Homo sapiens gene SHOX.1, encoding short stature homeobox.
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SUMMARY back to top
RefSeq summary
[SHOX] 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].

RefSeq annotates 2 representative transcripts (NM included in AceView variants .a and .b).

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at low level, only 4.6% of the average gene in this release. The sequence of this gene is defined by 6 GenBank accessions, some from bone marrow (seen once), eye (once), skeletal muscle (once). We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 6 distinct gt-ag introns. Transcription produces 2 alternatively spliced mRNAs. There are 2 non overlapping alternative last exons (see the diagram).
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant aAug10, bAug10).
Function: There are 53 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (OMIM: Langer mesomelic dysplasia; Leri-Weill dyschondrosteosis; short stature, idiopathic, autosomal; short stature, idiopathic, x-linked; Other sources: Abnormalities, Multiple; Chromosome Aberrations; Chromosome Disorders; Dwarfism; Growth Disorders and 6 others) and proposed to participate in processes (skeletal system development, transcription from RNA polymerase II promoter, multicellular organismal development, regulation of transcription, DNA-dependent). Proteins are expected to have molecular functions (sequence-specific DNA binding, transcription factor activity) and to localize in nucleus. A putative protein interactor has been described (CSNK2A1).
Protein coding potential: The 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete), containing domains Homeobox domain, OAR domain [Pfam]. Finally proteins from this gene may be modulated by acetylation; phosphorylation; ubiquitination, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome X, links to other databases and other names
Map: This gene SHOX.1 maps on chomosome X at position -19.44 (interpolated), at Xp22.33;Yp11.3 according to Entrez Gene. In AceView, it covers 35.07 kb, from 585075 to 620147 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from OMIM_127300, OMIM_249700, OMIM_300582, OMIM_604271, PhosphoSite, the SNP view, gene overviews from Entrez Gene 6473, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC. The previous AceView annotation is here.
Other names: The gene is also known as SHOX.1, SS, GCFX, PHOG, SHOXY or SHOX, LOC6473. It has been described as short stature homeobox protein, OTTHUMP00000022822, growth control factor, X-linked, short stature homeobox-containing protein, pseudoautosomal homeobox-containing osteogenic protein.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Shox2 (e=8 10-65).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes alr-1 (e=2 10-20), ceh-17 (e=4 10-19), unc-4 (e=6 10-19), ceh-8 (e=4 10-18), unc-42 (e=10-17), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes ANL2 (e=2 10-08), HB-7 (e=10-07), GL2 (e=10-07), AT4G17710 (e=9 10-07), HB-1 (e=10-06), HDG1 (e=2 10-06), PDF2 (e=2 10-06), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
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          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10 3757 bp 292 aa 691 bp 2187 bp 21 bp 2kb probably including promoter 22480 bp 1kb
bAug10 1955 bp 225 aa 695 bp 582 bp 21 bp 2kb probably including promoter 35072 bp 1kb

Gene neighbors and Navigator on chromosome Xp22.33;Yp11.3 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               53 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !