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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 Lamb-Shaffer Syndrome and Colorectal Cancer. Among its related pathways are ERK Signaling and Neural Crest Differentiation. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and transcription regulatory region DNA binding. An important paralog of this gene is SOX6.

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

Additional gene information for SOX5 Gene

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

Genomics for SOX5 Gene

GeneHancer (GH) Regulatory Elements for SOX5 Gene

Promoters and enhancers for SOX5 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J024559 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.6 553 4.4 PKNOX1 FOXA2 SIN3A FEZF1 GLI4 ZNF2 ZNF48 YY1 GLIS2 ZNF213 SOX5 GC12P024533
GH12J023948 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 650 +612.4 612441 2.5 HDAC1 PTBP1 PKNOX1 FOXA2 ZSCAN4 ARID4B FEZF1 DMAP1 ZBTB40 THRB GC12P023951 SOX5 LOC105369696
GH12J023584 Promoter 0.5 EPDnew 677.2 +978.1 978063 0.1 SOX5 LOC105369697 GC12P023453 GC12P023452
GH12J023585 Enhancer 0.9 FANTOM5 ENCODE 63.3 +976.9 976910 1.4 USF1 RFX1 MAX CHAMP1 CC2D1A SP1 POLR2A POU5F1 ZBTB33 SOX5 LOC105369697 GC12P023452 GC12P023453
GH12J023771 Enhancer 0.8 UCNEbase 10.4 +791.1 791104 0.3 RXRA HLF MAX REST YY1 SP1 JUND ATF3 HNF4A ZBTB33 LOC105369697 SOX5 LOC105369696 GC12P023951
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SOX5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SOX5 gene promoter:
  • AP-1
  • SRY
  • PPAR-gamma2
  • PPAR-gamma1
  • c-Jun
  • ATF-2

Genomic Locations for SOX5 Gene

Genomic Locations for SOX5 Gene
1,033,175 bases
Minus strand
1,032,941 bases
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:
    Recommended name:
    Transcription factor SOX-5
    Protein Accession:
    Secondary Accessions:
    • B7Z8V0
    • F5H5B0
    • Q86UK8
    • Q8J017
    • Q8J018
    • Q8J019
    • Q8J020
    • Q8N1D9
    • Q8N7E0
    • Q8TEA4

    Protein attributes for SOX5 Gene

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

    Alternative splice isoforms for SOX5 Gene


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

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SOX5 Gene


Suggested Antigen Peptide Sequences for SOX5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for SOX5 Gene

Function for SOX5 Gene

Molecular function for SOX5 Gene

UniProtKB/Swiss-Prot Function:
Binds specifically to the DNA sequence 5-AACAAT-3. Activates transcription of COL2A1 and AGC1 in vitro.
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

Phenotypes From GWAS Catalog for SOX5 Gene

Gene Ontology (GO) - Molecular Function for SOX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
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 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

Human Phenotype Ontology for SOX5 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

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

Clone Products

  • Addgene plasmids for SOX5

No data available for Enzyme Numbers (IUBMB) and HOMER Transcription for SOX5 Gene

Localization for SOX5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SOX5 Gene

Subcellular locations from

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 SOX5 gene
Compartment Confidence
nucleus 5
extracellular 2
cytoskeleton 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

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

2 BioSystems pathways 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:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0006366 transcription by RNA polymerase II TAS 8812465
GO:0032332 positive regulation of chondrocyte differentiation IDA 21401405
genes like me logo Genes that share ontologies with SOX5: view

No data available for SIGNOR curated interactions for SOX5 Gene

Drugs & Compounds for SOX5 Gene

No Compound Related Data Available

Transcripts for SOX5 Gene

mRNA/cDNA for SOX5 Gene

Unigene Clusters for SOX5 Gene

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

Clone Products

  • Addgene plasmids for SOX5

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: - - - -
SP5: - - -

Relevant External Links for SOX5 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SOX5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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 and MOPED for SOX5 Gene

