Sox5 (SRY-box transcription factor 5) - Rat Genome Database

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Gene: Sox5 (SRY-box transcription factor 5) Rattus norvegicus
Analyze
Symbol: Sox5
Name: SRY-box transcription factor 5
RGD ID: 620471
Description: Enables cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including asymmetric neuroblast division; cartilage development; and positive regulation of cell differentiation. Predicted to act upstream of or within several processes, including neurogenesis; regulation of DNA-templated transcription; and regulation of timing of neuron differentiation. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Orthologous to human SOX5 (SRY-box transcription factor 5); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Sox5l1; SRY (sex determining region Y)-box 5; SRY box 5; SRY-box containing gene 5; SRY-box containing gene 5-like 1; transcription factor SOX-5
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
mRatBN7.24176,781,375 - 177,736,833 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4176,785,892 - 177,736,852 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4183,088,517 - 183,461,996 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.04178,872,831 - 179,246,322 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.04177,493,406 - 177,866,892 (-)NCBIRnor_WKY
Rnor_6.04178,062,267 - 179,031,991 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4178,066,165 - 178,441,547 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04242,266,295 - 243,221,217 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44181,558,995 - 181,931,117 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14181,825,983 - 182,011,429 (-)NCBI
Celera4165,313,274 - 165,629,808 (-)NCBICelera
Cytogenetic Map4q44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(1->4)-beta-D-glucan  (ISO)
1,2-dichloroethane  (ISO)
17alpha-ethynylestradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
4,4'-sulfonyldiphenol  (ISO)
8-Br-cAMP  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
caffeine  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
deguelin  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
fenthion  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
genistein  (EXP,ISO)
glyphosate  (EXP)
leflunomide  (ISO)
methapyrilene  (ISO)
methidathion  (ISO)
methylmercury chloride  (ISO)
N,N-diethyl-m-toluamide  (EXP)
O-methyleugenol  (ISO)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
permethrin  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
potassium dichromate  (ISO)
propiconazole  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (ISO)
tributylstannane  (ISO)
trichloroethene  (EXP)
tris(2-butoxyethyl) phosphate  (ISO)
troglitazone  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis. Liu CF and Lefebvre V, Nucleic Acids Res. 2015 Sep 30;43(17):8183-203. doi: 10.1093/nar/gkv688. Epub 2015 Jul 6.
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Sox5 and Sox6 are required for notochord extracellular matrix sheath formation, notochord cell survival and development of the nucleus pulposus of intervertebral discs. Smits P and Lefebvre V, Development 2003 Mar;130(6):1135-48.
8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:9755172   PMID:15634692   PMID:17084361   PMID:18215621   PMID:20668334   PMID:20940257   PMID:21073445   PMID:21401405   PMID:22344693   PMID:23946438   PMID:24854956   PMID:26345464  
PMID:26525805  


Genomics

Comparative Map Data
Sox5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24176,781,375 - 177,736,833 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4176,785,892 - 177,736,852 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4183,088,517 - 183,461,996 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.04178,872,831 - 179,246,322 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.04177,493,406 - 177,866,892 (-)NCBIRnor_WKY
Rnor_6.04178,062,267 - 179,031,991 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4178,066,165 - 178,441,547 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04242,266,295 - 243,221,217 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44181,558,995 - 181,931,117 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14181,825,983 - 182,011,429 (-)NCBI
Celera4165,313,274 - 165,629,808 (-)NCBICelera
Cytogenetic Map4q44NCBI
SOX5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381223,529,504 - 24,562,650 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1223,529,504 - 24,562,544 (-)EnsemblGRCh38hg38GRCh38
GRCh371223,682,438 - 24,715,425 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361223,576,498 - 24,606,647 (-)NCBINCBI36Build 36hg18NCBI36
Celera1228,833,198 - 29,862,278 (-)NCBICelera
Cytogenetic Map12p12.1NCBI
