Human Gene SOX13 (uc001hal.3)
  Description: Homo sapiens SRY (sex determining region Y)-box 13 (SOX13), mRNA.
RefSeq Summary (NM_005686): This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. It has also been determined to be a type-1 diabetes autoantigen, also known as islet cell antibody 12. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr1:204,042,246-204,088,974 Size: 46,729 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr1:204,082,044-204,086,882 Size: 4,839 Coding Exon Count: 6 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:204,042,246-204,088,974)mRNA (may differ from genome)Protein (273 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCLynxMGIOMIMPubMed
TreefamUniProtKBWikipediaBioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SOX13
CDC HuGE Published Literature: SOX13
Positive Disease Associations: Iron
Related Studies:
  1. Iron
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 23.00 RPKM in Uterus
Total median expression: 436.44 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 -317.60595-0.534 Picture PostScript Text
3' UTR -977.562092-0.467 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
  ModBase Predicted Comparative 3D Structure on Q5SXX2
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     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  BC106038 - Homo sapiens SRY (sex determining region Y)-box 13, mRNA (cDNA clone MGC:117216 IMAGE:6502746), complete cds.
LF205350 - JP 2014500723-A/12853: Polycomb-Associated Non-Coding RNAs.
BC040649 - Homo sapiens SRY (sex determining region Y)-box 13, mRNA (cDNA clone IMAGE:4794944), with apparent retained intron.
AK304801 - Homo sapiens cDNA FLJ51471 complete cds, highly similar to SOX-13 protein.
AF116571 - Homo sapiens SRY-like DNA binding protein (SOX13) mRNA, complete cds.
AK314197 - Homo sapiens cDNA, FLJ94923.
AF083105 - Homo sapiens HMG box factor SOX-13 mRNA, complete cds.
AK304192 - Homo sapiens cDNA FLJ59817 complete cds, highly similar to SOX-13 protein.
MA440927 - JP 2018138019-A/12853: Polycomb-Associated Non-Coding RNAs.
AB587365 - Synthetic construct DNA, clone: pF1KB3072, Homo sapiens SOX13 gene for SRY (sex determining region Y)-box 13, without stop codon, in Flexi system.
EU446691 - Synthetic construct Homo sapiens clone IMAGE:100070219; IMAGE:100011900; FLH257349.01L SRY (sex determining region Y)-box 13 (SOX13) gene, encodes complete protein.
AF098915 - Homo sapiens type 1 diabetes autoantigen ICA12 mRNA, complete cds.
AK301782 - Homo sapiens cDNA FLJ58547 complete cds, highly similar to SOX-13 protein.
JD283358 - Sequence 264382 from Patent EP1572962.
JD142534 - Sequence 123558 from Patent EP1572962.
JD222882 - Sequence 203906 from Patent EP1572962.
JD140103 - Sequence 121127 from Patent EP1572962.
JD497718 - Sequence 478742 from Patent EP1572962.
JD497717 - Sequence 478741 from Patent EP1572962.
JD542657 - Sequence 523681 from Patent EP1572962.
JD542658 - Sequence 523682 from Patent EP1572962.
JD407479 - Sequence 388503 from Patent EP1572962.
JD212605 - Sequence 193629 from Patent EP1572962.
JD197996 - Sequence 179020 from Patent EP1572962.
JD413281 - Sequence 394305 from Patent EP1572962.
JD413283 - Sequence 394307 from Patent EP1572962.
JD413284 - Sequence 394308 from Patent EP1572962.
JD246637 - Sequence 227661 from Patent EP1572962.
JD246639 - Sequence 227663 from Patent EP1572962.
JD246640 - Sequence 227664 from Patent EP1572962.
JD185860 - Sequence 166884 from Patent EP1572962.
JD185861 - Sequence 166885 from Patent EP1572962.
JD481341 - Sequence 462365 from Patent EP1572962.
JD481340 - Sequence 462364 from Patent EP1572962.
JD364950 - Sequence 345974 from Patent EP1572962.
JD364949 - Sequence 345973 from Patent EP1572962.
JD308110 - Sequence 289134 from Patent EP1572962.
LF319523 - JP 2014500723-A/127026: Polycomb-Associated Non-Coding RNAs.
MA555100 - JP 2018138019-A/127026: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: BC040649, NM_005686, NP_005677, Q5SXX2, Q5SXX2_HUMAN, RP11-74C13.1-001
UCSC ID: uc001hal.3
RefSeq Accession: NM_005686
Protein: Q5SXX2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC040649.1
exon count: 7CDS single in 3' UTR: no RNA size: 3531
ORF size: 822CDS single in intron: no Alignment % ID: 99.23
txCdsPredict score: 1696.00frame shift in genome: no % Coverage: 99.38
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 2139# strange splices: 0
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.