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Aliases for SOX13 Gene

Aliases for SOX13 Gene

  • SRY-Box 13 2 2 3 5
  • SRY (Sex Determining Region Y)-Box 13 2 3 4
  • Type 1 Diabetes Autoantigen ICA12 3 4
  • SRY-Related HMG-Box Gene 13 2 3
  • Islet Cell Antibody 12 2 3
  • Islet Cell Antigen 12 3 4
  • Transcription Factor SOX-13 3
  • Type 1 Diabetes Autoantigen 2
  • SRY Box 13 2
  • Sox-13 3
  • ICA12 3

External Ids for SOX13 Gene

Previous GeneCards Identifiers for SOX13 Gene

  • GC01P201766
  • GC01P199503
  • GC01P200402
  • GC01P201259
  • GC01P201219
  • GC01P200774
  • GC01P202308
  • GC01P175207

Summaries for SOX13 Gene

Entrez Gene Summary for SOX13 Gene

  • 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]

GeneCards Summary for SOX13 Gene

SOX13 (SRY-Box 13) is a Protein Coding gene. Among its related pathways are Signaling by Wnt and ERK Signaling. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is SOX5.

UniProtKB/Swiss-Prot for SOX13 Gene

  • Binds to the sequence 5-AACAAT-3.

Gene Wiki entry for SOX13 Gene

Additional gene information for SOX13 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SOX13 Gene

Genomics for SOX13 Gene

GeneHancer (GH) Regulatory Elements for SOX13 Gene

Promoters and enhancers for SOX13 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J204072 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 655.5 +6.0 5957 13.2 HDGF CLOCK FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SOX13 ZC3H11A MDM4 PPP1R15B ENSG00000240219 KRT8P29 LAX1 PIK3C2B ENSG00000261065
GH01J204100 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 25.3 +30.5 30545 5.7 HDGF PKNOX1 CLOCK FOXA2 ARID4B NEUROD1 SIN3A DMAP1 ZBTB7B BRCA1 SOX13 LAX1 ERLNC1 ETNK2 KRT8P29 CNTN2 SNRPE PPP1R15B ENSG00000261065
GH01J203624 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.1 -444.9 -444930 7.2 HDGF PKNOX1 CLOCK SMAD1 ARNT SIN3A YBX1 ZNF2 ZBTB7B YY1 ATP2B4 ZC3H11A MDM4 SNRPE ZBED6 HNRNPA1P59 KDM5B PPP1R15B OPTC SOX13
GH01J204511 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.8 +444.0 443971 11.9 CLOCK ZFP64 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF213 E2F8 ZNF416 MDM4 ZC3H11A SNRPE ZBED6 PPP1R15B PIK3C2B LOC101929459 ENSG00000236108 NFASC SOX13
GH01J203298 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 10.8 -768.6 -768568 12.2 FEZF1 YBX1 YY1 ZNF213 ZNF143 NFYC MEF2D ZNF610 GLIS1 NBN BTG2 LINC01136 ZC3H11A HNRNPA1P59 KLHL12 ZBED6 SNRPE KDM5B FMOD LOC100506747
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SOX13 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SOX13 gene promoter:
  • GR-alpha
  • GR
  • GR-beta
  • SREBP-1a
  • SREBP-1c
  • SREBP-1b
  • RREB-1
  • IRF-7A
  • ZID
  • Sp1

Genomic Locations for SOX13 Gene

Genomic Locations for SOX13 Gene
chr1:204,073,109-204,127,743
(GRCh38/hg38)
Size:
54,635 bases
Orientation:
Plus strand
chr1:204,042,243-204,096,871
(GRCh37/hg19)
Size:
54,629 bases
Orientation:
Plus strand

Genomic View for SOX13 Gene

Genes around SOX13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SOX13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SOX13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SOX13 Gene

Proteins for SOX13 Gene

  • Protein details for SOX13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UN79-SOX13_HUMAN
    Recommended name:
    Transcription factor SOX-13
    Protein Accession:
    Q9UN79
    Secondary Accessions:
    • B4E2B0
    • O95275
    • O95826
    • Q3KQV7
    • Q5SXX1
    • Q9UHW7

    Protein attributes for SOX13 Gene

    Size:
    622 amino acids
    Molecular mass:
    69228 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAC83687.1; Type=Miscellaneous discrepancy; Note=Several frameshifts.; Evidence={ECO:0000305}; Sequence=AAF23875.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAG65072.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAI16596.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for SOX13 Gene

Post-translational modifications for SOX13 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SOX13 Gene

No data available for DME Specific Peptides for SOX13 Gene

Domains & Families for SOX13 Gene

Gene Families for SOX13 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SOX13 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SOX13 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SOX13: view

No data available for UniProtKB/Swiss-Prot for SOX13 Gene

Function for SOX13 Gene

Molecular function for SOX13 Gene

UniProtKB/Swiss-Prot Function:
Binds to the sequence 5-AACAAT-3.
GENATLAS Biochemistry:
SRY related HMB box gene 13,highly expressed in fetal kidney,lung,liver,with cow expression from thymus,spleen and muscle,modulator of LINE retroposons promoter activity

Phenotypes From GWAS Catalog for SOX13 Gene

Gene Ontology (GO) - Molecular Function for SOX13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA --
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity TAS 10198172
GO:0005515 protein binding IPI 21988832
genes like me logo Genes that share ontologies with SOX13: view
genes like me logo Genes that share phenotypes with SOX13: view