HuRef1223,452,599 - 24,484,456 (-)NCBIHuRef
CHM1_11223,650,324 - 24,680,623 (-)NCBICHM1_1
T2T-CHM13v2.01223,401,301 - 24,433,529 (-)NCBIT2T-CHM13v2.0
Sox5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396143,774,151 - 144,728,008 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6143,774,151 - 144,727,703 (-)EnsemblGRCm39 Ensembl
GRCm386143,828,425 - 144,782,287 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6143,828,425 - 144,781,977 (-)EnsemblGRCm38mm10GRCm38
MGSCv376143,781,349 - 144,158,078 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366143,790,051 - 144,166,639 (-)NCBIMGSCv36mm8
Celera6146,885,590 - 147,265,302 (-)NCBICelera
Cytogenetic Map6G3NCBI
cM Map676.14NCBI
Sox5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541318,831,931 - 19,204,217 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541318,831,931 - 19,676,371 (-)NCBIChiLan1.0ChiLan1.0
SOX5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan11272,249,780 - 73,280,539 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01262,361,631 - 62,780,805 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11264,973,019 - 65,391,500 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1264,971,818 - 65,388,694 (+)Ensemblpanpan1.1panPan2
SOX5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12722,857,661 - 23,855,709 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2723,452,985 - 23,851,380 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2722,515,990 - 23,511,350 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02723,058,695 - 24,061,457 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2723,059,559 - 24,061,452 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12722,871,574 - 23,867,072 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02722,890,892 - 23,887,914 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02722,685,794 - 23,683,255 (-)NCBIUU_Cfam_GSD_1.0
Sox5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494584,725,370 - 85,677,233 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365483,213,466 - 3,599,425 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365483,213,305 - 3,599,876 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOX5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl549,504,551 - 50,161,558 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1549,159,950 - 50,166,463 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2553,008,491 - 53,806,316 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SOX5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11123,298,622 - 24,131,712 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1123,303,325 - 23,715,492 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606910,803,456 - 11,833,677 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sox5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475214,985,942 - 15,378,465 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475214,986,146 - 15,382,687 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sox5
4331 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:114
Count of miRNA genes:90
Interacting mature miRNAs:98
Transcripts:ENSRNOT00000020729
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat

Markers in Region
D9Rat28  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,973,326 - 176,973,650 (+)MAPPERmRatBN7.2
Rnor_6.04178,253,454 - 178,253,777NCBIRnor6.0
Rnor_5.04242,456,468 - 242,456,791UniSTSRnor5.0
RGSC_v3.44181,645,676 - 181,646,000RGDRGSC3.4
RGSC_v3.44181,645,677 - 181,646,000UniSTSRGSC3.4
RGSC_v3.14181,890,801 - 181,891,124RGD
Celera4165,498,972 - 165,499,295UniSTS
RH 3.4 Map41062.3RGD
RH 3.4 Map41062.3UniSTS
Cytogenetic Map4q44UniSTS
D4Got154  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,951,334 - 176,951,490 (+)MAPPERmRatBN7.2
Rnor_6.04178,231,463 - 178,231,618NCBIRnor6.0
Rnor_5.04242,434,477 - 242,434,632UniSTSRnor5.0
RGSC_v3.44181,623,685 - 181,623,841RGDRGSC3.4
RGSC_v3.44181,623,686 - 181,623,841UniSTSRGSC3.4
RGSC_v3.14181,868,810 - 181,868,965RGD
Celera4165,476,979 - 165,477,134UniSTS
RH 3.4 Map41013.5RGD
RH 3.4 Map41013.5UniSTS
RH 2.0 Map41105.3RGD
Cytogenetic Map4q44UniSTS
BE108803  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,860,248 - 176,860,432 (+)MAPPERmRatBN7.2
Rnor_6.04178,141,125 - 178,141,308NCBIRnor6.0
Rnor_5.04242,344,099 - 242,344,282UniSTSRnor5.0
RGSC_v3.44180,472,699 - 180,472,882UniSTSRGSC3.4
Celera4165,387,487 - 165,387,670UniSTS
RH 3.4 Map41057.9UniSTS
Cytogenetic Map4q44UniSTS
RH134712  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,786,011 - 176,786,169 (+)MAPPERmRatBN7.2
Rnor_6.04178,066,907 - 178,067,064NCBIRnor6.0
Rnor_5.04242,270,935 - 242,271,092UniSTSRnor5.0
RGSC_v3.44180,399,064 - 180,399,221UniSTSRGSC3.4
Celera4165,313,400 - 165,313,557UniSTS
