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    SHOX SHOX homeobox [ Homo sapiens (human) ]

    Gene ID: 6473, updated on 1-Mar-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
    NEW
    Try the new Gene table
    Try the new Transcript table

    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)

    NEW Try the new Transcript table

    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)