Animal Models for SOX13 Gene

MGI Knock Outs for SOX13:
  • Sox13 Sox13<tm1a(EUCOMM)Wtsi>
  • Sox13 Sox13<tm1Jskg>

Animal Model Products

miRNA for SOX13 Gene

miRTarBase miRNAs that target SOX13

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SOX13 Gene

Localization for SOX13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SOX13 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SOX13 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SOX13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS,IDA --
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with SOX13: view

Pathways & Interactions for SOX13 Gene

genes like me logo Genes that share pathways with SOX13: view

Gene Ontology (GO) - Biological Process for SOX13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0009653 anatomical structure morphogenesis TAS 10198172
GO:0045586 regulation of gamma-delta T cell differentiation IEA --
genes like me logo Genes that share ontologies with SOX13: view

No data available for SIGNOR curated interactions for SOX13 Gene

Drugs & Compounds for SOX13 Gene

(1) Drugs for SOX13 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with SOX13: view

Transcripts for SOX13 Gene

mRNA/cDNA for SOX13 Gene

Unigene Clusters for SOX13 Gene

SRY (sex determining region Y)-box 13:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SOX13 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b ^ 14
SP1: - - -
SP2:
SP3:
SP4:

Relevant External Links for SOX13 Gene

GeneLoc Exon Structure for
SOX13
ECgene alternative splicing isoforms for
SOX13

Expression for SOX13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SOX13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SOX13 Gene

This gene is overexpressed in Placenta (44.4) and Platelet (24.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SOX13 Gene



Protein tissue co-expression partners for SOX13 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SOX13 Gene:

SOX13

SOURCE GeneReport for Unigene cluster for SOX13 Gene:

Hs.201671

mRNA Expression by UniProt/SwissProt for SOX13 Gene:

Q9UN79-SOX13_HUMAN
Tissue specificity: Highly expressed in kidney, lung, and liver and low expression in thymus, brain, spleen, and muscle.

Evidence on tissue expression from TISSUES for SOX13 Gene

  • Pancreas(4.3)
  • Kidney(4.2)
  • Nervous system(2.2)
genes like me logo Genes that share expression patterns with SOX13: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SOX13 Gene

Orthologs for SOX13 Gene

This gene was present in the common ancestor of animals.

Orthologs for SOX13 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SOX13 34 33
  • 99.62 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SOX13 34 33
  • 89.6 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SOX13 34 33
  • 88.56 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sox13 33
  • 88.13 (n)
mouse
(Mus musculus)
Mammalia Sox13 16 34 33
  • 87.77 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SOX13 34
  • 85 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SOX13 34
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves SOX13 34 33
  • 77.58 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SOX13 34
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sox13 33
  • 63.52 (n)
Str.11026 33
African clawed frog
(Xenopus laevis)
Amphibia xSox12 33
zebrafish
(Danio rerio)
Actinopterygii AL929022.1 34
  • 50 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Sox102F 34 35
  • 25 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea egl-13 34 35
  • 30 (a)
OneToMany
Species where no ortholog for SOX13 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SOX13 Gene

ENSEMBL:
Gene Tree for SOX13 (if available)
TreeFam:
Gene Tree for SOX13 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SOX13: view image

Paralogs for SOX13 Gene

Paralogs for SOX13 Gene

(2) SIMAP similar genes for SOX13 Gene using alignment to 4 proteins:

  • SOX13_HUMAN
  • E9PKD6_HUMAN
  • E9PPW0_HUMAN
  • H0YDQ5_HUMAN
genes like me logo Genes that share paralogs with SOX13: view

Variants for SOX13 Gene

Sequence variations from dbSNP and Humsavar for SOX13 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000091872 -- 204,112,941(+) C/T coding_sequence_variant, missense_variant
rs1000104109 -- 204,099,057(+) C/G intron_variant
rs1000243673 -- 204,099,459(+) T/A intron_variant
rs1000253949 -- 204,105,080(+) C/T intron_variant
rs1000394649 -- 204,118,084(+) C/T intron_variant

Variation tolerance for SOX13 Gene

Residual Variation Intolerance Score: 53.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.75; 46.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SOX13 Gene

Human Gene Mutation Database (HGMD)
SOX13
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SOX13

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for SOX13 Gene

Disorders for SOX13 Gene

Additional Disease Information for SOX13

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SOX13 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SOX13 Gene

Publications for SOX13 Gene

  1. The Sox-13 gene: structure, promoter characterization, and chromosomal localization. (PMID: 10198172) Roose J … Clevers H (Genomics 1999) 2 3 22 58
  2. Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study. (PMID: 19536175) Ehret GB … Chakravarti A (European journal of human genetics : EJHG 2009) 3 44 58
  3. SOX13 autoantibodies are likely to be a supplementary marker for type 1 diabetes in Korea. (PMID: 14679071) Park Y … Kim D (Annals of the New York Academy of Sciences 2003) 3 22 58
  4. Linkage studies of SOX13, the ICA12 autoantigen gene, in families with type 1 diabetes. (PMID: 11286511) Argentaro A … Harley VR (Molecular genetics and metabolism 2001) 3 22 58
  5. Genomic characterisation and fine mapping of the human SOX13 gene. (PMID: 10854791) Argentaro A … Harley VR (Gene 2000) 3 22 58

Products for SOX13 Gene

Sources for SOX13 Gene

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