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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 Hard Palate Cancer and Turner Syndrome. Gene Ontology (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

GeneHancer (GH) Regulatory Elements for SHOX2 Gene

Promoters and enhancers for SHOX2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J158101 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 661.2 +1.8 1791 6.4 ARNT SIN3A FEZF1 YBX1 ZNF280A GLIS2 ZNF143 ATF7 ZNF202 ZNF263 SHOX2 RSRC1 CCNL1 ENSG00000243675 MLF1 ENSG00000240207 GFM1 ENSG00000242536
GH03J158097 Enhancer 1.1 Ensembl ENCODE 10.9 +8.6 8567 1.5 CLOCK ARID4B SIN3A DMAP1 ZNF48 YY1 SLC30A9 ZNF207 ZNF143 NFKBIZ SHOX2 MLF1 ENSG00000242536 RSRC1
GH03J158057 Enhancer 1.2 VISTA UCNEbase 7.8 +47.4 47421 2.3 MEIS2 PKNOX1 SOX6 ATF2 CTBP1 POLR2A FOXK2 CUX1 TRIM28 SHOX2 ENSG00000242536 MLF1 GC03M158022
GH03J158419 Enhancer 1 Ensembl ENCODE 4.6 -314.3 -314347 1.9 BACH1 STAT5A BMI1 BATF IRF4 RELA NFATC1 EED ATF7 ETV6 GC03P158422 PIR31105 RSRC1 MLF1 ENSG00000271778 SHOX2 GC03P158403
GH03J158109 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 0.7 -3.9 -3869 1.8 FEZF1 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 ZNF610 GLIS1 RCOR2 RSRC1 CCNL1 LXN SHOX2 GC03M158221
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SHOX2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SHOX2 gene promoter:
  • CP2
  • COMP1
  • AREB6
  • CUTL1
  • POU3F2
  • aMEF-2

Genomic Locations for SHOX2 Gene

Genomic Locations for SHOX2 Gene
10,550 bases
Minus strand
10,493 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

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.
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

Phenotypes From GWAS Catalog for SHOX2 Gene

Gene Ontology (GO) - Molecular Function for SHOX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
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

miRNA for SHOX2 Gene

miRTarBase miRNAs that target SHOX2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHOX2

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 by RNA polymerase II 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

mRNA/cDNA for SHOX2 Gene

Unigene Clusters for SHOX2 Gene

Short stature homeobox 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHOX2

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 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(4.3)
genes like me logo Genes that share expression patterns with SHOX2: view

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 34 33
  • 99.81 (n)
(Ornithorhynchus anatinus)
Mammalia SHOX2 34
  • 99 (a)
(Monodelphis domestica)
Mammalia SHOX2 34
  • 97 (a)
(Canis familiaris)
Mammalia SHOX2 34 33
  • 94.16 (n)
(Rattus norvegicus)
Mammalia Shox2 33
  • 92.13 (n)
(Mus musculus)
Mammalia Shox2 16 34 33
  • 92.02 (n)
(Bos Taurus)
Mammalia SHOX2 34 33
  • 90.8 (n)
(Gallus gallus)
Aves SHOX2 34 33
  • 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 34 33
  • 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)
Evolutionary constrained regions (ECRs) for SHOX2: view image

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 Variation AA Info Type
rs770635670 likely-benign, not specified 158,105,793(-) CACCTCCTCC/CACCTCCTCCACCTCCTCC 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, inframe_insertion, upstream_transcript_variant
rs375389609 uncertain-significance, not specified 158,105,730(-) T/A/C 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, upstream_transcript_variant
rs747236738 uncertain-significance, not specified 158,105,803(-) G/A 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, synonymous_variant, upstream_transcript_variant
rs753047735 uncertain-significance, not specified 158,105,089(-) C/T 5_prime_UTR_variant, coding_sequence_variant, intron_variant, synonymous_variant
rs1000097517 -- 158,106,314(-) G/A upstream_transcript_variant

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)

Additional Variant Information for SHOX2 Gene

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

SNP Genotyping and Copy Number Assay Products

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

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

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

Additional Disease Information for SHOX2

Genetic Association Database
Human Genome Epidemiology 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 58
  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 58
  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 44 58
  4. 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 58
  5. An unappreciated role for RNA surveillance. (PMID: 14759258) Hillman RT … Brenner SE (Genome biology 2004) 3 4 58

Products for SHOX2 Gene

Sources for SHOX2 Gene

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