RH 3.4 Map41057.9UniSTS
Cytogenetic Map4q44UniSTS
Sox5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24176,786,012 - 176,786,632 (+)MAPPERmRatBN7.2
Rnor_6.04178,066,908 - 178,067,527NCBIRnor6.0
Rnor_5.04242,270,936 - 242,271,555UniSTSRnor5.0
RGSC_v3.44180,399,065 - 180,399,684UniSTSRGSC3.4
Celera4165,313,401 - 165,314,020UniSTS
Cytogenetic Map4q44UniSTS


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 6 6 6 47 11 2
Low 2 41 51 35 19 35 7 7 27 35 30 9 7
Below cutoff 1 2 1 4 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001014060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001271267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001415821 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001415822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001415823 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763349 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592402 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592403 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592404 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592405 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592406 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592407 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592408 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592409 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592410 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106953 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB073719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC121477 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC086415 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000020729   ⟹   ENSRNOP00000020729
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4176,785,892 - 177,736,852 (-)Ensembl
Rnor_6.0 Ensembl4178,067,051 - 178,168,690 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000055542   ⟹   ENSRNOP00000052404
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4176,785,892 - 177,159,525 (-)Ensembl
Rnor_6.0 Ensembl4178,066,787 - 178,441,547 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087434   ⟹   ENSRNOP00000073853
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4176,785,892 - 177,208,076 (-)Ensembl
Rnor_6.0 Ensembl4178,066,165 - 178,441,547 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096663   ⟹   ENSRNOP00000079278
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4176,785,892 - 177,736,852 (-)Ensembl
RefSeq Acc Id: NM_001271267   ⟹   NP_001258196
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,785,886 - 177,159,525 (-)NCBI
Rnor_6.04178,066,781 - 178,441,547 (-)NCBI
Rnor_5.04242,266,295 - 243,221,217 (-)NCBI
Celera4165,313,274 - 165,629,808 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237604   ⟹   XP_006237666
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,159,576 (-)NCBI
Rnor_6.04178,062,267 - 178,441,601 (-)NCBI
Rnor_5.04242,266,295 - 243,221,217 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763349   ⟹   XP_008761571
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,159,641 (-)NCBI
Rnor_6.04178,062,267 - 178,441,669 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763350   ⟹   XP_008761572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,715 - 176,893,809 (-)NCBI
Rnor_6.04178,062,267 - 178,174,280 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592402   ⟹   XP_017447891
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,736,833 (-)NCBI
Rnor_6.04178,062,267 - 179,031,991 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592404   ⟹   XP_017447893
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,154,286 (-)NCBI
Rnor_6.04178,062,267 - 178,436,745 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592405   ⟹   XP_017447894
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,159,641 (-)NCBI
Rnor_6.04178,062,267 - 178,441,669 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592406   ⟹   XP_017447895
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,736,831 (-)NCBI
Rnor_6.04178,062,267 - 179,031,991 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592407   ⟹   XP_017447896
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,159,575 (-)NCBI
Rnor_6.04178,062,267 - 178,441,601 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592408   ⟹   XP_017447897
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,159,641 (-)NCBI
Rnor_6.04178,062,267 - 178,441,669 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592409   ⟹   XP_017447898
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 176,889,262 (-)NCBI
Rnor_6.04178,062,267 - 178,169,792 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592410   ⟹   XP_017447899
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,715 - 176,893,809 (-)NCBI
