U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    SHOX2 SHOX homeobox 2 [ Homo sapiens (human) ]

    Gene ID: 6474, updated on 17-Jun-2024

    Summary

    Official Symbol
    SHOX2provided by HGNC
    Official Full Name
    SHOX homeobox 2provided by HGNC
    Primary source
    HGNC:HGNC:10854
    See related
    Ensembl:ENSG00000168779 MIM:602504; AllianceGenome:HGNC:10854
    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
    OG12; SHOT; OG12X
    Summary
    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]
    Expression
    Biased expression in fat (RPKM 3.0), lymph node (RPKM 1.2) and 4 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SHOX2 in Genome Data Viewer
    Location:
    3q25.32
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (158095905..158106420, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (160870630..160881158, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (157813694..157824209, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 66 member 1 like, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_65660 Neighboring gene VISTA enhancer hs638 Neighboring gene RN7SK pseudogene 46 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:157737752-157738378 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:157751099-157752298 Neighboring gene hs1251 and hs1262 enhancers downstream of SHOX2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20743 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:157820715-157821322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14847 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:157824397-157824900 Neighboring gene H3K27ac hESC enhancers GRCh37_chr3:157827539-157828040 and GRCh37_chr3:157828041-157828540 Neighboring gene VISTA enhancer hs636 Neighboring gene VISTA enhancer hs741 Neighboring gene arginine and serine rich coiled-coil 1 Neighboring gene MPRA-validated peak4879 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:158047255-158047784 Neighboring gene ribosomal protein L15 pseudogene 6 Neighboring gene LILRA2 pseudogene 1

    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?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cardiac pacemaker cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cardiac right atrium morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cartilage development involved in endochondral bone morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chondrocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic digestive tract morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic forelimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic skeletal joint morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mesenchymal cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in muscle tissue morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in osteoblast differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of axonogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of mesenchymal cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of skeletal muscle fiber development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of stem cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of branching morphogenesis of a nerve IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of chondrocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of regulation of heart rate ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sinoatrial node cell development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in sinoatrial node development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in sinoatrial valve development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in skeletal system development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in stem cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    short stature homeobox protein 2
    Names
    SHOX homologous gene on chromosome 3
    homeobox protein Og12X
    paired-related homeobox protein SHOT
    short stature homeobox 2

    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_047079.1 RefSeqGene

      Range
      4783..15298
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001163678.2NP_001157150.1  short stature homeobox protein 2 isoform c

      See identical proteins and their annotated locations for NP_001157150.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the coding region, compared to variant 1, resulting in an isoform (c) that is shorter than isoform b.
      Source sequence(s)
      AC112502, DA447204
      Consensus CDS
      CCDS54664.1
      UniProtKB/Swiss-Prot
      O60902
      Related
      ENSP00000419362.1, ENST00000483851.7
      Conserved Domains (2) summary
      pfam00046
      Location:143197
      Homeobox; Homeobox domain
      pfam03826
      Location:299315
      OAR; OAR domain
    2. NM_003030.4NP_003021.3  short stature homeobox protein 2 isoform b

      See identical proteins and their annotated locations for NP_003021.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (b).
      Source sequence(s)
      AA450208, AC112502, BC008829, BX331739
      Consensus CDS
      CCDS33884.2
      UniProtKB/Swiss-Prot
      O60902
      Related
      ENSP00000374240.4, ENST00000389589.8
      Conserved Domains (2) summary
      pfam00046
      Location:167220
      Homeobox; Homeobox domain
      pfam03826
      Location:335351
      OAR; OAR domain
    3. NM_006884.3NP_006875.2  short stature homeobox protein 2 isoform a

      See identical proteins and their annotated locations for NP_006875.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region, compared to variant 1, resulting in an isoform (a, also known as SHOX2a) that is shorter than isoform b.
      Source sequence(s)
      AA450208, AC112502, AJ002367, BC008829, BX331739, DA447204
      Consensus CDS
      CCDS43164.1
      UniProtKB/Swiss-Prot
      O60465, O60467, O60902, O60903
      Related
      ENSP00000397099.3, ENST00000441443.6
      Conserved Domains (2) summary
      pfam00046
      Location:143196
      Homeobox; Homeobox domain
      pfam03826
      Location:311327
      OAR; OAR 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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      158095905..158106420 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006713727.4XP_006713790.1  short stature homeobox protein 2 isoform X1

      See identical proteins and their annotated locations for XP_006713790.1

      Conserved Domains (2) summary
      pfam00046
      Location:167221
      Homeobox; Homeobox domain
      pfam03826
      Location:323339
      OAR; OAR domain
    2. XM_006713728.4XP_006713791.1  short stature homeobox protein 2 isoform X3

      See identical proteins and their annotated locations for XP_006713791.1

      UniProtKB/TrEMBL
      A0A0A0MSP8, A6NLG4, C9J3D0
      Conserved Domains (2) summary
      pfam00046
      Location:1468
      Homeobox; Homeobox domain
      pfam03826
      Location:170186
      OAR; OAR domain
    3. XM_017007053.2XP_016862542.1  short stature homeobox protein 2 isoform X2

      Related
      ENST00000490689.3
      Conserved Domains (2) summary
      pfam00046
      Location:2881
      Homeobox; Homeobox domain
      pfam03826
      Location:184200
      OAR; OAR domain
    4. XM_047448731.1XP_047304687.1  short stature homeobox protein 2 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      160870630..160881158 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347563.1XP_054203538.1  short stature homeobox protein 2 isoform X1

    2. XM_054347566.1XP_054203541.1  short stature homeobox protein 2 isoform X3

      UniProtKB/TrEMBL
      A0A0A0MSP8, A6NLG4, C9J3D0
    3. XM_054347564.1XP_054203539.1  short stature homeobox protein 2 isoform X2

    4. XM_054347565.1XP_054203540.1  short stature homeobox protein 2 isoform X2