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ZIC5 Zic family member 5 [ Homo sapiens (human) ]

Gene ID: 85416, updated on 12-Oct-2019

Summary

Official Symbol
ZIC5provided by HGNC
Official Full Name
Zic family member 5provided by HGNC
Primary source
HGNC:HGNC:20322
See related
Ensembl:ENSG00000139800 MIM:617896
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. The encoded protein may act as a transcriptional repressor. Studies in mouse and Xenopus support a role for this gene in neural crest development. Elevated expression of this gene has been observed in various human cancers and may contribute to cancer progression. This gene is closely linked to a related family member on chromosome 13. [provided by RefSeq, Mar 2017]
Expression
Restricted expression toward testis (RPKM 2.7) See more
Orthologs

Genomic context

See ZIC5 in Genome Data Viewer
Location:
13q32.3
Exon count:
4
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (99962964..99971909, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (100615275..100624178, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene citrate lyase beta like Neighboring gene uncharacterized LOC101927437 Neighboring gene CLYBL antisense RNA 1 Neighboring gene Zic family member 2 polyalanine repeat instability region Neighboring gene long intergenic non-protein coding RNA 554 Neighboring gene Zic family member 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide meta-analysis of myopia and hyperopia provides evidence for replication of 11 Loci.
NHGRI GWA Catalog

Pathways from BioSystems

  • Endoderm Differentiation, organism-specific biosystem (from WikiPathways)
    Endoderm Differentiation, organism-specific biosystemModel depicting endoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
  • Mesodermal Commitment Pathway, organism-specific biosystem (from WikiPathways)
    Mesodermal Commitment Pathway, organism-specific biosystemModel depicting mesodermal specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell l...
  • Neural Crest Differentiation, organism-specific biosystem (from WikiPathways)
    Neural Crest Differentiation, organism-specific biosystemGene regulatory network model of cranial neural crest cell (CNCC) development, adaped from PMID: 19575671. Most interactions in the model are proposed to regulate transcription of core factors involv...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
central nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
zinc finger protein ZIC 5
Names
Zic family member 5 (odd-paired homolog, Drosophila)
zinc finger protein of the cerebellum 5

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_053065.1 RefSeqGene

    Range
    5016..13961
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_033132.4NP_149123.2  zinc finger protein ZIC 5

    See identical proteins and their annotated locations for NP_149123.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the protein.
    Source sequence(s)
    AF378304, AL355338, CB129979
    Consensus CDS
    CCDS9494.2
    UniProtKB/Swiss-Prot
    Q96T25
    Related
    ENSP00000267294.3, ENST00000267294.4
    Conserved Domains (4) summary
    COG5048
    Location:429575
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:465485
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:551575
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:507534
    zf-H2C2_2; Zinc-finger double domain

RNA

  1. NR_146224.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate internal exon, resulting in a longer transcript compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL355338, CB129979
  2. NR_146225.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate 5' exon compared to variant 1, resulting in a shorter transcript compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AL355338, CB129979

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    99962964..99971909 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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