Human Gene SOX13 (uc001ham.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 chr1:204,042,246-204,096,871 Size: 54,626 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr1:204,082,044-204,095,262 Size: 13,219 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:204,042,246-204,096,871)mRNA (may differ from genome)Protein (622 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SOX13_HUMAN
DESCRIPTION: RecName: Full=Transcription factor SOX-13; AltName: Full=Islet cell antigen 12; AltName: Full=SRY (Sex determining region Y)-box 13; AltName: Full=Type 1 diabetes autoantigen ICA12;
FUNCTION: Binds to the sequence 5'-AACAAT-3' (By similarity).
INTERACTION: P56545:CTBP2; NbExp=2; IntAct=EBI-3928516, EBI-741533;
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Highly expressed in kidney, lung, and liver and low expression in thymus, brain, spleen, and muscle.
SIMILARITY: Contains 1 HMG box DNA-binding domain.
SEQUENCE CAUTION: Sequence=AAC83687.1; Type=Miscellaneous discrepancy; Note=Several frameshifts; Sequence=AAF23875.1; Type=Erroneous initiation; Sequence=BAG65072.1; Type=Erroneous initiation; Sequence=CAI16596.1; Type=Erroneous initiation;

-  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 -571.831609-0.355 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 Q9UN79
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0009653 anatomical structure morphogenesis
GO:0045586 regulation of gamma-delta T cell differentiation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  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.
LF319521 - JP 2014500723-A/127024: Polycomb-Associated Non-Coding RNAs.
JD178277 - Sequence 159301 from Patent EP1572962.
LF319520 - JP 2014500723-A/127023: Polycomb-Associated Non-Coding RNAs.
JD119682 - Sequence 100706 from Patent EP1572962.
JD510829 - Sequence 491853 from Patent EP1572962.
JD547482 - Sequence 528506 from Patent EP1572962.
JD498146 - Sequence 479170 from Patent EP1572962.
JD131207 - Sequence 112231 from Patent EP1572962.
JD366970 - Sequence 347994 from Patent EP1572962.
JD484805 - Sequence 465829 from Patent EP1572962.
JD545125 - Sequence 526149 from Patent EP1572962.
JD220722 - Sequence 201746 from Patent EP1572962.
JD161390 - Sequence 142414 from Patent EP1572962.
JD155558 - Sequence 136582 from Patent EP1572962.
JD298437 - Sequence 279461 from Patent EP1572962.
JD290345 - Sequence 271369 from Patent EP1572962.
JD547548 - Sequence 528572 from Patent EP1572962.
JD271058 - Sequence 252082 from Patent EP1572962.
JD210519 - Sequence 191543 from Patent EP1572962.
JD135452 - Sequence 116476 from Patent EP1572962.
JD148044 - Sequence 129068 from Patent EP1572962.
JD106178 - Sequence 87202 from Patent EP1572962.
JD255145 - Sequence 236169 from Patent EP1572962.
JD419196 - Sequence 400220 from Patent EP1572962.
JD292098 - Sequence 273122 from Patent EP1572962.
JD292099 - Sequence 273123 from Patent EP1572962.
JD205124 - Sequence 186148 from Patent EP1572962.
JD466800 - Sequence 447824 from Patent EP1572962.
JD427140 - Sequence 408164 from Patent EP1572962.
JD553516 - Sequence 534540 from Patent EP1572962.
JD436451 - Sequence 417475 from Patent EP1572962.
JD501202 - Sequence 482226 from Patent EP1572962.
JD558164 - Sequence 539188 from Patent EP1572962.
JD265737 - Sequence 246761 from Patent EP1572962.
JD413244 - Sequence 394268 from Patent EP1572962.
JD094341 - Sequence 75365 from Patent EP1572962.
JD190162 - Sequence 171186 from Patent EP1572962.
JD412188 - Sequence 393212 from Patent EP1572962.
JD490949 - Sequence 471973 from Patent EP1572962.
JD284394 - Sequence 265418 from Patent EP1572962.
MA555098 - JP 2018138019-A/127024: Polycomb-Associated Non-Coding RNAs.
MA555097 - JP 2018138019-A/127023: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UN79 (Reactome details) participates in the following event(s):

R-HSA-5665608 TCF:Beta-catenin binds SOX proteins
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-195721 Signaling by WNT
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B4E2B0, NM_005686, NP_005677, O95275, O95826, Q3KQV7, Q5SXX1, Q9UHW7, Q9UN79, SOX13_HUMAN
UCSC ID: uc001ham.3
RefSeq Accession: NM_005686
Protein: Q9UN79 (aka SOX13_HUMAN or SX13_HUMAN)
CCDS: CCDS44299.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005686.2
exon count: 14CDS single in 3' UTR: no RNA size: 4088
ORF size: 1869CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3829.00frame shift in genome: no % Coverage: 99.63
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: 0# 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.