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hoxc11b homeobox C11b [ Danio rerio (zebrafish) ]

Gene ID: 570925, updated on 27-Mar-2024

Summary

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Official Symbol
hoxc11bprovided by ZNC
Official Full Name
homeobox C11bprovided by ZNC
Primary source
ZFIN:ZDB-GENE-000822-3
See related
Ensembl:ENSDARG00000102631 AllianceGenome:ZFIN:ZDB-GENE-000822-3
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
hoxa11; im:7165141
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 anatomical structure development 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 presumptive telencephalon; pronephric duct; pronephric mesoderm; pronephros; and tail bud. Orthologous to human HOXC11 (homeobox C11). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
all
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Genomic context

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See hoxc11b 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 (2177123..2183983)
105 previous assembly GRCz10 (GCF_000002035.5) 11 NC_007122.6 (2121753..2126122, complement)

Chromosome 11 - NC_007122.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100534851 Neighboring gene homeobox C12b Neighboring gene uncharacterized LOC110440087 Neighboring gene microRNA 196c Neighboring gene homeobox C6b

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. Zebrafish hox genes: genomic organization and modified colinear expression patterns in the trunk. Prince VE, et al. Development, 1998 Feb. PMID 9425136
  2. HOX epimutations driven by maternal SMCHD1/LRIF1 haploinsufficiency trigger homeotic transformations in genetically wildtype offspring. Xue S, et al. Nat Commun, 2022 Jun 23. PMID 35739109, Free PMC Article
  3. MicroRNA-directed cleavage of HOXB8 mRNA. Yekta S, et al. Science, 2004 Apr 23. PMID 15105502
  4. Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum). Mehta TK, et al. Proc Natl Acad Sci U S A, 2013 Oct 1. PMID 24043829, Free PMC Article
  5. Zebrafish hox clusters and vertebrate genome evolution. Amores A, et al. Science, 1998 Nov 27. PMID 9831563

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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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
  
Process Evidence Code Pubs
involved_in anatomical structure development 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 C11b; homeobox protein Hox-C11a
Names
homeo box C11b

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_007122.7 Reference GRCz11 Primary Assembly

    Range
    2177123..2183983
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009300573.3 → XP_009298848.1  homeobox protein Hox-C11a

    See identical proteins and their annotated locations for XP_009298848.1

    UniProtKB/TrEMBL
    A0A0R4IDM3, A0A8N7T8D8
    Related
    ENSDARP00000131152.3, ENSDART00000164839.3
    Conserved Domains (2) summary
    pfam00046
    Location:237 → 290
    Homeobox; Homeobox domain
    pfam12045
    Location:41 → 180
    DUF3528; Protein of unknown function (DUF3528)

  2. XM_694457.9 → XP_699549.1  homeobox protein Hox-C11a

    See identical proteins and their annotated locations for XP_699549.1

    UniProtKB/TrEMBL
    A0A0R4IDM3, A0A8N7T8D8
    Related
    ENSDARP00000156809.1, ENSDART00000186854.1
    Conserved Domains (2) summary
    pfam00046
    Location:237 → 290
    Homeobox; Homeobox domain
    pfam12045
    Location:41 → 180
    DUF3528; Protein of unknown function (DUF3528)
Nucleotide Protein Strain
Heading Accession and Version

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