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Zic4 zinc finger protein of the cerebellum 4 [ Mus musculus (house mouse) ]

Gene ID: 22774, updated on 3-Apr-2024

Summary

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Official Symbol
Zic4provided by MGI
Official Full Name
zinc finger protein of the cerebellum 4provided by MGI
Primary source
MGI:MGI:107201
See related
Ensembl:ENSMUSG00000036972 AllianceGenome:MGI:107201
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
Summary
Enables RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in central nervous system development and regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including central nervous system; embryo mesenchyme; future brain; genitourinary system; and retina. Used to study Dandy-Walker syndrome. Orthologous to human ZIC4 (Zic family member 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in whole brain E14.5 (RPKM 6.3), CNS E14 (RPKM 5.8) and 4 other tissues See more
Orthologs
human all
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Genomic context

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Location:
9 E3.2; 9 48.26 cM
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (91247636..91271404)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (91365631..91389351)

Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA A730094K22 gene Neighboring gene methionyl aminopeptidase 1 pseudogene Neighboring gene predicted gene, 40546 Neighboring gene predicted gene, 40545 Neighboring gene zinc finger protein of the cerebellum 1 Neighboring gene predicted gene 29478 Neighboring gene predicted gene, 39400

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Identification and characterization of Zic4, a new member of the mouse Zic gene family. Aruga J, et al. Gene, 1996 Jun 26. PMID 8682319
  2. The germinal zones of the basal ganglia but not the septum generate GABAergic interneurons for the cortex. Rubin AN, et al. J Neurosci, 2010 Sep 8. PMID 20826668, Free PMC Article
  3. Differential gene expression in the developing lateral geniculate nucleus and medial geniculate nucleus reveals novel roles for Zic4 and Foxp2 in visual and auditory pathway development. Horng S, et al. J Neurosci, 2009 Oct 28. PMID 19864579, Free PMC Article
  4. High-depth spatial transcriptome analysis by photo-isolation chemistry. Honda M, et al. Nat Commun, 2021 Jul 20. PMID 34285220, Free PMC Article
  5. If the skull fits: magnetic resonance imaging and microcomputed tomography for combined analysis of brain and skull phenotypes in the mouse. Nieman BJ, et al. Physiol Genomics, 2012 Oct 17. PMID 22947655, Free PMC Article

See all (42) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. These findings identify roles for two differentially expressed genes, Zic4 and Foxp2, in the development of the principal auditory relay nucleus, the medial geniculate nucleus, and principal visual relay nucleus, the lateral geniculate nucleus
    Title: Differential gene expression in the developing lateral geniculate nucleus and medial geniculate nucleus reveals novel roles for Zic4 and Foxp2 in visual and auditory pathway development.
  3. Zic4 has an expression pattern distinct from, but partly overlapping with, other members of the Zic gene family
    Title: Zic4, a zinc-finger transcription factor, is expressed in the developing mouse nervous system.
  4. Results describe the molecular properties of Zic4 and Zic5 proteins.
    Title: Molecular properties of Zic4 and Zic5 proteins: functional diversity within Zic family.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2)  1 citation
  • Endonuclease-mediated (3) 

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding 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 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 sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in central nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
  
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 IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
zinc finger protein ZIC 4
Names
Zic family member 4 (odd-paired homolog, Drosophila)

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_001374749.1 → NP_001361678.1  zinc finger protein ZIC 4 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC116582
    Consensus CDS
    CCDS90639.1
    UniProtKB/Swiss-Prot
    Q61467, Q8BG91
    Related
    ENSMUSP00000069568.6, ENSMUST00000066384.7
    Conserved Domains (3) summary
    COG5048
    Location:150 → 295
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:185 → 205
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:129 → 173
    zf_ZIC; Zic proteins zinc finger domain

  2. NM_001421110.1 → NP_001408039.1  zinc finger protein ZIC 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC116582
    UniProtKB/TrEMBL
    G3UYE7

  3. NM_001421111.1 → NP_001408040.1  zinc finger protein ZIC 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC116582
    UniProtKB/TrEMBL
    G3UYE7

  4. NM_001421112.1 → NP_001408041.1  zinc finger protein ZIC 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC116582
    UniProtKB/TrEMBL
    G3UYE7

  5. NM_001421113.1 → NP_001408042.1  zinc finger protein ZIC 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC116582
    UniProtKB/TrEMBL
    G3UYE7

  6. NM_001421114.1 → NP_001408043.1  zinc finger protein ZIC 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC116582
    UniProtKB/TrEMBL
    G3UYE7

  7. NM_001421115.1 → NP_001408044.1  zinc finger protein ZIC 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC116582
    UniProtKB/TrEMBL
    G3UYE7

  8. NM_001421116.1 → NP_001408045.1  zinc finger protein ZIC 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC116582
    UniProtKB/TrEMBL
    G3UYE7

  9. NM_001421117.1 → NP_001408046.1  zinc finger protein ZIC 4 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC116582

  10. NM_009576.3 → NP_033602.2  zinc finger protein ZIC 4 isoform 2

    See identical proteins and their annotated locations for NP_033602.2

    Status: VALIDATED

    Source sequence(s)
    AC116582
    Consensus CDS
    CCDS23404.1
    UniProtKB/TrEMBL
    G3UYE7
    Related
    ENSMUSP00000134053.2, ENSMUST00000172646.8
    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    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

  1. NC_000075.7 Reference GRCm39 C57BL/6J

    Range
    91247636..91271404
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036154852.1 → XP_036010745.1  zinc finger protein ZIC 4 isoform X7

