Human Gene SOX15 (ENST00000250055.3_9) from GENCODE V47lift37
  Description: SRY-box transcription factor 15 (from RefSeq NM_006942.2)
Gencode Transcript: ENST00000250055.3_9
Gencode Gene: ENSG00000129194.8_11
Transcript (Including UTRs)
   Position: hg19 chr17:7,491,496-7,493,412 Size: 1,917 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr17:7,491,696-7,492,994 Size: 1,299 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:7,491,496-7,493,412)mRNA (may differ from genome)Protein (233 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SOX15_HUMAN
DESCRIPTION: RecName: Full=Protein SOX-15; AltName: Full=Protein SOX-12; AltName: Full=Protein SOX-20;
FUNCTION: Binds to the 5'-AACAAT-3' sequence.
SUBCELLULAR LOCATION: Nucleus (Potential).
TISSUE SPECIFICITY: Widely expressed in fetal and adult tissues examined, highest level found in fetal spinal cord and adult brain and testis.
SIMILARITY: Contains 1 HMG box DNA-binding domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 39.64 RPKM in Esophagus - Mucosa
Total median expression: 218.11 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -161.80418-0.387 Picture PostScript Text
3' UTR -41.30200-0.206 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009071 - HMG_superfamily

Pfam Domains:
PF00505 - HMG (high mobility group) box
PF09011 - HMG-box domain

SCOP Domains:
47095 - HMG-box

ModBase Predicted Comparative 3D Structure on O60248
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006325 chromatin organization
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0008584 male gonad development
GO:0014718 positive regulation of satellite cell activation involved in skeletal muscle regeneration
GO:0030154 cell differentiation
GO:0043403 skeletal muscle tissue regeneration
GO:0045843 negative regulation of striated muscle tissue development
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048627 myoblast development
GO:0070318 positive regulation of G0 to G1 transition
GO:2000288 positive regulation of myoblast proliferation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0044798 nuclear transcription factor complex


-  Descriptions from all associated GenBank mRNAs
  AJ006222 - Homo sapiens mRNA for HMG-box transcription factor SOX-20, partial.
BC072003 - Homo sapiens SRY (sex determining region Y)-box 15, mRNA (cDNA clone MGC:88706 IMAGE:4653140), complete cds.
BC000985 - Homo sapiens SRY (sex determining region Y)-box 15, mRNA (cDNA clone MGC:5138 IMAGE:3447385), complete cds.
AB006867 - Homo sapiens mRNA for hSOX20 protein, complete cds.
JD334835 - Sequence 315859 from Patent EP1572962.
JD370428 - Sequence 351452 from Patent EP1572962.
JD522037 - Sequence 503061 from Patent EP1572962.
KJ892187 - Synthetic construct Homo sapiens clone ccsbBroadEn_01581 SOX15 gene, encodes complete protein.
DQ890736 - Synthetic construct clone IMAGE:100003366; FLH165566.01X; RZPDo839D12160D SRY (sex determining region Y)-box 15 (SOX15) gene, encodes complete protein.
DQ893908 - Synthetic construct Homo sapiens clone IMAGE:100008368; FLH165565.01L; RZPDo839D12159D SRY (sex determining region Y)-box 15 (SOX15) gene, encodes complete protein.
AK301687 - Homo sapiens cDNA FLJ55408 complete cds, highly similar to SOX-15 protein.
JD566367 - Sequence 547391 from Patent EP1572962.
JD227868 - Sequence 208892 from Patent EP1572962.
JD338819 - Sequence 319843 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DWU7, D3DTQ0, ENST00000250055.1, ENST00000250055.2, NM_006942, O60248, P35717, Q9Y6W7, SOX12, SOX15_HUMAN, SOX20, SOX26, SOX27, uc317faq.1, uc317faq.2
UCSC ID: ENST00000250055.3_9
RefSeq Accession: NM_006942.2
Protein: O60248 (aka SOX15_HUMAN or SX15_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.