U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    hoxc3a homeobox C3a [ Danio rerio (zebrafish) ]

    Gene ID: 30421, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    hoxc3aprovided by ZNC
    Official Full Name
    homeobox C3aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-980526-532
    See related
    Ensembl:ENSDARG00000070339 AllianceGenome:ZFIN:ZDB-GENE-980526-532
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    HOX-114; zgc:110503
    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; embryonic skeletal system morphogenesis; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of DNA-templated transcription. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See hoxc3a in Genome Data Viewer
    Location:
    chromosome: 23
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 23 NC_007134.7 (36087200..36149042)
    105 previous assembly GRCz10 (GCF_000002035.5) 23 NC_007134.6 (35988497..36050251)

    Chromosome 23 - NC_007134.7Genomic Context describing neighboring genes Neighboring gene homeobox C10a Neighboring gene homeobox C12a Neighboring gene si:dkey-81p22.11 Neighboring gene homeobox C11a Neighboring gene microRNA 196a-1 Neighboring gene homeobox C9a Neighboring gene microRNA 10b-2 Neighboring gene homeobox C8a Neighboring gene homeobox C6a Neighboring gene homeobox C5a Neighboring gene uncharacterized LOC110438326 Neighboring gene homeobox C4a Neighboring gene homeobox C1a

    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: 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Characterization of retinoic acid-induced neurobehavioral effects in developing zebrafish. Wang Y, et al. Environ Toxicol Chem, 2014 Feb. PMID 24395056
    2. Development of oculomotor circuitry independent of hox3 genes. Ma LH, et al. Nat Commun, 2014 Jun 25. PMID 24964400, Free PMC Article
    3. A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish. Kawakami K, et al. Dev Cell, 2004 Jul. PMID 15239961
    4. Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes. Punnamoottil B, et al. Dev Biol, 2010 Apr 15. PMID 20144609
    5. Antisense RNAs during early vertebrate development are divided in groups with distinct features. Pillay S, et al. Genome Res, 2021 Jun. PMID 33795334, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC192333

    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 anterior/posterior pattern specification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in embryonic skeletal system morphogenesis 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

    Go to the top of the page Help
    Preferred Names
    homeobox protein Hox-C3a
    Names
    homeo box C3a
    homeobox gene C-3a
    homeobox protein Zf-114
    hox[zf-114]

    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_001134685.2 → NP_001128157.2  homeobox protein Hox-C3a

      See identical proteins and their annotated locations for NP_001128157.2

      Status: PROVISIONAL

      Source sequence(s)
      BX005254
      UniProtKB/Swiss-Prot
      P28174
      UniProtKB/TrEMBL
      A0A8M9P4Z9
      Related
      ENSDARP00000129398.1, ENSDART00000154825.3
      Conserved Domains (2) summary
      pfam00046
      Location:162 → 214
      Homeobox; Homeobox domain
      cl27820
      Location:123 → 246
      Abdominal-A; Homeobox protein

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007134.7 Reference GRCz11 Primary Assembly

      Range
      36087200..36149042
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021469727.2 → XP_021325402.1  homeobox protein Hox-C3a isoform X1

      UniProtKB/Swiss-Prot
      P28174
      UniProtKB/TrEMBL
      A0A8M9P4Z9
      Conserved Domains (2) summary
      pfam00046
      Location:162 → 214
      Homeobox; Homeobox domain
      cl27820
      Location:123 → 246
      Abdominal-A; Homeobox protein

    2. XM_005162365.5 → XP_005162422.1  homeobox protein Hox-C3a isoform X1

      See identical proteins and their annotated locations for XP_005162422.1

      UniProtKB/Swiss-Prot
      P28174
      UniProtKB/TrEMBL
      A0A8M9P4Z9
      Conserved Domains (2) summary
      pfam00046
      Location:162 → 214
      Homeobox; Homeobox domain
      cl27820
      Location:123 → 246
      Abdominal-A; Homeobox protein

    3. XM_005162367.5 → XP_005162424.1  homeobox protein Hox-C3a isoform X1

      See identical proteins and their annotated locations for XP_005162424.1

      UniProtKB/Swiss-Prot
      P28174
      UniProtKB/TrEMBL
      A0A8M9P4Z9
      Conserved Domains (2) summary
      pfam00046
      Location:162 → 214
      Homeobox; Homeobox domain
      cl27820
      Location:123 → 246
      Abdominal-A; Homeobox protein

    4. XM_005162366.5 → XP_005162423.1  homeobox protein Hox-C3a isoform X1

      See identical proteins and their annotated locations for XP_005162423.1

      UniProtKB/Swiss-Prot
      P28174
      UniProtKB/TrEMBL
      A0A8M9P4Z9
      Conserved Domains (2) summary
      pfam00046
      Location:162 → 214
      Homeobox; Homeobox domain
      cl27820
      Location:123 → 246
      Abdominal-A; Homeobox protein
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P28174.1 GenPept UniProtKB/Swiss-Prot:P28174

    Gene LinkOut

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

    Molecular Biology Databases
    Research Materials