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hoxc6b homeobox C6b [ Danio rerio (zebrafish) ]

Gene ID: 58045, updated on 27-Mar-2024

Summary

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Official Symbol
hoxc6bprovided by ZNC
Official Full Name
homeobox C6bprovided by ZNC
Primary source
ZFIN:ZDB-GENE-000822-1
See related
Ensembl:ENSDARG00000101954 AllianceGenome:ZFIN:ZDB-GENE-000822-1
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
hoxy6
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 anterior/posterior pattern specification and 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 several structures, including margin; musculature system; neuroectoderm; paraxial mesoderm; and tail bud. Orthologous to human HOXC6 (homeobox C6). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
all
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Genomic context

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See hoxc6b in Genome Data Viewer
Location:
chromosome: 11
Exon count:
3
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 11 NC_007122.7 (2198433..2204754)
105 previous assembly GRCz10 (GCF_000002035.5) 11 NC_007122.6 (2100982..2107204, complement)

Chromosome 11 - NC_007122.7Genomic Context describing neighboring genes Neighboring gene homeobox C11b Neighboring gene uncharacterized LOC110440087 Neighboring gene microRNA 196c Neighboring gene single-strand-selective monofunctional uracil-DNA glycosylase 1 Neighboring gene heterogeneous nuclear ribonucleoprotein A1a

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
  • 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. Differences in expression pattern and function between zebrafish hoxc13 orthologs: recruitment of Hoxc13b into an early embryonic role. Thummel R, et al. Dev Biol, 2004 Oct 15. PMID 15385162
  2. Vagus Motor Neuron Topographic Map Determined by Parallel Mechanisms of hox5 Expression and Time of Axon Initiation. Barsh GR, et al. Curr Biol, 2017 Dec 18. PMID 29225029, Free PMC Article
  3. A histone H3 lysine 27 demethylase regulates animal posterior development. Lan F, et al. Nature, 2007 Oct 11. PMID 17851529
  4. MicroRNA-directed cleavage of HOXB8 mRNA. Yekta S, et al. Science, 2004 Apr 23. PMID 15105502
  5. Hox gene clusters in blunt snout bream, Megalobrama amblycephala and comparison with those of zebrafish, fugu and medaka genomes. Zou SM, et al. Gene, 2007 Oct 1. PMID 17618068

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

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 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
  
Process Evidence Code Pubs
involved_in anterior/posterior pattern specification IBA
Inferred from Biological aspect of Ancestor
more info
  
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
homeobox protein Hox-C6b
Names
homeo box C6b
homeobox gene Y-6

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_001328159.1 → NP_001315088.1  homeobox protein Hox-C6b isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    CABZ01085067
    UniProtKB/Swiss-Prot
    O57377, Q4PR82, Q9PWM5
    UniProtKB/TrEMBL
    A0A8M1P8V2

  2. NM_131530.2 → NP_571605.2  homeobox protein Hox-C6b isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    CABZ01085067
    UniProtKB/Swiss-Prot
    O57377, Q4PR82, Q9PWM5
    UniProtKB/TrEMBL
    A0A2R8Q006, A0A8M1PC79
    Related
    ENSDARP00000146904.1, ENSDART00000173139.2

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_007122.7 Reference GRCz11 Primary Assembly

    Range
    2198433..2204754
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005172774.4 → XP_005172831.1  homeobox protein Hox-C6b isoform X1

    See identical proteins and their annotated locations for XP_005172831.1

    UniProtKB/Swiss-Prot
    O57377, Q4PR82, Q9PWM5
    UniProtKB/TrEMBL
    A0A2R8QUV2, A0A8M2BK36
    Related
    ENSDARP00000134791.3, ENSDART00000160515.3
    Conserved Domains (1) summary
    pfam00046
    Location:140 → 192
    Homeobox; Homeobox domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9PWM5.1 GenPept UniProtKB/Swiss-Prot:Q9PWM5

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