Sox17 (SRY-box transcription factor 17) - Rat Genome Database

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Gene: Sox17 (SRY-box transcription factor 17) Rattus norvegicus
Analyze
Symbol: Sox17
Name: SRY-box transcription factor 17
RGD ID: 1305371
Description: Enables sequence-specific double-stranded DNA binding activity. Involved in response to alkaloid. Located in nucleus. Biomarker of cholangiocarcinoma and pulmonary hypertension. Human ortholog(s) of this gene implicated in intracranial aneurysm; patent ductus arteriosus; and vesicoureteral reflux. Orthologous to human SOX17 (SRY-box transcription factor 17); PARTICIPATES IN Wnt signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC312936; SRY (sex determining region Y)-box 17; SRY box 17; SRY-box containing gene 17; transcription factor SOX-17
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8519,814,345 - 19,819,859 (+)NCBIGRCr8
mRatBN7.2515,016,660 - 15,022,228 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl515,016,731 - 15,022,228 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx517,215,894 - 17,221,391 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0518,819,700 - 18,825,180 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0518,550,534 - 18,556,035 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0514,890,318 - 14,895,907 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl514,890,408 - 14,895,907 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0519,675,563 - 19,681,084 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4515,241,405 - 15,246,904 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1515,244,440 - 15,246,899 (+)NCBI
Celera514,398,084 - 14,403,591 (+)NCBICelera
Cytogenetic Map5q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-bromo-2'-deoxyuridine  (ISO)
5-fluorouracil  (ISO)
6-aminonicotinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acetic acid  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
all-trans-retinol  (ISO)
angiotensin II  (ISO)
Aroclor 1254  (EXP)
arsenite(3-)  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromochloroacetic acid  (ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (ISO)
calciol  (ISO)
camptothecin  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
CHIR 99021  (ISO)
Chlorophacinone  (ISO)
chloroprene  (ISO)
chlorpyrifos  (ISO)
chrysene  (ISO)
columbamine  (ISO)
Cuprizon  (EXP)
diethylstilbestrol  (ISO)
dimethyl sulfoxide  (ISO)
diniconazole  (ISO)
dinoseb  (ISO)
diquat  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
fenvalerate  (EXP)
fluazinam  (ISO)
flusilazole  (ISO)
folic acid  (ISO)
gefitinib  (ISO)
genistein  (EXP,ISO)
gentamycin  (EXP)
hexaconazole  (ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
isoprenaline  (ISO)
isotretinoin  (ISO)
lead(0)  (ISO)
Licochalcone B  (ISO)
lipopolysaccharide  (ISO)
maleic acid  (ISO)
methamphetamine  (EXP)
mianserin  (ISO)
mifepristone  (EXP)
monocrotaline  (EXP)
N-acetyl-L-cysteine  (ISO)
N-nitrosodiethylamine  (ISO)
naphthalene  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
remdesivir  (ISO)
resveratrol  (EXP,ISO)
ritanserin  (ISO)
SB 431542  (ISO)
SCH 23390  (EXP)
silicon dioxide  (ISO)
sorafenib  (ISO)
sunitinib  (ISO)
tetrachloroethene  (ISO)
tetraphene  (ISO)
thalidomide  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
topotecan  (EXP)
trichloroethene  (EXP,ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
valproic acid  (ISO)
vandetanib  (ISO)
vinclozolin  (EXP)
ziprasidone  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
angiogenesis  (IBA,ISO)
cardiac cell fate determination  (ISO)
cardiogenic plate morphogenesis  (ISO)
cell migration involved in gastrulation  (ISO)
cellular response to leukemia inhibitory factor  (ISO)
common bile duct development  (ISO)
embryonic foregut morphogenesis  (ISO)
embryonic heart tube development  (ISO)
embryonic heart tube morphogenesis  (ISO)
embryonic organ development  (ISO)
