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hoxa9a homeobox A9a [ Danio rerio (zebrafish) ]

Gene ID: 58047, updated on 27-Mar-2024

Summary

Official Symbol
hoxa9aprovided by ZNC
Official Full Name
homeobox A9aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-000823-1
See related
Ensembl:ENSDARG00000105013 AllianceGenome:ZFIN:ZDB-GENE-000823-1
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
z-10; hoxx9; fd07f09; wu:fd07f09; zgc:110505
Summary
Predicted to enable DNA-binding transcription factor activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in embryonic skeletal system morphogenesis; regionalization; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated and transcription, DNA-templated. Predicted to be active in nucleus. Is expressed in several structures, including margin; mesoderm; musculature system; nervous system; and tail bud. Orthologous to human HOXA9 (homeobox A9). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
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Genomic context

See hoxa9a in Genome Data Viewer
Location:
chromosome: 19
Exon count:
2
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (19750101..19752139)
105 previous assembly GRCz10 (GCF_000002035.5) 19 NC_007130.6 (20177150..20179188)

Chromosome 19 - NC_007130.7Genomic Context describing neighboring genes Neighboring gene homeobox A10a, pseudogene Neighboring gene microRNA 196a-2 Neighboring gene homeobox A4a Neighboring gene homeobox A5a Neighboring gene si:busm1-227p06.3, pseudogene Neighboring gene homeobox A3a

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

General gene information

Markers

Clone Names

  • MGC110505

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 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
acts_upstream_of_or_within DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
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
 
involved_in proximal/distal pattern formation 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

Preferred Names
homeobox protein Hox-A9a
Names
homeo box A9a
homeobox gene X-9

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_131532.2NP_571607.2  homeobox protein Hox-A9a

    See identical proteins and their annotated locations for NP_571607.2

    Status: PROVISIONAL

    Source sequence(s)
    BC090700
    UniProtKB/Swiss-Prot
    O57376, Q4PRA8, Q5CZU7, Q9PWL6
    UniProtKB/TrEMBL
    B2GSB0
    Related
    ENSDARP00000140324.1, ENSDART00000168041.2
    Conserved Domains (2) summary
    pfam00046
    Location:187240
    Homeobox; Homeobox domain
    pfam04617
    Location:1171
    Hox9_act; Hox9 activation region

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_007130.7 Reference GRCz11 Primary Assembly

    Range
    19750101..19752139
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)