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

    Gene ID: 22774, updated on 4-Jan-2025

    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, Jan 2025]
    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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    See Zic4 in Genome Data Viewer
    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. 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
    3. 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
    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. Zic4, a zinc-finger transcription factor, is expressed in the developing mouse nervous system. Gaston-Massuet C, et al. Dev Dyn, 2005 Jul. PMID 15895369

    See all (43) 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)
    • Endonuclease-mediated (3) 
    • Targeted (2)  1 citation

    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
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    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
      Related
      ENSMUSP00000133958.2, ENSMUST00000173933.8

    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
      UniProtKB/TrEMBL
      Q8C5L0

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

      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

      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

      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

      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

      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

      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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