    UniProtKB/TrEMBL
    G3UYE7
    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  2. XM_030244259.2 → XP_030100119.1  zinc finger protein ZIC 4 isoform X5

    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  3. XM_036154848.1 → XP_036010741.1  zinc finger protein ZIC 4 isoform X3

    Conserved Domains (3) summary
    COG5048
    Location:200 → 345
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:235 → 255
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:179 → 223
    zf_ZIC; Zic proteins zinc finger domain

  4. XM_036154854.1 → XP_036010747.1  zinc finger protein ZIC 4 isoform X10

    Conserved Domains (2) summary
    COG5189
    Location:100 → 160
    SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
    sd00017
    Location:110 → 132
    ZF_C2H2; C2H2 Zn finger [structural motif]

  5. XM_011242719.2 → XP_011241021.1  zinc finger protein ZIC 4 isoform X1

    Conserved Domains (3) summary
    COG5048
    Location:200 → 345
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:235 → 255
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:179 → 223
    zf_ZIC; Zic proteins zinc finger domain

  6. XM_017313291.2 → XP_017168780.1  zinc finger protein ZIC 4 isoform X5

    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  7. XM_036154851.1 → XP_036010744.1  zinc finger protein ZIC 4 isoform X5

    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  8. XM_011242720.3 → XP_011241022.1  zinc finger protein ZIC 4 isoform X2

    Conserved Domains (3) summary
    COG5048
    Location:191 → 336
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:226 → 246
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:170 → 214
    zf_ZIC; Zic proteins zinc finger domain

  9. XM_030244258.1 → XP_030100118.1  zinc finger protein ZIC 4 isoform X5

    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  10. XM_006511078.4 → XP_006511141.1  zinc finger protein ZIC 4 isoform X5

    See identical proteins and their annotated locations for XP_006511141.1

    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  11. XM_030244261.1 → XP_030100121.1  zinc finger protein ZIC 4 isoform X7

    UniProtKB/TrEMBL
    G3UYE7
    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  12. XM_030244274.1 → XP_030100134.1  zinc finger protein ZIC 4 isoform X11

    UniProtKB/TrEMBL
    Q8C5L0
    Conserved Domains (2) summary
    COG5189
    Location:20 → 80
    SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
    sd00017
    Location:30 → 52
    ZF_C2H2; C2H2 Zn finger [structural motif]

  13. XM_036154849.1 → XP_036010742.1  zinc finger protein ZIC 4 isoform X5

    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  14. XM_017313292.2 → XP_017168781.1  zinc finger protein ZIC 4 isoform X5

    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  15. XM_011242723.3 → XP_011241025.1  zinc finger protein ZIC 4 isoform X5

    See identical proteins and their annotated locations for XP_011241025.1

    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  16. XM_036154850.1 → XP_036010743.1  zinc finger protein ZIC 4 isoform X5

    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  17. XM_036154855.1 → XP_036010748.1  zinc finger protein ZIC 4 isoform X11

    UniProtKB/TrEMBL
    Q8C5L0
    Conserved Domains (2) summary
    COG5189
    Location:20 → 80
    SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
    sd00017
    Location:30 → 52
    ZF_C2H2; C2H2 Zn finger [structural motif]

  18. XM_030244260.2 → XP_030100120.1  zinc finger protein ZIC 4 isoform X6

    Conserved Domains (3) summary
    COG5048
    Location:149 → 294
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:184 → 204
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:128 → 172
    zf_ZIC; Zic proteins zinc finger domain

  19. XM_030244268.1 → XP_030100128.1  zinc finger protein ZIC 4 isoform X7

    UniProtKB/TrEMBL
    G3UYE7
    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  20. XM_011242722.3 → XP_011241024.1  zinc finger protein ZIC 4 isoform X4

    Conserved Domains (3) summary
    COG5048
    Location:149 → 294
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:184 → 204
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:128 → 172
    zf_ZIC; Zic proteins zinc finger domain

  21. XM_011242726.3 → XP_011241028.1  zinc finger protein ZIC 4 isoform X5

    See identical proteins and their annotated locations for XP_011241028.1

    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  22. XM_011242725.1 → XP_011241027.1  zinc finger protein ZIC 4 isoform X5

    See identical proteins and their annotated locations for XP_011241027.1

    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  23. XM_006511079.1 → XP_006511142.1  zinc finger protein ZIC 4 isoform X5

    See identical proteins and their annotated locations for XP_006511142.1

    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  24. XM_030244263.1 → XP_030100123.1  zinc finger protein ZIC 4 isoform X7

    UniProtKB/TrEMBL
    G3UYE7
    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  25. XM_006511067.4 → XP_006511130.1  zinc finger protein ZIC 4 isoform X5

    See identical proteins and their annotated locations for XP_006511130.1

    Conserved Domains (3) summary
    COG5048
    Location:143 → 288
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:178 → 198
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:122 → 166
    zf_ZIC; Zic proteins zinc finger domain

  26. XM_030244270.2 → XP_030100130.1  zinc finger protein ZIC 4 isoform X8

    Conserved Domains (3) summary
    COG5048
    Location:73 → 218
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:108 → 128
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:52 → 96
    zf_ZIC; Zic proteins zinc finger domain

  27. XM_036154853.1 → XP_036010746.1  zinc finger protein ZIC 4 isoform X9

    Conserved Domains (3) summary
    COG5048
    Location:73 → 218
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:108 → 128
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam18366
    Location:52 → 96
    zf_ZIC; Zic proteins zinc finger domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q61467.2 GenPept UniProtKB/Swiss-Prot:Q61467

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