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SHOX SHOX homeobox [ Homo sapiens (human) ]

Gene ID: 6473, updated on 17-Jun-2024

Summary

Official Symbol
SHOXprovided by HGNC
Official Full Name
SHOX homeoboxprovided by HGNC
Primary source
HGNC:HGNC:10853
See related
Ensembl:ENSG00000185960 Ensembl:ENSG00000292354 MIM:312865; MIM:400020; AllianceGenome:HGNC:10853
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
SS; GCFX; PHOG; SHOX1; SHOXY
Summary
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]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

See SHOX in Genome Data Viewer
Location:
X;Y
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (624344..659411)
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (624344..659411)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (464175..499150)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (478002..512484)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (585079..620146)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (535079..570146)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene fatty acid binding protein 5 pseudogene 13 Neighboring gene keratin 18 pseudogene 53 Neighboring gene CNE-2 enhancer upstream of SHOX Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrY:534047-534914 Neighboring gene meiotic recombination hotspot SHOX Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:639405-639905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:644837-645338 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:727399-727565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:753798-754298 Neighboring gene SHOX downstream enhancer, distal recombination region Neighboring gene CNE4 enhancer downstream of SHOX Neighboring gene CNE5 enhancer downstream of SHOX Neighboring gene SHOX downstream enhancer, proximal recombination region Neighboring gene CNE6 enhancer downstream of SHOX Neighboring gene CNE7 enhancer downstream of SHOX Neighboring gene CNE8 enhancer downstream of SHOX Neighboring gene CNE9 enhancer downstream of SHOX Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:941763-942262 Neighboring gene H3K27ac hESC enhancers GRCh37_chrX:958477-959001 and GRCh37_chrY:908292-908926 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:959002-959525 Neighboring gene ribosomal protein L14 pseudogene 5 Neighboring gene NANOG hESC enhancer GRCh37_chrX:1104952-1105491 Neighboring gene repetin pseudogene

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene fatty acid binding protein 5 pseudogene 13 Neighboring gene keratin 18 pseudogene 53 Neighboring gene CNE-2 enhancer upstream of SHOX Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrY:534047-534914 Neighboring gene meiotic recombination hotspot SHOX Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:639405-639905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:644837-645338 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:727399-727565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:753798-754298 Neighboring gene SHOX downstream enhancer, distal recombination region Neighboring gene CNE4 enhancer downstream of SHOX Neighboring gene CNE5 enhancer downstream of SHOX Neighboring gene SHOX downstream enhancer, proximal recombination region Neighboring gene CNE6 enhancer downstream of SHOX Neighboring gene CNE7 enhancer downstream of SHOX Neighboring gene CNE8 enhancer downstream of SHOX Neighboring gene CNE9 enhancer downstream of SHOX Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:941763-942262 Neighboring gene H3K27ac hESC enhancers GRCh37_chrX:958477-959001 and GRCh37_chrY:908292-908926 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:959002-959525 Neighboring gene ribosomal protein L14 pseudogene 5 Neighboring gene NANOG hESC enhancer GRCh37_chrX:1104952-1105491 Neighboring gene repetin pseudogene

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
short stature homeobox protein
Names
growth control factor, X-linked
pseudoautosomal homeobox-containing osteogenic protein
short stature homeobox

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

  1. NG_009385.2 RefSeqGene

    Range
    5001..40068
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_710

mRNA and Protein(s)

  1. NM_000451.4NP_000442.1  short stature homeobox protein isoform SHOXa

    See identical proteins and their annotated locations for NP_000442.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (SHOXa).
    Source sequence(s)
    BX004827
    Consensus CDS
    CCDS14107.1
    UniProtKB/Swiss-Prot
    O00412, O00413, O15266, O15267
    UniProtKB/TrEMBL
    Q6IT45
    Related
    ENSP00000508521.1, ENSP00000518640.1, ENST00000686671.1, ENST00000711142.1
    Conserved Domains (2) summary
    pfam00046
    Location:120174
    Homeobox; Homeobox domain
    pfam03826
    Location:272288
    OAR; OAR domain
  2. NM_006883.2NP_006874.1  short stature homeobox protein isoform SHOXb

    See identical proteins and their annotated locations for NP_006874.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 3' terminal exon compared to transcript variant 1, and encodes a shorter isoform (SHOXb) with a different C-terminus compared to isoform SHOXa.
    Source sequence(s)
    BX004827
    Consensus CDS
    CCDS14106.1
    UniProtKB/Swiss-Prot
    O15266
    Related
    ENSP00000335505.3, ENSP00000518641.1, ENST00000334060.8, ENST00000711143.1
    Conserved Domains (1) summary
    pfam00046
    Location:120173
    Homeobox; Homeobox 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

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    624344..659411
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

    Range
    624344..659411
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    464175..499150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    478002..512484
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)