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zfhx4 zinc finger homeobox 4 [ Danio rerio (zebrafish) ]

Gene ID: 556453, updated on 17-Aug-2024

Summary

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Official Symbol
zfhx4provided by ZNC
Official Full Name
zinc finger homeobox 4provided by ZNC
Primary source
ZFIN:ZDB-GENE-070530-3
See related
Ensembl:ENSDARG00000075542 AllianceGenome:ZFIN:ZDB-GENE-070530-3
Gene type
protein coding
RefSeq status
MODEL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
im:7159242; si:ch211-94d7.1
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be active in nucleus. Is expressed in brain; midbrain neural keel; pharyngeal arch; and retinal ganglion cell layer. Orthologous to human ZFHX4 (zinc finger homeobox 4). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 24
Exon count:
12
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 24 NC_007135.7 (23242309..23323441, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 24 NC_007135.6 (23097139..23178254, complement)

Chromosome 24 - NC_007135.7Genomic Context describing neighboring genes Neighboring gene si:dkey-7n6.2 Neighboring gene peroxisomal biogenesis factor 2 Neighboring gene hepatocyte nuclear factor 4, gamma Neighboring gene G protein-coupled receptor 141

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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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Related articles in PubMed

  1. Mutant-specific gene expression profiling identifies SRY-related HMG box 11b (SOX11b) as a novel regulator of vascular development in zebrafish. Schmitt CE, et al. Mol Cells, 2013 Feb. PMID 23456338, Free PMC Article
  2. Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos. Armant O, et al. Dev Biol, 2013 Aug 15. PMID 23684812, Free PMC Article
  3. A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos. Rosenthal SM, et al. Mol Cell Proteomics, 2021. PMID 34332124, Free PMC Article
  4. Expression of Protein-Coding Gene Orthologs in Zebrafish and Mouse Inner Ear Non-sensory Supporting Cells. Giffen KP, et al. Front Neurosci, 2019. PMID 31680844, Free PMC Article
  5. Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches. Diotel N, et al. J Comp Neurol, 2015 Jun 1. PMID 25556858, Free PMC Article

See all (7) citations in PubMed

GeneRIFs: Gene References Into Functions

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
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 nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
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 IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
zinc finger homeobox protein 4

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007135.7 Reference GRCz11 Primary Assembly

    Range
    23242309..23323441 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_679268.9 → XP_684360.5  zinc finger homeobox protein 4 isoform X1

    See identical proteins and their annotated locations for XP_684360.5

    UniProtKB/TrEMBL
    A0A8N7TAH7, F6NXU9
    Related
    ENSDARP00000143509.1, ENSDART00000176903.2
    Conserved Domains (7) summary
    smart00389
    Location:2069 → 2128
    HOX; Homeodomain
    COG5576
    Location:2465 → 2620
    COG5576; Homeodomain-containing transcription factor [Transcription]
    sd00017
    Location:1505 → 1527
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00020
    Location:1361 → 1381
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00046
    Location:2168 → 2221
    Homeobox; Homeobox domain
    pfam11825
    Location:2995 → 3058
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
    pfam14945
    Location:3089 → 3130
    LLC1; Normal lung function maintenance, Low in Lung Cancer 1 protein

  2. XM_005162749.4 → XP_005162806.1  zinc finger homeobox protein 4 isoform X2

    UniProtKB/TrEMBL
    A0A8M2B9P4, E7FCF7
    Related
    ENSDARP00000101036.3, ENSDART00000112256.4
    Conserved Domains (7) summary
    smart00389
    Location:2030 → 2089
    HOX; Homeodomain
    COG5576
    Location:2426 → 2581
    COG5576; Homeodomain-containing transcription factor [Transcription]
    sd00017
    Location:1466 → 1488
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00020
    Location:1322 → 1342
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00046
    Location:2129 → 2182
    Homeobox; Homeobox domain
    pfam11825
    Location:2956 → 3019
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
    pfam14945
    Location:3050 → 3091
    LLC1; Normal lung function maintenance, Low in Lung Cancer 1 protein

  3. XM_005162746.4 → XP_005162803.1  zinc finger homeobox protein 4 isoform X1

    See identical proteins and their annotated locations for XP_005162803.1

    UniProtKB/TrEMBL
    A0A8N7TAH7, F6NXU9
    Related
    ENSDARP00000122306.1, ENSDART00000135846.3
    Conserved Domains (7) summary
    smart00389
    Location:2069 → 2128
    HOX; Homeodomain
    COG5576
    Location:2465 → 2620
    COG5576; Homeodomain-containing transcription factor [Transcription]
    sd00017
    Location:1505 → 1527
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00020
    Location:1361 → 1381
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00046
    Location:2168 → 2221
    Homeobox; Homeobox domain
    pfam11825
    Location:2995 → 3058
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
    pfam14945
    Location:3089 → 3130
    LLC1; Normal lung function maintenance, Low in Lung Cancer 1 protein

  4. XM_005162747.4 → XP_005162804.1  zinc finger homeobox protein 4 isoform X1

    See identical proteins and their annotated locations for XP_005162804.1

    UniProtKB/TrEMBL
    A0A8N7TAH7, F6NXU9
    Conserved Domains (7) summary
    smart00389
    Location:2069 → 2128
    HOX; Homeodomain
    COG5576
    Location:2465 → 2620
    COG5576; Homeodomain-containing transcription factor [Transcription]
    sd00017
    Location:1505 → 1527
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00020
    Location:1361 → 1381
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00046
    Location:2168 → 2221
    Homeobox; Homeobox domain
    pfam11825
    Location:2995 → 3058
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
    pfam14945
    Location:3089 → 3130
    LLC1; Normal lung function maintenance, Low in Lung Cancer 1 protein

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018395175.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    200654..216348 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021473783.1 → XP_021329458.1  zinc finger homeobox protein 4 isoform X3

    UniProtKB/TrEMBL
    A0A8M9PR14
    Conserved Domains (6) summary
    smart00389
    Location:988 → 1047
    HOX; Homeodomain
    sd00017
    Location:424 → 446
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00020
    Location:280 → 300
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00046
    Location:1087 → 1140
    Homeobox; Homeobox domain
    pfam00096
    Location:474 → 495
    zf-C2H2; Zinc finger, C2H2 type
    cl27820
    Location:1384 → 1539
    Abdominal-A; Homeobox protein
Nucleotide Protein Strain
Heading Accession and Version

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