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Aliases for SHOX2 Gene

Aliases for SHOX2 Gene

  • Short Stature Homeobox 2 2 3 5
  • Paired-Related Homeobox Protein SHOT 3 4
  • Homeobox Protein Og12X 3 4
  • OG12X 3 4
  • SHOT 3 4
  • SHOX Homologous Gene On Chromosome 3 3
  • Short Stature Homeobox Protein 2 3
  • OG12 3

External Ids for SHOX2 Gene

Previous GeneCards Identifiers for SHOX2 Gene

  • GC03M154850
  • GC03M158760
  • GC03M159095
  • GC03M159135
  • GC03M159297
  • GC03M157813
  • GC03M155210

Summaries for SHOX2 Gene

Entrez Gene Summary for SHOX2 Gene

  • 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]

GeneCards Summary for SHOX2 Gene

SHOX2 (Short Stature Homeobox 2) is a Protein Coding gene. Diseases associated with SHOX2 include Turner Syndrome and Hard Palate Cancer. GO annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is SHOX.

UniProtKB/Swiss-Prot for SHOX2 Gene

  • May be a growth regulator and have a role in specifying neural systems involved in processing somatosensory information, as well as in face and body structure formation.

Gene Wiki entry for SHOX2 Gene

Additional gene information for SHOX2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SHOX2 Gene

Genomics for SHOX2 Gene

Regulatory Elements for SHOX2 Gene

Enhancers for SHOX2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03H158057 1.9 VISTA 7.7 +47.4 47421 2.3 PKNOX1 SOX6 ATF2 CTBP1 FOXK2 POLR2A CUX1 TRIM28 SHOX2 ENSG00000242536 MLF1 GC03M158022
GH03H158097 1.2 Ensembl ENCODE 10.9 +8.6 8568 1.5 ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF207 ZNF143 ZHX2 MXD4 NFYC SHOX2 MLF1 RSRC1 ENSG00000242536
GH03H158101 1 ENCODE 11.2 +1.8 1791 6.4 ARNT SIN3A FEZF1 YBX1 GLIS2 ZNF143 ATF7 ZNF202 SP3 SMARCA4 SHOX2 CCNL1 MLF1 ENSG00000240207 GFM1 RSRC1 ENSG00000242536
GH03H158419 1 Ensembl ENCODE 4.6 -314.3 -314347 1.9 BACH1 BMI1 BATF RELA EED ATF7 RUNX3 IKZF2 CREM SMARCA5 RSRC1 MLF1 ENSG00000271778 SHOX2 PIR31105 GC03P158422 GC03P158403
GH03H158329 0.2 Ensembl 7 -223.5 -223499 0.8 SHOX2 MLF1 LOC100422604 RPL15P6
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SHOX2 on UCSC Golden Path with GeneCards custom track

Promoters for SHOX2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000160989 403 601 RB1 ARNT SIN3A YBX1 NFXL1 BMI1 GLIS2 EGR1 ZNF366 ZNF143

Genomic Locations for SHOX2 Gene

Genomic Locations for SHOX2 Gene
10,550 bases
Minus strand

Genomic View for SHOX2 Gene

Genes around SHOX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHOX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHOX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SHOX2 Gene

Proteins for SHOX2 Gene

  • Protein details for SHOX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Short stature homeobox protein 2
    Protein Accession:
    Secondary Accessions:
    • O60465
    • O60467
    • O60903

    Protein attributes for SHOX2 Gene

    331 amino acids
    Molecular mass:
    34953 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAC39662.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAA05341.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAA05342.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SHOX2 Gene


neXtProt entry for SHOX2 Gene

Post-translational modifications for SHOX2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SHOX2 Gene

Domains & Families for SHOX2 Gene

Gene Families for SHOX2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the paired homeobox family. Bicoid subfamily.
  • Belongs to the paired homeobox family. Bicoid subfamily.
genes like me logo Genes that share domains with SHOX2: view

Function for SHOX2 Gene

Molecular function for SHOX2 Gene

GENATLAS Biochemistry:
murine homeo box Og12X homolog,strongly expressed in developing craniofacial,brain,heart and in the mesenchym of developing limbs,highly homologous to SHOX
UniProtKB/Swiss-Prot Function:
May be a growth regulator and have a role in specifying neural systems involved in processing somatosensory information, as well as in face and body structure formation.

Phenotypes From GWAS Catalog for SHOX2 Gene

Gene Ontology (GO) - Molecular Function for SHOX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with SHOX2: view
genes like me logo Genes that share phenotypes with SHOX2: view

Animal Models for SHOX2 Gene

MGI Knock Outs for SHOX2:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SHOX2 Gene

Localization for SHOX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHOX2 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SHOX2 gene
Compartment Confidence
nucleus 5
mitochondrion 2
cytosol 2
extracellular 1

Gene Ontology (GO) - Cellular Components for SHOX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with SHOX2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SHOX2 Gene

Pathways & Interactions for SHOX2 Gene

SuperPathways for SHOX2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SHOX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0001501 skeletal system development TAS 9482898
GO:0001649 osteoblast differentiation IEA --
GO:0002053 positive regulation of mesenchymal cell proliferation IEA --
GO:0002062 chondrocyte differentiation IEA --
genes like me logo Genes that share ontologies with SHOX2: view

No data available for Pathways by source and SIGNOR curated interactions for SHOX2 Gene

Drugs & Compounds for SHOX2 Gene

No Compound Related Data Available

Transcripts for SHOX2 Gene

Unigene Clusters for SHOX2 Gene

Short stature homeobox 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SHOX2 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b · 7c
SP1: - - -
SP2: - - - -
SP3: - - - - -
SP4: -

Relevant External Links for SHOX2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SHOX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SHOX2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SHOX2 Gene

This gene is overexpressed in Artery - Tibial (x7.2), Nerve - Tibial (x6.2), and Adipose - Subcutaneous (x5.1).

