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Aliases for SOX5 Gene

Aliases for SOX5 Gene

  • SRY-Box 5 2 3 5
  • SRY (Sex Determining Region Y)-Box 5 2 3
  • Transcription Factor SOX-5 3
  • SRY Box 5 2
  • L-SOX5B 3
  • L-SOX5F 3
  • L-SOX5 3
  • LAMSHF 3

External Ids for SOX5 Gene

Previous GeneCards Identifiers for SOX5 Gene

  • GC12M024046
  • GC12M023696
  • GC12M023585
  • GC12M023576

Summaries for SOX5 Gene

Entrez Gene Summary for SOX5 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 the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. The encoded protein may play a role in chondrogenesis. A pseudogene of this gene is located on chromosome 8. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for SOX5 Gene

SOX5 (SRY-Box 5) is a Protein Coding gene. Diseases associated with SOX5 include Developmental And Speech Delay Due To Sox5 Deficiency and 12P12.1 Microdeletion Syndrome. Among its related pathways are ERK Signaling and Mesenchymal Stem Cell Differentiation Pathways and Lineage-specific Markers. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and transcription regulatory region DNA binding. An important paralog of this gene is MIR6073.

UniProtKB/Swiss-Prot for SOX5 Gene

  • Binds specifically to the DNA sequence 5-AACAAT-3. Activates transcription of COL2A1 and AGC1 in vitro.

Gene Wiki entry for SOX5 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SOX5 Gene

Genomics for SOX5 Gene

Regulatory Elements for SOX5 Gene

Enhancers for SOX5 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12F023585 1.2 FANTOM5 ENCODE 63.3 +976.9 976911 1.4 RFX1 MAX CHAMP1 BCL11A POLR2A POU5F1 ZSCAN29 ZBTB33 SOX5 LOC105369697 GC12P023453
GH12F023626 1.2 FANTOM5 31.9 +935.7 935712 0.1 SOX5 LOC105369697 GC12P023453
GH12F023593 0.8 FANTOM5 17.6 +968.6 968578 0.4 ZBTB33 CHAMP1 ZNF7 SOX5 LOC105369697 GC12P023453
GH12F023677 0.4 FANTOM5 14.9 +885.1 885088 0.3 SOX5 LOC105369697 GC12P023671 GC12P023722
GH12F023921 0.5 Ensembl 11.4 +640.9 640869 0.4 ZNF121 PKNOX1 PRDM1 SOX5 GC12P023951 LOC105369696
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around SOX5 on UCSC Golden Path with GeneCards custom track

Promoters for SOX5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000427736 268 3999 SIN3A FEZF1 GLI4 ZNF48 ZNF2 GLIS2 KLF7 YY2 REST ZNF264

Genomic Location for SOX5 Gene

Chromosome:
12
Start:
23,529,495 bp from pter
End:
24,562,669 bp from pter
Size:
1,033,175 bases
Orientation:
Minus strand

Genomic View for SOX5 Gene

Genes around SOX5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SOX5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SOX5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SOX5 Gene

Proteins for SOX5 Gene

  • Protein details for SOX5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P35711-SOX5_HUMAN
    Recommended name:
    Transcription factor SOX-5
    Protein Accession:
    P35711
    Secondary Accessions:
    • B7Z8V0
    • F5H5B0
    • Q86UK8
    • Q8J017
    • Q8J018
    • Q8J019
    • Q8J020
    • Q8N1D9
    • Q8N7E0
    • Q8TEA4

    Protein attributes for SOX5 Gene

    Size:
    763 amino acids
    Molecular mass:
    84026 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAB49537.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SOX5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SOX5 Gene

Post-translational modifications for SOX5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SOX5 Gene

Domains & Families for SOX5 Gene

Gene Families for SOX5 Gene

Protein Domains for SOX5 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SOX5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P35711

UniProtKB/Swiss-Prot:

SOX5_HUMAN :
  • Contains 1 HMG box DNA-binding domain.
Domain:
  • Contains 1 HMG box DNA-binding domain.
genes like me logo Genes that share domains with SOX5: view

Function for SOX5 Gene

Molecular function for SOX5 Gene

GENATLAS Biochemistry:
SRY related HMG box gene 5,expressed in brain,testis and various tissues,with alternatively spliced isoforms,including a long form expressed in chondrogenesis coactivator in association with SOX6 and SOX9 of the chondrocyte-specific enhancer of COL2A1,modulator of LINE retroposons promoter activity
UniProtKB/Swiss-Prot Function:
Binds specifically to the DNA sequence 5-AACAAT-3. Activates transcription of COL2A1 and AGC1 in vitro.

Gene Ontology (GO) - Molecular Function for SOX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding TAS 8812465
GO:0005515 protein binding IPI 21262861
genes like me logo Genes that share ontologies with SOX5: view
genes like me logo Genes that share phenotypes with SOX5: view

Animal Models for SOX5 Gene

MGI Knock Outs for SOX5:

Animal Model Products

Transcription Factor Targets for SOX5 Gene

Selected GeneGlobe predicted Target genes for SOX5

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and HOMER Transcription for SOX5 Gene

Localization for SOX5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SOX5 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SOX5 Gene COMPARTMENTS Subcellular localization image for SOX5 gene
Compartment Confidence
nucleus 4
cytosol 1

Gene Ontology (GO) - Cellular Components for SOX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with SOX5: view

Pathways & Interactions for SOX5 Gene

genes like me logo Genes that share pathways with SOX5: view

Pathways by source for SOX5 Gene

1 Qiagen pathway for SOX5 Gene

Gene Ontology (GO) - Biological Process for SOX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription from RNA polymerase II promoter TAS 8812465
GO:0032332 positive regulation of chondrocyte differentiation IDA 21401405
GO:0055059 asymmetric neuroblast division IGI 23946438
genes like me logo Genes that share ontologies with SOX5: view

No data available for SIGNOR curated interactions for SOX5 Gene

Transcripts for SOX5 Gene

Unigene Clusters for SOX5 Gene

SRY (sex determining region Y)-box 5:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SOX5 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19
SP1: - - -
SP2: - - - - -
SP3: - - - -
SP4:
SP5: - - -
SP6:
SP7:

Relevant External Links for SOX5 Gene

GeneLoc Exon Structure for
SOX5
ECgene alternative splicing isoforms for
SOX5

Expression for SOX5 Gene

mRNA expression in normal human tissues for SOX5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SOX5 Gene

This gene is overexpressed in Fetal Brain (33.5), Adipocyte (27.0), and Brain (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SOX5 Gene



Protein tissue co-expression partners for SOX5 Gene

NURSA nuclear receptor signaling pathways regulating expression of SOX5 Gene:

SOX5

SOURCE GeneReport for Unigene cluster for SOX5 Gene:

Hs.657542
genes like me logo Genes that share expression patterns with SOX5: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for SOX5 Gene

Orthologs for SOX5 Gene

This gene was present in the common ancestor of animals.

Orthologs for SOX5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SOX5 34 35
  • 99.73 (n)
oppossum
(Monodelphis domestica)
Mammalia SOX5 35
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SOX5 34 35
  • 95.74 (n)
dog
(Canis familiaris)
Mammalia SOX5 34 35
  • 95.6 (n)
mouse
(Mus musculus)
Mammalia Sox5 34 16 35
  • 90.43 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 90 (a)
OneToMany
-- 35
  • 90 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Sox5 34
  • 89.86 (n)
chicken
(Gallus gallus)
Aves SOX5 34 35
  • 88.97 (n)
lizard
(Anolis carolinensis)
Reptilia SOX5 35
  • 94 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sox5 34
  • 77.48 (n)
zebrafish
(Danio rerio)
Actinopterygii sox5 34 35
  • 71.09 (n)
fruit fly
(Drosophila melanogaster)
Insecta Sox102F 36 35
  • 80 (a)
worm
(Caenorhabditis elegans)
Secernentea egl-13 36 35
  • 70 (a)
Species where no ortholog for SOX5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 SOX5 Gene

