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shox2 shox homeobox 2 [ Danio rerio (zebrafish) ]

Gene ID: 394171, updated on 27-Mar-2024

Summary

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Official Symbol
shox2provided by ZNC
Official Full Name
shox homeobox 2provided by ZNC
Primary source
ZFIN:ZDB-GENE-040426-1457
See related
Ensembl:ENSDARG00000075713 AllianceGenome:ZFIN:ZDB-GENE-040426-1457
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
zgc:65884; zgc:77344
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Acts upstream of or within heart development and regulation of heart contraction. Predicted to be active in nucleus. Is expressed in apical ectodermal ridge pectoral fin bud; heart; nervous system; and pectoral fin. Human ortholog(s) of this gene implicated in lung cancer. Orthologous to human SHOX2 (short stature homeobox 2). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 15
Exon count:
6
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 15 NC_007126.7 (2181622..2188473, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 15 NC_007126.6 (2218531..2224764, complement)

Chromosome 15 - NC_007126.7Genomic Context describing neighboring genes Neighboring gene dedicator of cytokinesis 10 Neighboring gene trace amine associated receptor 12m Neighboring gene arginine/serine-rich coiled-coil 1 Neighboring gene hephaestin-like 1a

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. Functional Characterization of Rare Variants in the SHOX2 Gene Identified in Sinus Node Dysfunction and Atrial Fibrillation. Hoffmann S, et al. Front Genet, 2019. PMID 31354791, Free PMC Article
  2. In vivo loss of function study reveals the short stature homeobox-containing (shox) gene plays indispensable roles in early embryonic growth and bone formation in zebrafish. Sawada R, et al. Dev Dyn, 2015 Feb. PMID 25483930
  3. A 3D Searchable Database of Transgenic Zebrafish Gal4 and Cre Lines for Functional Neuroanatomy Studies. Marquart GD, et al. Front Neural Circuits, 2015. PMID 26635538, Free PMC Article
  4. Islet1 is a direct transcriptional target of the homeodomain transcription factor Shox2 and rescues the Shox2-mediated bradycardia. Hoffmann S, et al. Basic Res Cardiol, 2013 Mar. PMID 23455426, Free PMC Article
  5. Targeted mutation reveals essential functions of the homeodomain transcription factor Shox2 in sinoatrial and pacemaking development. Blaschke RJ, et al. Circulation, 2007 Apr 10. PMID 17372176

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Network-driven discovery yields new insight into Shox2-dependent cardiac rhythm control.
    Title: Network-driven discovery yields new insight into Shox2-dependent cardiac rhythm control.
  2. Shox2 deficiency interferes with pacemaking function in zebrafish embryos. Shox2 has a critical function in the recruitment of sinus venosus myocardium comprising the sinoatrial nodal region.
    Title: Targeted mutation reveals essential functions of the homeodomain transcription factor Shox2 in sinoatrial and pacemaking development.
Submit: New GeneRIF Correction

General gene information

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Homology

Clone Names

  • MGC65884

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 sequence-specific double-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within heart development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within regulation of heart contraction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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
short stature homeobox protein 2
Names
short stature homeobox 2

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_201196.1 → NP_957490.1  short stature homeobox protein 2

    See identical proteins and their annotated locations for NP_957490.1

    Status: PROVISIONAL

    Source sequence(s)
    BC056324
    UniProtKB/TrEMBL
    Q6P103, Q7SZN8
    Related
    ENSDARP00000018280.7, ENSDART00000009564.9
    Conserved Domains (2) summary
    pfam00046
    Location:111 → 164
    Homeobox; Homeobox domain
    pfam03826
    Location:278 → 294
    OAR; OAR domain

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_007126.7 Reference GRCz11 Primary Assembly

    Range
    2181622..2188473 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021481366.1 → XP_021337041.1  short stature homeobox protein 2 isoform X2

    UniProtKB/TrEMBL
    A0A8M9QLB7
    Conserved Domains (2) summary
    pfam00046
    Location:45 → 98
    Homeobox; Homeobox domain
    pfam03826
    Location:212 → 229
    OAR; OAR domain

  2. XM_021481367.1 → XP_021337042.1  short stature homeobox protein 2 isoform X3

    UniProtKB/TrEMBL
    A0A8M9Q089
    Related
    ENSDARP00000121424.1, ENSDART00000138941.2
    Conserved Domains (2) summary
    pfam00046
    Location:45 → 98
    Homeobox; Homeobox domain
    pfam03826
    Location:200 → 217
    OAR; OAR domain

  3. XM_021481365.1 → XP_021337040.1  short stature homeobox protein 2 isoform X1

    UniProtKB/TrEMBL
    A0A8M9QPS7
    Conserved Domains (2) summary
    pfam00046
    Location:111 → 164
    Homeobox; Homeobox domain
    pfam03826
    Location:266 → 283
    OAR; OAR domain
Nucleotide Protein
Heading Accession and Version

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