 296

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18366
Location:219 → 264

zf_ZIC; Zic proteins zinc finger domain
NM_009573.4 → NP_033599.2 zinc finger protein ZIC 1

See identical proteins and their annotated locations for NP_033599.2

Status: VALIDATED

Description

Transcript Variant: Variants 1 and 2 encode the same protein.

Source sequence(s)

AK141431, BC063247, BY261991, CD741655, CN666056

Consensus CDS

CCDS23403.1

UniProtKB/Swiss-Prot

P46684, Q6PAK5, Q80Y18

UniProtKB/TrEMBL

Q3TWA9

Related

ENSMUSP00000034927.7, ENSMUST00000034927.13

Conserved Domains (3) summary

COG5189
Location:298 → 382

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

sd00017
Location:276 → 296

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18366
Location:219 → 264

zf_ZIC; Zic proteins zinc finger domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000075.7 Reference GRCm39 C57BL/6J

Range

91240111..91250136 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036154847.1 → XP_036010740.1 zinc finger protein ZIC 1 isoform X1

UniProtKB/Swiss-Prot

P46684, Q6PAK5, Q80Y18

UniProtKB/TrEMBL

Q3TWA9

Conserved Domains (3) summary

COG5189
Location:298 → 382

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

sd00017
Location:276 → 296

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam18366
Location:219 → 264

zf_ZIC; Zic proteins zinc finger domain