U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    Hoxc6 homeo box C6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 252885, updated on 2-Nov-2024

    Summary

    Go to the top of the page Help
    Symbol
    Hoxc6provided by RGD
    Full Name
    homeo box C6provided by RGD
    Primary source
    RGD:620626
    See related
    EnsemblRapid:ENSRNOG00000063956 AllianceGenome:RGD:620626
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    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 embryonic skeletal system development. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Orthologous to human HOXC6 (homeobox C6). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 62.2), Uterus (RPKM 29.7) and 5 other tissues See more
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Hoxc6 in Genome Data Viewer
    Location:
    7q36
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (136013679..136051601)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (134138017..134148899)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (144612230..144626036)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene homeobox C9 Neighboring gene homeobox C8 Neighboring gene microRNA 615 Neighboring gene homeo box C5 Neighboring gene homeo box C4 Neighboring gene uncharacterized LOC102547409 Neighboring gene uncharacterized LOC102547667

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Abnormal expression of homeobox c6 in the atherosclerotic aorta and its effect on proliferation and migration of rat vascular smooth muscle cells. Long X, et al. Acta Biochim Biophys Sin (Shanghai), 2020 Sep 8. PMID 32785574
    2. Bisphenol-A induces expression of HOXC6, an estrogen-regulated homeobox-containing gene associated with breast cancer. Hussain I, et al. Biochim Biophys Acta, 2015 Jun. PMID 25725483, Free PMC Article
    3. Changes in homeobox-containing gene expression during ectopic bone formation induced by bone morphogenetic protein. Iimura T, et al. Biochem Biophys Res Commun, 1994 Jun 15. PMID 7911662
    4. Hox patterning of the vertebrate rib cage. McIntyre DC, et al. Development, 2007 Aug. PMID 17626057
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Abnormal expression of homeobox c6 in the atherosclerotic aorta and its effect on proliferation and migration of rat vascular smooth muscle cells.
      Title: Abnormal expression of homeobox c6 in the atherosclerotic aorta and its effect on proliferation and migration of rat vascular smooth muscle cells.
    2. Our studies demonstrate that HOXC6, which is a critical player in mammary gland development, is upregulated in multiple cases of breast cancer, and is transcriptionally regulated by E2 and BPA, in vitro and in vivo.
      Title: Bisphenol-A induces expression of HOXC6, an estrogen-regulated homeobox-containing gene associated with breast cancer.
    Submit: New GeneRIF Correction

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific 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 HMG box domain binding 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 anterior/posterior pattern specification ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cartilage development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in embryonic organ morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within embryonic skeletal system development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II 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
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    homeobox protein Hox-C6

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001398518.1 → NP_001385447.1  homeobox protein Hox-C6

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/TrEMBL
      A0A8I6GM16, A6KCZ0
      Related
      ENSRNOP00000022217.5, ENSRNOT00000022217.8
      Conserved Domains (1) summary
      pfam00046
      Location:145 → 198
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086025.1 Reference GRCr8

      Range
      136013679..136051601
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063263014.1 → XP_063119084.1  homeobox protein Hox-C6 isoform X1

      UniProtKB/TrEMBL
      A6KCZ2, D3ZK87

    2. XM_063263017.1 → XP_063119087.1  homeobox protein Hox-C6 isoform X3

    3. XM_063263022.1 → XP_063119092.1  homeobox protein Hox-C6 isoform X5

      UniProtKB/TrEMBL
      G3V841

    4. XM_063263015.1 → XP_063119085.1  homeobox protein Hox-C6 isoform X1

      UniProtKB/TrEMBL
      A6KCZ2, D3ZK87

    5. XM_063263016.1 → XP_063119086.1  homeobox protein Hox-C6 isoform X3

    6. XM_063263019.1 → XP_063119089.1  homeobox protein Hox-C6 isoform X3

    7. XM_063263021.1 → XP_063119091.1  homeobox protein Hox-C6 isoform X5

      UniProtKB/TrEMBL
      G3V841

    8. XM_039080396.2 → XP_038936324.1  homeobox protein Hox-C6 isoform X2

      Conserved Domains (1) summary
      pfam00046
      Location:153 → 206
      Homeobox; Homeobox domain

    9. XM_063263020.1 → XP_063119090.1  homeobox protein Hox-C6 isoform X4

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Other Literature Sources
    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools