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Aliases for SHOX Gene

Aliases for SHOX Gene

  • Short Stature Homeobox 2 3
  • Pseudoautosomal Homeobox-Containing Osteogenic Protein 3 4
  • PHOG 3 4
  • Short Stature Homeobox-Containing Protein 4
  • Growth Control Factor, X-Linked 3
  • Short Stature Homeobox Protein 3
  • SHOXY 3
  • GCFX 3
  • SS 3

External Ids for SHOX Gene

Previous GeneCards Identifiers for SHOX Gene

  • GC0XP000427
  • GC0YU900006
  • GC0XP000527
  • GC0YP000555
  • GC0XP000585

Summaries for SHOX Gene

Entrez Gene Summary for SHOX Gene

  • This gene belongs to the paired homeobox family and is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes. Defects in this gene are associated with idiopathic growth retardation and in the short stature phenotype of Turner syndrome patients. This gene is highly conserved across species from mammals to fish to flies. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for SHOX Gene

SHOX (Short Stature Homeobox) is a Protein Coding gene. Diseases associated with SHOX include leri-weill dyschondrosteosis and langer mesomelic dysplasia. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and transcription regulatory region sequence-specific DNA binding. An important paralog of this gene is PHOX2B.

UniProtKB/Swiss-Prot for SHOX Gene

  • Controls fundamental aspects of growth and development

Gene Wiki entry for SHOX Gene

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

Genomics for SHOX Gene

Regulatory Elements for SHOX Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for SHOX Gene

624,344 bp from pter
659,411 bp from pter
35,068 bases
Plus strand

Genomic View for SHOX Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SHOX Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SHOX Gene

Proteins for SHOX Gene

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

    Protein Symbol:
    Recommended name:
    Short stature homeobox protein
    Protein Accession:
    Secondary Accessions:
    • O00412
    • O00413
    • O15267

    Protein attributes for SHOX Gene

    292 amino acids
    Molecular mass:
    32236 Da
    Quaternary structure:
    No Data Available
    • The gene coding for this protein is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes

    Alternative splice isoforms for SHOX Gene


neXtProt entry for SHOX Gene

Proteomics data for SHOX Gene at MOPED

Post-translational modifications for SHOX Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SHOX Gene

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for SHOX

No data available for DME Specific Peptides for SHOX Gene

Domains for SHOX Gene

Gene Families for SHOX Gene

  • PAR1 :Pseudoautosomal regions / PAR1
  • PRD :Homeoboxes / PRD class

Suggested Antigen Peptide Sequences for SHOX Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • O15266
  • Contains 1 homeobox DNA-binding domain.
  • Belongs to the paired homeobox family. Bicoid subfamily.
genes like me logo Genes that share domains with SHOX: view

Function for SHOX Gene

Molecular function for SHOX Gene

GENATLAS Biochemistry:
short stature homeo box-containing gene,with two alternatively spliced forms SHOXa widely expressed,and SHOXb predominantly found in bone marrow,fibroblast,homolog to murine OG-12a,OG-12b
UniProtKB/Swiss-Prot Function:
Controls fundamental aspects of growth and development
UniProtKB/Swiss-Prot Induction:
By retinoic acid and phorbol-12-myristate 13-acetate (PMA)

Gene Ontology (GO) - Molecular Function for SHOX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0003700 sequence-specific DNA binding transcription factor activity TAS 9259282
GO:0005515 protein binding IPI 21262861
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with SHOX: view

Phenotypes for SHOX Gene

genes like me logo Genes that share phenotypes with SHOX: view

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for SHOX Gene

Localization for SHOX Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHOX Gene

Subcellular locations from

Jensen Localization Image for SHOX Gene COMPARTMENTS Subcellular localization image for SHOX gene
Compartment Confidence
nucleus 3

Gene Ontology (GO) - Cellular Components for SHOX Gene

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

Pathways for SHOX Gene

SuperPathways for SHOX Gene

No Data Available

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Homeobox (HOX) Genes in human,mouse,rat

Gene Ontology (GO) - Biological Process for SHOX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 9590292
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription from RNA polymerase II promoter TAS 9259282
genes like me logo Genes that share ontologies with SHOX: view

No data available for Pathways by source for SHOX Gene

Compounds for SHOX Gene

(2) Novoseek inferred chemical compound relationships for SHOX Gene

Compound -log(P) Hits PubMed IDs
steroid 0 2
estrogen 0 6
genes like me logo Genes that share compounds with SHOX: view

Transcripts for SHOX Gene

mRNA/cDNA for SHOX Gene

(8) Selected AceView cDNA sequences:
(3) Additional mRNA sequences :
(2) REFSEQ mRNAs :
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SHOX Gene

Short stature homeobox:
Representative Sequences:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SHOX

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

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

No ASD Table

Relevant External Links for SHOX Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SHOX Gene

mRNA expression in normal human tissues for SHOX Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Adipose - Subcutaneous (17.9), Muscle - Skeletal (7.1), Artery - Tibial (6.8), and Skin - Sun Exposed (Lower leg) (4.2).

Protein differential expression in normal tissues for SHOX Gene

This gene is overexpressed in Adipocyte (69.0).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for SHOX Gene

SOURCE GeneReport for Unigene cluster for SHOX Gene Hs.105932

mRNA Expression by UniProt/SwissProt for SHOX Gene

Tissue specificity: SHOXA is expressed in skeletal muscle, placenta, pancreas, heart and bone marrow fibroblast and SHOXB is highly expressed in bone marrow fibroblast followed by kidney and skeletal muscle. SHOXB is not expressed in brain, kidney, liver and lung. Highly expressed in osteogenic cells
genes like me logo Genes that share expressions with SHOX: view

Expression partners for SHOX Gene

In Situ Assay Products

Orthologs for SHOX Gene

This gene was present in the common ancestor of animals.