ENSEMBL:
Gene Tree for SOX5 (if available)
TreeFam:
Gene Tree for SOX5 (if available)

Paralogs for SOX5 Gene

Paralogs for SOX5 Gene

Pseudogenes.org Pseudogenes for SOX5 Gene

genes like me logo Genes that share paralogs with SOX5: view

Variants for SOX5 Gene

Sequence variations from dbSNP and Humsavar for SOX5 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs869025321 Pathogenic 23,604,491(-) CTCCA(G/T)GAGGG reference, stop-gained
rs869312867 Likely pathogenic 23,536,610(-) AAGCC(C/G)GTCTC reference, missense
rs1002245 -- 23,991,348(+) AAAAA(A/T)ATata intron-variant
rs1002815 -- 23,634,432(+) GAGTA(A/G)ATACA intron-variant
rs1002816 -- 23,634,650(+) GCACA(G/T)AGAGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SOX5 Gene

Variant ID Type Subtype PubMed ID
dgv178e201 CNV deletion 23290073
dgv2410n54 CNV loss 21841781
dgv2411n54 CNV loss 21841781
dgv261e214 CNV loss 21293372
dgv468e212 CNV loss 25503493
dgv782n106 CNV deletion 24896259
dgv783n106 CNV deletion 24896259
dgv91n21 CNV gain 19592680
esv1006653 CNV deletion 20482838
esv1146003 CNV insertion 17803354
esv1554693 CNV insertion 17803354
esv2016346 CNV deletion 18987734
esv2090158 CNV deletion 18987734
esv2422312 CNV duplication 17116639
esv26543 CNV loss 19812545
esv2660296 CNV deletion 23128226
esv2664283 CNV deletion 23128226
esv2669713 CNV deletion 23128226
esv2676176 CNV deletion 23128226
esv2676317 CNV deletion 23128226
esv2677220 CNV deletion 23128226
esv2745636 CNV deletion 23290073
esv2745637 CNV deletion 23290073
esv2745638 CNV deletion 23290073
esv2745639 CNV deletion 23290073
esv2745640 CNV deletion 23290073
esv2745642 CNV deletion 23290073
esv2745643 CNV deletion 23290073
esv2745644 CNV deletion 23290073
esv2745647 CNV deletion 23290073
esv2745648 CNV deletion 23290073
esv3253496 CNV deletion 24192839
esv3303211 CNV mobile element insertion 20981092
esv3305135 CNV mobile element insertion 20981092
esv3308213 CNV mobile element insertion 20981092
esv3340 CNV loss 18987735
esv33613 CNV gain 17666407
esv3388111 CNV insertion 20981092
esv3402812 CNV insertion 20981092
esv3409691 CNV insertion 20981092
esv34159 CNV loss 18971310
esv3436335 CNV insertion 20981092
esv3548886 CNV deletion 23714750
esv3548890 CNV deletion 23714750
esv3548891 CNV deletion 23714750
esv3548892 CNV deletion 23714750
esv3548893 CNV deletion 23714750
esv3580192 CNV loss 25503493
esv3580193 CNV loss 25503493
esv3628849 CNV loss 21293372
esv3628850 CNV loss 21293372
esv3628851 CNV loss 21293372
esv3628853 CNV loss 21293372
esv3628856 CNV loss 21293372
esv3628857 OTHER inversion 21293372
esv3628858 CNV loss 21293372
esv3628861 CNV gain 21293372
esv3628863 CNV loss 21293372
esv3628865 CNV loss 21293372
esv3628866 CNV loss 21293372
esv3628869 CNV loss 21293372
esv3628870 CNV gain 21293372
esv3628871 CNV loss 21293372
esv3628873 CNV loss 21293372
esv3892160 CNV loss 25118596
esv3892161 CNV loss 25118596
esv4942 CNV loss 18987735
esv5104 CNV loss 18987735
esv9507 CNV loss 19470904
esv993084 CNV insertion 20482838
nsv1046463 CNV gain 25217958
nsv1053666 CNV loss 25217958
nsv1069652 CNV deletion 25765185
nsv1069653 CNV deletion 25765185
nsv1070099 CNV deletion 25765185
nsv1145587 CNV deletion 24896259
nsv433520 CNV loss 18776910
nsv469167 CNV loss 19166990
nsv469168 CNV loss 19166990
nsv469169 CNV gain 19166990
nsv470276 CNV loss 18288195
nsv475434 CNV novel sequence insertion 20440878
nsv518599 CNV loss 19592680
nsv519893 CNV loss 19592680
nsv525031 CNV loss 19592680
nsv557759 CNV loss 21841781
nsv557760 CNV loss 21841781
nsv557761 CNV loss 21841781
nsv557762 CNV loss 21841781
nsv557767 CNV loss 21841781
nsv557768 CNV loss 21841781
nsv557769 CNV loss 21841781
nsv557770 CNV loss 21841781
nsv557771 CNV loss 21841781
nsv557772 CNV loss 21841781
nsv557773 CNV loss 21841781
nsv557774 CNV loss 21841781
nsv557775 CNV gain 21841781
nsv642 CNV deletion 18451855
nsv643 CNV insertion 18451855
nsv645 CNV deletion 18451855
nsv818896 CNV gain 17921354
nsv826282 CNV loss 20364138
nsv832350 CNV loss 17160897
nsv832351 CNV gain+loss 17160897
nsv832352 CNV gain 17160897
nsv958671 CNV deletion 24416366
nsv958699 CNV deletion 24416366

