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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]
SOX5 (SRY-Box Transcription Factor 5) is a Protein Coding gene. Diseases associated with SOX5 include Lamb-Shaffer Syndrome and Optic Nerve Hypoplasia, Bilateral. Among its related pathways are Neural Crest Differentiation and ERK Signaling. 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.
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 |
---|---|---|---|---|---|---|---|---|---|---|
GH12J024559 | Promoter/Enhancer | 2.2 | EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER | 250.7 | +0.4 | 435 | 4.7 | ZBTB10 FEZF1 CEBPA ZEB1 ZIC2 SIN3A FOXA2 KLF7 ZNF341 RXRA | HSALNG0089869 SOX5 lnc-SOX5-5 piR-48759-054 LINC00477 | |
GH12J023943 | Promoter/Enhancer | 1.9 | EPDnew Ensembl ENCODE CraniofacialAtlas | 250 | +615.2 | 615156 | 7.9 | FEZF1 ZEB1 FOXA2 ZNF740 VEZF1 SAP130 TRIM25 ZNF341 RXRA TEAD3 | SOX5 piR-49713-004 RF00994-221 lnc-SOX5-5 | |
GH12J023584 | Promoter | 0.3 | EPDnew | 277.2 | +978.1 | 978095 | 0.1 | SOX5 ENSG00000256473 piR-33432-106 ETNK1 lnc-SOX5-5 | ||
GH12J023585 | Enhancer | 1 | FANTOM5 Ensembl ENCODE | 63.4 | +977.1 | 977077 | 1.6 | YY1 RBM22 ZBTB33 TAF1 RFX1 EGR1 SP1 POU5F1 POLR2A CHAMP1 | SOX5 ENSG00000256473 piR-33432-106 lnc-SOX5-5 ETNK1 | |
GH12J023626 | Enhancer | 0.4 | FANTOM5 Ensembl | 31.9 | +935.4 | 935400 | 1 | SOX5 LOC105369697 ENSG00000256473 lnc-SOX5-5 |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0000976 | transcription regulatory region sequence-specific DNA binding | IDA | 26525805 |
GO:0000978 | RNA polymerase II proximal promoter sequence-specific DNA binding | IBA | 21873635 |
GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific | ISA | -- |
GO:0000987 | proximal promoter sequence-specific DNA binding | IEA | -- |
GO:0003677 | DNA binding | IEA | -- |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0000785 | chromatin | ISA | -- |
GO:0005634 | nucleus | IBA | 21873635 |
SuperPathway | Contained pathways | ||
---|---|---|---|
1 | Mesenchymal Stem Cell Differentiation Pathways and Lineage-specific Markers | ||
2 | ERK Signaling |
Molecular Mechanisms of Cancer
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|
3 | Endochondral Ossification | ||
4 | Neural Crest Differentiation |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0001502 | cartilage condensation | ISS | -- |
GO:0002062 | chondrocyte differentiation | ISS | -- |
GO:0006355 | regulation of transcription, DNA-templated | IEA | -- |
GO:0006357 | regulation of transcription by RNA polymerase II | IBA | 21873635 |
GO:0006366 | transcription by RNA polymerase II | TAS | 8812465 |
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: |
This gene was present in the common ancestor of animals.
Organism | Taxonomy | Gene | Similarity | Type | Details |
---|---|---|---|---|---|
Chimpanzee (Pan troglodytes) |
Mammalia | SOX5 30 31 |
|
OneToOne | |
Oppossum (Monodelphis domestica) |
Mammalia | SOX5 31 |
|
OneToOne | |
Cow (Bos Taurus) |
Mammalia | SOX5 30 31 |
|
OneToOne | |
Dog (Canis familiaris) |
Mammalia | SOX5 30 31 |
|
OneToOne | |
Mouse (Mus musculus) |
Mammalia | Sox5 30 17 31 |
|
OneToOne | |
Platypus (Ornithorhynchus anatinus) |
Mammalia | -- 31 |
|
OneToMany | |
-- 31 |
|
OneToMany | |||
Rat (Rattus norvegicus) |
Mammalia | Sox5 30 |
|
||
Chicken (Gallus gallus) |
Aves | SOX5 30 31 |
|
OneToOne | |
Lizard (Anolis carolinensis) |
Reptilia | SOX5 31 |
|
OneToOne | |
Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | sox5 30 |
|
||
Zebrafish (Danio rerio) |
Actinopterygii | sox5 30 31 |
|
OneToOne | |
Fruit Fly (Drosophila melanogaster) |
Insecta | Sox102F 31 32 |
|
OneToMany | |
Worm (Caenorhabditis elegans) |
Secernentea | egl-13 31 32 |
|
OneToMany |
SNP ID | Clinical significance and condition | Chr 12 pos | Variation | AA Info | Type |
---|---|---|---|---|---|
835565 | Uncertain Significance: not provided | 23,895,899(-) |
T/C NM_006940.6(SOX5):c.164A>G (p.His55Arg) |
MISSENSE | |
872102 | Pathogenic: not provided | 23,604,385(-) |
A/C NM_006940.6(SOX5):c.1164+2T>G |
SPLICE_DONOR | |
872103 | Pathogenic: not provided | 23,755,687(-) |
C/T NM_006940.6(SOX5):c.519G>A (p.Trp173Ter) |
NONSENSE | |
873457 | Likely Pathogenic: Lamb-shaffer syndrome | 23,536,652(-) |
T/C NM_006940.6(SOX5):c.1789A>G (p.Met597Val) |
MISSENSE | |
973345 | Likely Pathogenic: Lamb-shaffer syndrome | 23,543,309(-) |
C/T NM_006940.6(SOX5):c.1673G>A (p.Arg558His) |
MISSENSE |
Disorder | Aliases | PubMed IDs |
---|---|---|
lamb-shaffer syndrome |
|
|
optic nerve hypoplasia, bilateral |
|
|
colorectal cancer |
|
|
strabismus |
|
|
campomelic dysplasia |
|
|