Protein differential expression in normal tissues from HIPED for SHOX2 Gene

This gene is overexpressed in Pancreas (25.0), Platelet (17.9), and Urine (13.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SHOX2 Gene

Protein tissue co-expression partners for SHOX2 Gene

NURSA nuclear receptor signaling pathways regulating expression of SHOX2 Gene:


SOURCE GeneReport for Unigene cluster for SHOX2 Gene:


mRNA Expression by UniProt/SwissProt for SHOX2 Gene:

Tissue specificity: Expressed in heart, skeletal muscle, liver, lung, bone marrow fibroblast, pancreas and placenta.

Evidence on tissue expression from TISSUES for SHOX2 Gene

  • Muscle(4.2)
genes like me logo Genes that share expression patterns with SHOX2: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SHOX2 Gene

Orthologs for SHOX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SHOX2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SHOX2 33 34
  • 99.81 (n)
(Ornithorhynchus anatinus)
Mammalia SHOX2 34
  • 99 (a)
(Monodelphis domestica)
Mammalia SHOX2 34
  • 97 (a)
(Canis familiaris)
Mammalia SHOX2 33 34
  • 94.16 (n)
(Rattus norvegicus)
Mammalia Shox2 33
  • 92.13 (n)
(Mus musculus)
Mammalia Shox2 33 16 34
  • 92.02 (n)
(Bos Taurus)
Mammalia SHOX2 33 34
  • 90.8 (n)
(Gallus gallus)
Aves SHOX2 33 34
  • 82.34 (n)
(Anolis carolinensis)
Reptilia SHOX2 34
  • 89 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia shox2 33
  • 78.86 (n)
(Danio rerio)
Actinopterygii shox2 33 34
  • 78.37 (n)
zgc65884 33
fruit fly
(Drosophila melanogaster)
Insecta CG34367 34
  • 33 (a)
(Caenorhabditis elegans)
Secernentea alr-1 34
  • 19 (a)
Species where no ortholog for SHOX2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SHOX2 Gene

Gene Tree for SHOX2 (if available)
Gene Tree for SHOX2 (if available)

Paralogs for SHOX2 Gene

Paralogs for SHOX2 Gene

(14) SIMAP similar genes for SHOX2 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with SHOX2: view

Variants for SHOX2 Gene

Sequence variations from dbSNP and Humsavar for SHOX2 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs770635670 Likely benign 158,105,792(+) TCCTA(-/CACCTCCTC)CACCT upstream-variant-2KB, cds-indel, utr-variant-5-prime
rs375389609 Uncertain significance 158,105,730(+) GCCCA(A/T)GTCCA upstream-variant-2KB, reference, missense, utr-variant-5-prime
rs747236738 Uncertain significance 158,105,803(+) CCTCC(A/G)CCTCC upstream-variant-2KB, reference, synonymous-codon, utr-variant-5-prime
rs753047735 Uncertain significance 158,105,089(+) AGAAG(C/T)AGCGT intron-variant, reference, synonymous-codon, utr-variant-5-prime
rs1000097517 -- 158,106,314(+) GGGGC(A/G)GGGGC upstream-variant-2KB

Variation tolerance for SHOX2 Gene

Residual Variation Intolerance Score: 13.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.60; 12.93% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SHOX2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for SHOX2 Gene

Disorders for SHOX2 Gene

MalaCards: The human disease database

(21) MalaCards diseases for SHOX2 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
turner syndrome
  • bonnevie-ullrich syndrome
hard palate cancer
  • hard palate
sinoatrial node disease
  • sa node
leri-weill dyschondrosteosis
  • leri weill dyschondrosteosis
cornelia de lange syndrome
  • brachmann de lange syndrome
- elite association - COSMIC cancer census association via MalaCards
Search SHOX2 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SHOX2

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with SHOX2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SHOX2 Gene

Publications for SHOX2 Gene

  1. A new human homeobox gene OGI2X is a member of the most conserved homeobox gene family and is expressed during heart development in mouse. (PMID: 9466998) Semina EV … Murray JC (Human molecular genetics 1998) 2 3 4 22 60
  2. SHOT, a SHOX-related homeobox gene, is implicated in craniofacial, brain, heart, and limb development. (PMID: 9482898) Blaschke RJ … Rappold GA (Proceedings of the National Academy of Sciences of the United States of America 1998) 2 3 4 22 60
  3. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PMID: 19453261) Yerges LM … MrOS Research Group (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2009) 3 45 60
  4. An unappreciated role for RNA surveillance. (PMID: 14759258) Hillman RT … Brenner SE (Genome biology 2004) 3 4 60
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60

Products for SHOX2 Gene

Sources for SHOX2 Gene

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