Variation tolerance for SOX5 Gene

Residual Variation Intolerance Score: 2.48% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.58; 12.52% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SOX5 Gene

Human Gene Mutation Database (HGMD)
SOX5
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SOX5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SOX5 Gene

Disorders for SOX5 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SOX5 Gene - From: Orphanet and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SOX5 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SOX5_HUMAN
  • Lamb-Shaffer syndrome (LAMSHF) [MIM:616803]: An autosomal dominant, neurodevelopmental disorder characterized by global developmental delay, intellectual disability, language and motor impairment, and distinct facial features. Additional variable skeletal abnormalities may also be present. {ECO:0000269 PubMed:22290657, ECO:0000269 PubMed:23220431, ECO:0000269 PubMed:23498568, ECO:0000269 PubMed:26111154}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SOX5

Genetic Association Database (GAD)
SOX5
Human Genome Epidemiology (HuGE) Navigator
SOX5
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SOX5
genes like me logo Genes that share disorders with SOX5: view

No data available for Genatlas for SOX5 Gene

Publications for SOX5 Gene

  1. Cloning and characterization of SOX5, a new member of the human SOX gene family. (PMID: 8812465) Wunderle V.M. … Goodfellow P.N. (Genomics 1996) 2 3 4 22 64
  2. Identification and characterization of the human long form of Sox5 (L-SOX5) gene. (PMID: 12406576) Ikeda T. … Ikegawa S. (Gene 2002) 3 4 22 64
  3. Haploinsufficiency of SOX5, a member of the SOX (SRY-related HMG-box) family of transcription factors is a cause of intellectual disability. (PMID: 23220431) Schanze I. … Zenker M. (Eur J Med Genet 2013) 3 4 64
  4. Deletion 12p12 involving SOX5 in two children with developmental delay and dysmorphic features. (PMID: 23498568) Lee R.W. … Batista D. (Pediatr. Neurol. 2013) 3 4 64
  5. Haploinsufficiency of SOX5 at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic features. (PMID: 22290657) Lamb A.N. … Shaffer L.G. (Hum. Mutat. 2012) 3 4 64

Products for SOX5 Gene

Sources for SOX5 Gene

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