Rnor_6.04178,062,267 - 178,174,275 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039106952   ⟹   XP_038962880
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,237,409 (-)NCBI
RefSeq Acc Id: XM_039106953   ⟹   XP_038962881
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 177,736,833 (-)NCBI
RefSeq Acc Id: XM_039106955   ⟹   XP_038962883
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24176,781,375 - 176,889,262 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001258196   ⟸   NM_001271267
- UniProtKB: Q5U1X4 (UniProtKB/Swiss-Prot),   F1M8W4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237666   ⟸   XM_006237604
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008761571   ⟸   XM_008763349
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008761572   ⟸   XM_008763350
- Peptide Label: isoform X12
- UniProtKB: Q5U1X4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447895   ⟸   XM_017592406
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017447891   ⟸   XM_017592402
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017447897   ⟸   XM_017592408
- Peptide Label: isoform X8
- UniProtKB: A0A0G2K6K9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447894   ⟸   XM_017592405
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017447896   ⟸   XM_017592407
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017447893   ⟸   XM_017592404
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017447899   ⟸   XM_017592410
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017447898   ⟸   XM_017592409
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: ENSRNOP00000052404   ⟸   ENSRNOT00000055542
RefSeq Acc Id: ENSRNOP00000073853   ⟸   ENSRNOT00000087434
RefSeq Acc Id: ENSRNOP00000020729   ⟸   ENSRNOT00000020729
RefSeq Acc Id: XP_038962881   ⟸   XM_039106953
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038962880   ⟸   XM_039106952
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038962883   ⟸   XM_039106955
- Peptide Label: isoform X11
RefSeq Acc Id: ENSRNOP00000079278   ⟸   ENSRNOT00000096663
Protein Domains
HMG box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M8W4-F1-model_v2 AlphaFold F1M8W4 1-763 view protein structure

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:620471 AgrOrtholog
BioCyc Gene G2FUF-42476 BioCyc
Ensembl Genes ENSRNOG00000027869 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020729.7 UniProtKB/TrEMBL
  ENSRNOP00000052404 ENTREZGENE
  ENSRNOP00000052404.3 UniProtKB/Swiss-Prot
  ENSRNOP00000073853 ENTREZGENE
  ENSRNOP00000073853.2 UniProtKB/TrEMBL
  ENSRNOP00000079278 ENTREZGENE
  ENSRNOP00000079278.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020729.7 UniProtKB/TrEMBL
  ENSRNOT00000055542 ENTREZGENE
  ENSRNOT00000055542.4 UniProtKB/Swiss-Prot
  ENSRNOT00000087434 ENTREZGENE
  ENSRNOT00000087434.2 UniProtKB/TrEMBL
  ENSRNOT00000096663 ENTREZGENE
  ENSRNOT00000096663.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7131922 IMAGE-MGC_LOAD
InterPro HMG_box_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:140587 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105885 IMAGE-MGC_LOAD
NCBI Gene 140587 ENTREZGENE
PANTHER FI18025P1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRANSCRIPTION FACTOR SOX-5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sox5 PhenoGen
PROSITE HMG_BOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HMG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K6K9 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZMP4_RAT UniProtKB/TrEMBL
  A0A8L2QAC4_RAT UniProtKB/TrEMBL
  F1M8W4 ENTREZGENE
  Q5U1X4 ENTREZGENE
  SOX5_RAT UniProtKB/Swiss-Prot
UniProt Secondary F1LQN4 UniProtKB/Swiss-Prot
  Q5U1X4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-05 Sox5  SRY-box transcription factor 5  Sox5  SRY box 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-12 Sox5  SRY box 5  Sox5  SRY (sex determining region Y)-box 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-02 Sox5  SRY (sex determining region Y)-box 5  Sox5l1  SRY-box containing gene 5-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-04-17 Sox5l1  SRY-box containing gene 5-like 1  Sox5  SRY (sex determining region Y)-box 5  Data Merged 737654 PROVISIONAL
2010-04-20 Sox5  SRY (sex determining region Y)-box 5  LOC312831  similar to SRY (sex determining region Y)-box 5 isoform a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 LOC312831  similar to SRY (sex determining region Y)-box 5 isoform a      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-07-08 Sox5  SRY-box containing gene 5    SRY (sex determining region Y)-box 5  Name updated 1299863 APPROVED
2002-08-07 Sox5  SRY (sex determining region Y)-box 5      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference