SHOX2 SHOX homeobox 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SHOX2provided by HGNC
Official Full Name: SHOX homeobox 2provided by HGNC
Primary source: HGNC:HGNC:10854
See related: Ensembl:ENSG00000168779 MIM:602504; AllianceGenome:HGNC:10854
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: mouse all
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Genomic context

Location:: 3q25.32

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (158095905..158106420, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (160870630..160881158, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (157813694..157824209, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

lncRNA SNHG11 promotes the development of colorectal cancer by mediating miR-339-3p/SHOX2.
Title: lncRNA SNHG11 promotes the development of colorectal cancer by mediating miR-339-3p/SHOX2.
SHOX2 methylation in Vietnamese patients with lung cancer.
Title: SHOX2 methylation in Vietnamese patients with lung cancer.
[Diagnostic Efficacy of SHOX2 Gene Hypermethylation for Lung Cancer: A Meta-Analysis].
Title: [Diagnostic Efficacy of SHOX2 Gene Hypermethylation for Lung Cancer: A Meta-Analysis].
SHOX2 cooperates with STAT3 to promote breast cancer metastasis through the transcriptional activation of WASF3.
Title: SHOX2 cooperates with STAT3 to promote breast cancer metastasis through the transcriptional activation of WASF3.
[SHOX2 promotes migration, invasion and stemness of bladder cancer cells in vitro].
Title: [SHOX2 promotes migration, invasion and stemness of bladder cancer cells in vitro].
A Novel Diagnosis Method Based on Methylation Analysis of SHOX2 and Serum Biomarker for Early Stage Lung Cancer.
Title: A Novel Diagnosis Method Based on Methylation Analysis of SHOX2 and Serum Biomarker for Early Stage Lung Cancer.
combined detection of RASSF1A and SHOX2 gene methylation was identified as an excellent method for the screening and surveillance of lung cancer that exhibits high sensitivity and specificity
Title: Signaling pathways and clinical application of RASSF1A and SHOX2 in lung cancer.
SHOX2 is regulated by IGF2-AS in the gastric adenocarcinoma.
Title: IGF2-AS affects the prognosis and metastasis of gastric adenocarcinoma via acting as a ceRNA of miR-503 to regulate SHOX2.
SHOX2 and PTGER4 methylation detection in blood plasma has certain value in the early diagnosis of lung cancer
Title: [DNA methylation detection of SHOX2 and PTGER4 in plasma contributes to differential diagnosis of pulmonary nodule patients].
Post-therapeutic SHOX2 and SEPT9 circulating cell-free DNA(ccfDNA) methylation levels correlated with UICC stage (all P <0.01). SEPT9 ccfDNA methylation further allowed for an accurate pre- and post-therapeutic detection of distant metastases.
Title: Potential of quantitative SEPT9 and SHOX2 methylation in plasmatic circulating cell-free DNA as auxiliary staging parameter in colorectal cancer: a prospective observational cohort study.

Submit: New GeneRIF Correction See all GeneRIFs (37)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH92222 (e-PCR)
- UniSTS:88362

SGC44267 (e-PCR)
- UniSTS:41936

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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	ISA Inferred from Sequence Alignment more info
enables sequence-specific double-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in cardiac pacemaker cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in cardiac right atrium morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cartilage development involved in endochondral bone morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in chondrocyte development	IEA Inferred from Electronic Annotation more info
involved_in embryonic digestive tract morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic forelimb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic skeletal joint morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in mesenchymal cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in muscle tissue morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in nervous system development	TAS Traceable Author Statement more info	PubMed
involved_in osteoblast differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of axonogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of mesenchymal cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of skeletal muscle fiber development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of stem cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in regulation of branching morphogenesis of a nerve	IEA Inferred from Electronic Annotation more info
involved_in regulation of chondrocyte differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of regulation of heart rate	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in sinoatrial node cell development	ISS Inferred from Sequence or Structural Similarity more info
involved_in sinoatrial node development	ISS Inferred from Sequence or Structural Similarity more info
involved_in sinoatrial valve development	ISS Inferred from Sequence or Structural Similarity more info
involved_in skeletal system development	TAS Traceable Author Statement more info	PubMed
involved_in smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in stem cell proliferation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: short stature homeobox protein 2

Names: SHOX homologous gene on chromosome 3; homeobox protein Og12X; paired-related homeobox protein SHOT; 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.

Genomic

NG_047079.1 RefSeqGene

Range

4783..15298

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001163678.2 → NP_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, ENST00000483851.7

Conserved Domains (2) summary

pfam00046
Location:143 → 197

Homeobox; Homeobox domain

pfam03826
Location:299 → 315

OAR; OAR domain
NM_003030.4 → NP_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:167 → 220

Homeobox; Homeobox domain

pfam03826
Location:335 → 351

OAR; OAR domain
NM_006884.3 → NP_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

O60465, O60467, O60902, O60903

Related

ENSP00000397099.3, ENST00000441443.6

Conserved Domains (2) summary

pfam00046
Location:143 → 196

Homeobox; Homeobox domain

pfam03826
Location:311 → 327

OAR; OAR domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

158095905..158106420 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006713727.4 → XP_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:167 → 221

Homeobox; Homeobox domain

pfam03826
Location:323 → 339

OAR; OAR domain
XM_006713728.4 → XP_006713791.1 short stature homeobox protein 2 isoform X3

See identical proteins and their annotated locations for XP_006713791.1

UniProtKB/TrEMBL

A0A0A0MSP8, A6NLG4, C9J3D0

Conserved Domains (2) summary

pfam00046
Location:14 → 68

Homeobox; Homeobox domain

pfam03826
Location:170 → 186

OAR; OAR domain
XM_017007053.2 → XP_016862542.1 short stature homeobox protein 2 isoform X2

Related

ENST00000490689.3

Conserved Domains (2) summary

pfam00046
Location:28 → 81

Homeobox; Homeobox domain

pfam03826
Location:184 → 200

OAR; OAR domain
XM_047448731.1 → XP_047304687.1 short stature homeobox protein 2 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

160870630..160881158 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054347563.1 → XP_054203538.1 short stature homeobox protein 2 isoform X1
XM_054347566.1 → XP_054203541.1 short stature homeobox protein 2 isoform X3

UniProtKB/TrEMBL

A0A0A0MSP8, A6NLG4, C9J3D0
XM_054347564.1 → XP_054203539.1 short stature homeobox protein 2 isoform X2
XM_054347565.1 → XP_054203540.1 short stature homeobox protein 2 isoform X2