Sox3 (SRY-box transcription factor 3) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Sox3 (SRY-box transcription factor 3) Rattus norvegicus
Analyze
Symbol: Sox3
Name: SRY-box transcription factor 3
RGD ID: 1591839
Description: Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including Sertoli cell development; diencephalon development; and face development. Predicted to act upstream of or within animal organ morphogenesis; forebrain development; and spermatid differentiation. Predicted to be located in nucleoplasm. Human ortholog(s) of this gene implicated in X-linked panhypopituitarism. Orthologous to human SOX3 (SRY-box transcription factor 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; (+)-catechin (ortholog); 17beta-estradiol (ortholog).
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: LOC679158; similar to SRY (sex determining region Y)-box 3; SRY-box 3; SRY-box containing gene 3; transcription factor SOX-3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X144,344,892 - 144,346,971 (-)NCBIGRCr8
mRatBN7.2X139,308,608 - 139,310,687 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX139,309,329 - 139,310,678 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX141,520,105 - 141,522,187 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X145,061,083 - 145,063,164 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X142,616,774 - 142,618,855 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X144,035,162 - 144,037,364 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX144,035,883 - 144,037,294 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X144,060,911 - 144,062,696 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X146,510,409 - 146,511,936 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX135,369,404 - 135,371,527 (-)NCBICelera
Cytogenetic MapXq36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleoplasm  (IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Transcription factor SOX3 is involved in X-linked mental retardation with growth hormone deficiency. Laumonnier F, etal., Am J Hum Genet. 2002 Dec;71(6):1450-5. Epub 2002 Nov 8.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
7. SOX3 is required during the formation of the hypothalamo-pituitary axis. Rizzoti K, etal., Nat Genet 2004 Mar;36(3):247-55. Epub 2004 Feb 15.
Additional References at PubMed
PMID:8625802   PMID:11875113   PMID:15893302   PMID:17728342   PMID:21183788   PMID:25759379  


Genomics

Comparative Map Data
Sox3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X144,344,892 - 144,346,971 (-)NCBIGRCr8
mRatBN7.2X139,308,608 - 139,310,687 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX139,309,329 - 139,310,678 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX141,520,105 - 141,522,187 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X145,061,083 - 145,063,164 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X142,616,774 - 142,618,855 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X144,035,162 - 144,037,364 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX144,035,883 - 144,037,294 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X144,060,911 - 144,062,696 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X146,510,409 - 146,511,936 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX135,369,404 - 135,371,527 (-)NCBICelera
Cytogenetic MapXq36NCBI
SOX3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X140,502,985 - 140,505,069 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX140,502,985 - 140,505,069 (-)EnsemblGRCh38hg38GRCh38
GRCh37X139,585,150 - 139,587,234 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X139,412,818 - 139,414,891 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X139,310,671 - 139,312,745NCBI
CeleraX139,957,265 - 139,959,338 (-)NCBICelera
Cytogenetic MapXq27.1NCBI
HuRefX128,852,437 - 128,854,510 (-)NCBIHuRef
CHM1_1X139,496,277 - 139,498,350 (-)NCBICHM1_1
T2T-CHM13v2.0X138,814,872 - 138,816,956 (-)NCBIT2T-CHM13v2.0
Sox3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X59,934,972 - 59,937,045 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX59,934,972 - 59,937,036 (-)EnsemblGRCm39 Ensembl
GRCm38X60,891,366 - 60,893,430 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX60,891,366 - 60,893,430 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X58,144,541 - 58,146,605 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X43,982,954 - 43,989,787 (-)NCBIMGSCv36mm8
MGSCv36X57,152,743 - 57,153,870 (-)NCBIMGSCv36mm8
CeleraX47,327,987 - 47,330,119 (-)NCBICelera
Cytogenetic MapXA6NCBI
cM MapX33.66NCBI
Sox3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554894,817,753 - 4,819,131 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554894,817,753 - 4,819,858 (+)NCBIChiLan1.0ChiLan1.0
SOX3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X139,951,885 - 139,954,109 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X139,955,485 - 139,957,710 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X129,654,296 - 129,656,446 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SOX3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X110,361,354 - 110,363,458 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX110,362,124 - 110,363,458 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX96,180,957 - 96,183,063 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X112,345,866 - 112,347,975 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX112,346,638 - 112,347,975 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X109,479,743 - 109,481,849 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X111,665,269 - 111,667,378 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X111,344,119 - 111,346,231 (-)NCBIUU_Cfam_GSD_1.0
Sox3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X108,393,513 - 108,401,350 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365137,218,583 - 7,221,085 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOX3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX115,019,232 - 115,020,578 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X115,017,704 - 115,020,601 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X131,290,259 - 131,292,684 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SOX3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X115,608,059 - 115,610,248 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX115,608,810 - 115,610,150 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606553,045,641 - 53,047,778 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sox3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248086,167,512 - 6,168,891 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248086,167,512 - 6,169,603 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sox3
6 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat

Markers in Region
Sox3  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.4X146,511,270 - 146,511,330UniSTSRGSC3.4
CeleraX135,370,791 - 135,370,851UniSTS
Sox1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0X144,062,046 - 144,062,209NCBIRnor5.0
RGSC_v3.4X146,511,248 - 146,511,449UniSTSRGSC3.4
CeleraX135,370,769 - 135,370,970UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

circulatory system nervous system reproductive system
High
Medium 16 1
Low 12 40 22
Below cutoff 6 11 9

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000083615
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX139,309,329 - 139,310,678 (-)Ensembl
Rnor_6.0 EnsemblX144,035,883 - 144,037,294 (-)Ensembl
RefSeq Acc Id: NM_001401192   ⟹   NP_001388121
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X144,344,892 - 144,346,971 (-)NCBI
mRatBN7.2X139,308,608 - 139,310,687 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001388121 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ACJ31784 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000078873
  ENSRNOP00000078873.1
Reference Protein Sequences
RefSeq Acc Id: NP_001388121   ⟸   NM_001401192
- UniProtKB: A0A8I5ZM42 (UniProtKB/TrEMBL)
Protein Domains
HMG box

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1591839 AgrOrtholog
BioCyc Gene G2FUF-869 BioCyc
Ensembl Genes ENSRNOG00000058173 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000083615 ENTREZGENE
  ENSRNOT00000083615.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
InterPro HMG_box_dom UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/TrEMBL
  SOX_fam UniProtKB/TrEMBL
NCBI Gene 679158 ENTREZGENE
PANTHER PTHR10270:SF111 UniProtKB/TrEMBL
  SOX TRANSCRIPTION FACTOR UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/TrEMBL
  SOXp UniProtKB/TrEMBL
PhenoGen Sox3 PhenoGen
PROSITE HMG_BOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000058173 RatGTEx
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/TrEMBL
UniProt A0A8I5ZM42 ENTREZGENE, UniProtKB/TrEMBL
  B7T0X1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-05 Sox3  SRY-box transcription factor 3  Sox3  SRY-box 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-12-17 Sox3  SRY-box 3  LOC679158  similar to SRY (sex determining region Y)-box 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC679158  similar to SRY (sex determining region Y)-box 3      Symbol and Name status set to provisional 70820 PROVISIONAL