Protein tissue co-expression partners for SOX5 Gene

NURSA nuclear receptor signaling pathways regulating expression of SOX5 Gene:


SOURCE GeneReport for Unigene cluster for SOX5 Gene:


Evidence on tissue expression from TISSUES for SOX5 Gene

  • Nervous system(4.8)
  • Liver(4.2)
  • Heart(4.1)
genes like me logo Genes that share expression patterns with SOX5: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
(Pan troglodytes)
Mammalia SOX5 34 33
  • 99.73 (n)
(Monodelphis domestica)
Mammalia SOX5 34
  • 98 (a)
(Bos Taurus)
Mammalia SOX5 34 33
  • 95.74 (n)
(Canis familiaris)
Mammalia SOX5 34 33
  • 95.6 (n)
(Mus musculus)
Mammalia Sox5 16 34 33
  • 90.43 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 90 (a)
-- 34
  • 90 (a)
(Rattus norvegicus)
Mammalia Sox5 33
  • 89.86 (n)
(Gallus gallus)
Aves SOX5 34 33
  • 88.97 (n)
(Anolis carolinensis)
Reptilia SOX5 34
  • 94 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia sox5 33
  • 77.48 (n)
(Danio rerio)
Actinopterygii sox5 34 33
  • 71.09 (n)
fruit fly
(Drosophila melanogaster)
Insecta Sox102F 34 35
  • 27 (a)
(Caenorhabditis elegans)
Secernentea egl-13 34 35
  • 31 (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

Gene Tree for SOX5 (if available)
Gene Tree for SOX5 (if available)
Evolutionary constrained regions (ECRs) for SOX5: view image

Paralogs for SOX5 Gene

Paralogs for SOX5 Gene

(14) SIMAP similar genes for SOX5 Gene using alignment to 9 proteins:

  • F5H0I3_HUMAN
  • F5H876_HUMAN
  • G3V0H1_HUMAN
  • I3L0A5_HUMAN
  • T2CZM2_HUMAN 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 Variation AA Info Type
rs1057518845 likely-pathogenic, Aplasia/Hypoplasia of the nails, Central hypotonia, Generalized hypotonia, Strabismus, Thoracolumbar scoliosis 23,755,726(-) T/G genic_upstream_transcript_variant, splice_acceptor_variant
rs1057518928 likely-pathogenic, Epileptic encephalopathy, Generalized hypotonia, Severe global developmental delay 23,665,471(-) G/A coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs869025321 pathogenic, Lamb-shaffer syndrome 23,604,491(-) C/A coding_sequence_variant, genic_upstream_transcript_variant, stop_gained
rs869312867 likely-pathogenic, Cerebral visual impairment and intellectual disability 23,536,610(-) G/C coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1000000723 -- 23,852,264(-) A/G genic_upstream_transcript_variant, 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)

Additional Variant Information for SOX5 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for SOX5 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SOX5 Gene - From: HGMD, LncRNADisease, OMIM, ClinVar, GTR, Orphanet, and GeneCards

Disorder Aliases PubMed IDs
lamb-shaffer syndrome
  • lamshf
colorectal cancer
  • crc
- elite association - COSMIC cancer census association via MalaCards
Search SOX5 in MalaCards View complete list of genes associated with diseases


  • 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.

Additional Disease Information for SOX5

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 VM … Goodfellow PN (Genomics 1996) 2 3 4 22 58
  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 58
  3. Deletion 12p12 involving SOX5 in two children with developmental delay and dysmorphic features. (PMID: 23498568) Lee RW … Batista D (Pediatric neurology 2013) 3 4 58
  4. 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 (European journal of medical genetics 2013) 3 4 58
  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 AN … Shaffer LG (Human mutation 2012) 3 4 58

Products for SOX5 Gene

  • Addgene plasmids for SOX5

Sources for SOX5 Gene

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