Orthologs for SHOX Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia SHOX 35
  • 87.67 (n)
  • 92.12 (a)
  • 89 (a)
(Canis familiaris)
Mammalia SHOX 35
  • 90.26 (n)
  • 95.53 (a)
  • 96 (a)
(Monodelphis domestica)
Mammalia SHOX 36
  • 93 (a)
(Ornithorhynchus anatinus)
Mammalia SHOX 36
  • 71 (a)
(Gallus gallus)
Aves SHOX 35
  • 84.77 (n)
  • 93.13 (a)
  • 93 (a)
(Anolis carolinensis)
Reptilia SHOX 36
  • 85 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia shox 35
  • 75.09 (n)
  • 88.24 (a)
(Danio rerio)
Actinopterygii shox 35
  • 75.85 (n)
  • 87.28 (a)
shox 36
  • 79 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG34367 36
  • 32 (a)
(Caenorhabditis elegans)
Secernentea alr-1 36
  • 18 (a)
Species with no ortholog for SHOX:
  • 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)
  • chimpanzee (Pan troglodytes)
  • 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)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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 SHOX Gene

Gene Tree for SHOX (if available)
Gene Tree for SHOX (if available)

Paralogs for SHOX Gene

Paralogs for SHOX Gene

Selected SIMAP similar genes for SHOX Gene using alignment to 1 proteins:

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

Variants for SHOX Gene

Sequence variations from dbSNP and Humsavar for SHOX Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
VAR_012346 Leri-Weill dyschondrosteosis (LWD)
VAR_019414 Leri-Weill dyschondrosteosis (LWD)
VAR_019415 Leri-Weill dyschondrosteosis (LWD)
VAR_019416 Langer mesomelic dysplasia (LMD)

Structural Variations from Database of Genomic Variants (DGV) for SHOX Gene

Variant ID Type Subtype PubMed ID
nsv469571 CNV Loss 16826518
esv2739493 CNV Deletion 23290073
esv2739494 CNV Deletion 23290073
esv2739495 CNV Deletion 23290073
esv2739497 CNV Deletion 23290073
dgv1346e201 CNV Deletion 23290073
esv2743216 CNV Deletion 23290073
nsv507942 CNV Insertion 20534489
nsv9923 CNV Loss 18304495
esv2739498 CNV Deletion 23290073
esv2739499 CNV Deletion 23290073
esv2664240 CNV Deletion 23128226
esv2676175 CNV Deletion 23128226
esv2739500 CNV Deletion 23290073
esv2739501 CNV Deletion 23290073
esv2739502 CNV Deletion 23290073
esv2739503 CNV Deletion 23290073
esv2739504 CNV Deletion 23290073
esv2739505 CNV Deletion 23290073
esv2739506 CNV Deletion 23290073
esv2739508 CNV Deletion 23290073
nsv10004 CNV Loss 18304495

Relevant External Links for SHOX Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHOX Gene

Disorders for SHOX Gene


  • Leri-Weill dyschondrosteosis (LWD) [MIM:127300]: Dominantly inherited skeletal dysplasia characterized by moderate short stature predominantly because of short mesomelic limb segments. It is often associated with the Madelung deformity of the wrist, comprising bowing of the radius and dorsal dislocation of the distal ulna. {ECO:0000269 PubMed:11030412, ECO:0000269 PubMed:11403039}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Langer mesomelic dysplasia (LMD) [MIM:249700]: Autosomal recessive rare skeletal dysplasia characterized by severe short stature owing to shortening and maldevelopment of the mesomelic and rhizomelic segments of the limbs. Associated malformations are rarely reported and intellect is normal in all affected subjects reported to date. {ECO:0000269 PubMed:11889214}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Short stature, idiopathic, X-linked (ISS) [MIM:300582]: A condition defined by a standing height more than 2 standard deviations below the mean (or below the 2.5 percentile) for sex and chronological age, compared with a well-nourished, genetically relevant population, in the absence of specific causative disorders. {ECO:0000269 PubMed:9140395}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for SHOX Gene

(19) Novoseek inferred disease relationships for SHOX Gene

Disease -log(P) Hits PubMed IDs
leri-weill dyschondrosteosis 99 52
madelungs deformity 97.8 20
langer mesomelic dysplasia 97.7 13
short stature 93.2 148
turners syndrome 91 46

Relevant External Links for SHOX

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with SHOX: view

No data available for OMIM and Genatlas for SHOX Gene

Publications for SHOX Gene

  1. Pseudoautosomal deletions encompassing a novel homeobox gene cause growth failure in idiopathic short stature and Turner syndrome. (PMID: 9140395) Rao E. … Rappold G.A. (Nat. Genet. 1997) 2 3 4 23
  2. PHOG, a candidate gene for involvement in the short stature of Turner syndrome. (PMID: 9259282) Ellison J.W. … Chiong W. (Hum. Mol. Genet. 1997) 2 3 4 23
  3. SHOX point mutations in dyschondrosteosis. (PMID: 11403039) Huber C. … Cormier-Daire V. (J. Med. Genet. 2001) 3 4 23
  4. Mutations in short stature homeobox containing gene (SHOX) in dyschondrosteosis but not in hypochondroplasia. (PMID: 11030412) Grigelioniene G. … Hagenaes L. (Hum. Genet. 2000) 3 4 23
  5. SHOX nullizygosity and haploinsufficiency in a Japanese family: implication for the development of Turner skeletal features. (PMID: 11889214) Ogata T. … Hattori T. (J. Clin. Endocrinol. Metab. 2002) 3 4 23

Products for SHOX Gene

Sources for SHOX Gene

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