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SHOX2 short stature homeobox 2 [ Homo sapiens (human) ]

Gene ID: 6474, updated on 21-Dec-2019

Summary

Official Symbol
SHOX2provided by HGNC
Official Full Name
short stature homeobox 2provided by HGNC
Primary source
HGNC:HGNC:10854
See related
Ensembl:ENSG00000168779 MIM:602504
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
OG12; SHOT; OG12X
Summary
This gene is a member of the homeobox family of genes that encode proteins containing a 60-amino acid residue motif that represents a DNA binding domain. Homeobox genes have been characterized extensively as transcriptional regulators involved in pattern formation in both invertebrate and vertebrate species. Several human genetic disorders are caused by aberrations in human homeobox genes. This locus represents a pseudoautosomal homeobox gene that is thought to be responsible for idiopathic short stature, and it is implicated in the short stature phenotype of Turner syndrome patients. This gene is considered to be a candidate gene for Cornelia de Lange syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2009]
Expression
Biased expression in fat (RPKM 3.0), lymph node (RPKM 1.2) and 4 other tissues See more
Orthologs

Genomic context

See SHOX2 in Genome Data Viewer
Location:
3q25.32
Exon count:
7
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (158095905..158106420, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (157813800..157823952, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 46 Neighboring gene hs1251 and hs1262 enhancers downstream of SHOX2 Neighboring gene VISTA enhancer hs636 Neighboring gene arginine and serine rich coiled-coil 1 Neighboring gene VISTA enhancer hs741

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cardiac atrium morphogenesis IEA
Inferred from Electronic Annotation
more info
 
cartilage development involved in endochondral bone morphogenesis IEA
Inferred from Electronic Annotation
more info
 
chondrocyte development IEA
Inferred from Electronic Annotation
more info
 
embryonic digestive tract morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic skeletal joint morphogenesis IEA
Inferred from Electronic Annotation
more info
 
heart development TAS
Traceable Author Statement
more info
PubMed 
heart valve development IEA
Inferred from Electronic Annotation
more info
 
muscle tissue morphogenesis IEA
Inferred from Electronic Annotation
more info
 
nervous system development TAS
Traceable Author Statement
more info
PubMed 
osteoblast differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of axonogenesis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of mesenchymal cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of skeletal muscle fiber development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
regulation of branching morphogenesis of a nerve IEA
Inferred from Electronic Annotation
more info
 
regulation of chondrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
skeletal system development TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 

General protein information

Preferred Names
short stature homeobox protein 2
Names
SHOX homologous gene on chromosome 3
homeobox protein Og12X
paired-related homeobox protein SHOT

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_047079.1 RefSeqGene

    Range
    5040..15192
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001163678.2NP_001157150.1  short stature homeobox protein 2 isoform c

    See identical proteins and their annotated locations for NP_001157150.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the coding region, compared to variant 1, resulting in an isoform (c) that is shorter than isoform b.
    Source sequence(s)
    AC112502, DA447204
    Consensus CDS
    CCDS54664.1
    UniProtKB/Swiss-Prot
    O60902
    Related
    ENSP00000419362.1, ENST00000483851.6
    Conserved Domains (2) summary
    pfam00046
    Location:143196
    Homeobox; Homeobox domain
    pfam03826
    Location:299315
    OAR; OAR domain
  2. NM_003030.4NP_003021.3  short stature homeobox protein 2 isoform b

    See identical proteins and their annotated locations for NP_003021.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (b).
    Source sequence(s)
    AA450208, AC112502, BC008829, BX331739
    Consensus CDS
    CCDS33884.2
    UniProtKB/Swiss-Prot
    O60902
    Related
    ENSP00000374240.4, ENST00000389589.8
    Conserved Domains (2) summary
    pfam00046
    Location:167220
    Homeobox; Homeobox domain
    pfam03826
    Location:335351
    OAR; OAR domain
  3. NM_006884.3NP_006875.2  short stature homeobox protein 2 isoform a

    See identical proteins and their annotated locations for NP_006875.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region, compared to variant 1, resulting in an isoform (a, also known as SHOX2a) that is shorter than isoform b.
    Source sequence(s)
    AA450208, AC112502, AJ002367, BC008829, BX331739, DA447204
    Consensus CDS
    CCDS43164.1
    UniProtKB/Swiss-Prot
    O60902
    Related
    ENSP00000397099.3, ENST00000441443.6
    Conserved Domains (2) summary
    pfam00046
    Location:143196
    Homeobox; Homeobox domain
    pfam03826
    Location:311327
    OAR; OAR domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    158095905..158106420 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006713727.3XP_006713790.1  short stature homeobox protein 2 isoform X1

    See identical proteins and their annotated locations for XP_006713790.1

    Conserved Domains (2) summary
    pfam00046
    Location:167220
    Homeobox; Homeobox domain
    pfam03826
    Location:323338
    OAR; OAR domain
  2. XM_017007055.1XP_016862544.1  short stature homeobox protein 2 isoform X3

    UniProtKB/Swiss-Prot
    O60902
    UniProtKB/TrEMBL
    A6NLG4
    Related
    ENSP00000398704.4, ENST00000425436.7
    Conserved Domains (2) summary
    pfam03826
    Location:170186
    OAR; OAR domain
    pfam00046
    Location:1468
    Homeobox; Homeobox domain
  3. XM_017007054.1XP_016862543.1  short stature homeobox protein 2 isoform X2

    Conserved Domains (2) summary
    pfam00046
    Location:2881
    Homeobox; Homeobox domain
    pfam03826
    Location:184200
    OAR; OAR domain
  4. XM_006713728.3XP_006713791.1  short stature homeobox protein 2 isoform X3

    See identical proteins and their annotated locations for XP_006713791.1

    UniProtKB/Swiss-Prot
    O60902
    UniProtKB/TrEMBL
    A6NLG4
    Conserved Domains (2) summary
    pfam03826
    Location:170186
    OAR; OAR domain
    pfam00046
    Location:1468
    Homeobox; Homeobox domain
  5. XM_017007053.1XP_016862542.1  short stature homeobox protein 2 isoform X2

    Conserved Domains (2) summary
    pfam00046
    Location:2881
    Homeobox; Homeobox domain
    pfam03826
    Location:184200
    OAR; OAR domain
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