endocardial cell differentiation  (ISO)
endocardium formation  (ISO)
endoderm development  (ISO)
endoderm formation  (IBA,ISO)
endodermal cell differentiation  (ISO)
endodermal cell fate determination  (ISO)
endodermal cell fate specification  (ISO)
endodermal digestive tract morphogenesis  (ISO)
gallbladder development  (ISO)
gastrulation  (ISO)
gene expression  (ISO)
heart development  (IBA,ISO)
heart looping  (ISO)
inner cell mass cellular morphogenesis  (ISO)
metanephros development  (ISO)
negative regulation of canonical Wnt signaling pathway  (IBA,ISO)
negative regulation of cell growth  (ISO)
negative regulation of Wnt signaling pathway  (ISO)
outflow tract morphogenesis  (ISO)
positive regulation of DNA-templated transcription  (ISO)
positive regulation of endodermal cell differentiation  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of protein catabolic process  (ISO)
positive regulation of stem cell differentiation  (ISO)
positive regulation of transcription by RNA polymerase II  (IBA,ISO)
protein destabilization  (ISO)
protein stabilization  (ISO)
regulation of cardiac cell fate specification  (ISO)
regulation of cell differentiation  (ISO)
regulation of DNA-templated transcription  (ISO)
regulation of embryonic development  (ISO)
regulation of stem cell division  (ISO)
regulation of stem cell proliferation  (ISO)
regulation of transcription by RNA polymerase II  (ISO)
response to alkaloid  (IEP)
rostrocaudal neural tube patterning  (ISO)
signal transduction involved in regulation of gene expression  (ISO)
spermatogenesis  (ISO)
stem cell differentiation  (ISO)
stem cell fate specification  (ISO)
ureter development  (ISO)
vasculogenesis  (IBA,ISO)
Wnt signaling pathway  (IEA)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Susceptibility loci for intracranial aneurysm in European and Japanese populations. Bilguvar K, etal., Nat Genet. 2008 Dec;40(12):1472-7. doi: 10.1038/ng.240. Epub 2008 Nov 9.
2. Differential gene expression profiling of cultured neu-transformed versus spontaneously-transformed rat cholangiocytes and of corresponding cholangiocarcinomas. Dumur CI, etal., Exp Mol Pathol. 2010 Dec;89(3):227-35. Epub 2010 Sep 9.
3. Genome-wide association study of intracranial aneurysms confirms role of Anril and SOX17 in disease risk. Foroud T, etal., Stroke. 2012 Nov;43(11):2846-52. doi: 10.1161/STROKEAHA.112.656397. Epub 2012 Sep 6.
4. 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.
5. Identification of rare sequence variation underlying heritable pulmonary arterial hypertension. Gräf S, etal., Nat Commun. 2018 Apr 12;9(1):1416. doi: 10.1038/s41467-018-03672-4.
6. Common genetic variants in pulmonary arterial hypertension. Gu S, etal., Lancet Respir Med. 2019 Mar;7(3):190-191. doi: 10.1016/S2213-2600(18)30448-X. Epub 2018 Dec 5.
7. Association of SOX17 Gene Polymorphisms and Intracranial Aneurysm: A Case-Control Study and Meta-Analysis. Hong EP, etal., World Neurosurg. 2018 Feb;110:e823-e829. doi: 10.1016/j.wneu.2017.11.108. Epub 2017 Nov 27.
8. Deficiency of endothelium-specific transcription factor Sox17 induces intracranial aneurysm. Lee S, etal., Circulation. 2015 Mar 17;131(11):995-1005. doi: 10.1161/CIRCULATIONAHA.114.012568. Epub 2015 Jan 16.
9. Associations among Genetic Variants and Intracranial Aneurysm in a Chinese Population. Li B, etal., Yonsei Med J. 2019 Jul;60(7):651-658. doi: 10.3349/ymj.2019.60.7.651.
10. Genetic polymorphisms in Sox17 associated with intracranial aneurysm in Chinese Han people: a genotype-phenotype study. Li M, etal., Neuropsychiatr Dis Treat. 2019 Apr 2;15:779-783. doi: 10.2147/NDT.S193478. eCollection 2019.
11. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
12. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
13. Sox17 Deficiency Promotes Pulmonary Arterial Hypertension via HGF/c-Met Signaling. Park CS, etal., Circ Res. 2022 Oct 28;131(10):792-806. doi: 10.1161/CIRCRESAHA.122.320845. Epub 2022 Oct 7.
14. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
15. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
17. Comprehensive gene review and curation RGD comprehensive gene curation
18. Conserved regulatory motifs at phenylethanolamine N-methyltransferase (PNMT) are disrupted by common functional genetic variation: an integrated computational/experimental approach. Rodríguez-Flores JL, etal., Mamm Genome. 2010 Apr;21(3-4):195-204. doi: 10.1007/s00335-010-9253-y. Epub 2010 Mar 5.
19. SOX17 Deficiency Mediates Pulmonary Hypertension: At the Crossroads of Sex, Metabolism, and Genetics. Sangam S, etal., Am J Respir Crit Care Med. 2023 Apr 15;207(8):1055-1069. doi: 10.1164/rccm.202203-0450OC.
20. SOX17 Enhancer Variants Disrupt Transcription Factor Binding And Enhancer Inactivity Drives Pulmonary Hypertension. Walters R, etal., Circulation. 2023 May 23;147(21):1606-1621. doi: 10.1161/CIRCULATIONAHA.122.061940. Epub 2023 Apr 17.
21. Upregulated miR-194-5p suppresses retinal microvascular endothelial cell dysfunction and mitigates the symptoms of hypertensive retinopathy in mice by targeting SOX17 and VEGF signaling. Wan Q, etal., Cell Cycle. 2023 Feb;22(3):331-346. doi: 10.1080/15384101.2022.2119514. Epub 2022 Oct 5.
22. SOX17 Loss-of-Function Mutation Underlying Familial Pulmonary Arterial Hypertension. Wang TM, etal., Int Heart J. 2021 May 29;62(3):566-574. doi: 10.1536/ihj.20-711. Epub 2021 May 1.
23. Dll4 Suppresses Transcytosis for Arterial Blood-Retinal Barrier Homeostasis. Yang JM, etal., Circ Res. 2020 Mar 13;126(6):767-783. doi: 10.1161/CIRCRESAHA.119.316476. Epub 2020 Feb 12.
24. Genome-wide association study of intracranial aneurysm identifies three new risk loci. Yasuno K, etal., Nat Genet. 2010 May;42(5):420-5. doi: 10.1038/ng.563. Epub 2010 Apr 4.
25. SOX17 loss-of-function variation underlying familial congenital heart disease. Zhao L, etal., Eur J Med Genet. 2021 May;64(5):104211. doi: 10.1016/j.ejmg.2021.104211. Epub 2021 Mar 29.
26. Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease. Zhu N, etal., Genome Med. 2018 Jul 20;10(1):56. doi: 10.1186/s13073-018-0566-x.
27. SOX17 is a Critical Factor in Maintaining Endothelial Function in Pulmonary Hypertension by an Exosome-Mediated Autocrine Manner. Zou X, etal., Adv Sci (Weinh). 2023 May;10(14):e2206139. doi: 10.1002/advs.202206139. Epub 2023 Mar 15.
Additional References at PubMed
PMID:8636240   PMID:11973269   PMID:12477932   PMID:15082719   PMID:15220343   PMID:16574095   PMID:16895970   PMID:17360443   PMID:17610846   PMID:17655922   PMID:17875931   PMID:17940068  
PMID:18413743   PMID:18462699   PMID:18682240   PMID:19328208   PMID:19515696   PMID:19619492   PMID:19736317   PMID:19913509   PMID:20123909   PMID:20228271   PMID:20308546   PMID:20439489  
PMID:20802155   PMID:20960469   PMID:21146513   PMID:21305474   PMID:22292085   PMID:22344693   PMID:23824537   PMID:25209250  


Genomics

Comparative Map Data
Sox17
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8519,814,345 - 19,819,859 (+)NCBIGRCr8
mRatBN7.2515,016,660 - 15,022,228 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl515,016,731 - 15,022,228 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx517,215,894 - 17,221,391 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0518,819,700 - 18,825,180 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0518,550,534 - 18,556,035 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0514,890,318 - 14,895,907 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl514,890,408 - 14,895,907 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0519,675,563 - 19,681,084 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4515,241,405 - 15,246,904 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1515,244,440 - 15,246,899 (+)NCBI
Celera514,398,084 - 14,403,591 (+)NCBICelera
Cytogenetic Map5q12NCBI
SOX17
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38854,457,935 - 54,460,892 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl854,457,935 - 54,460,892 (+)EnsemblGRCh38hg38GRCh38
GRCh37855,370,495 - 55,373,452 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36855,533,048 - 55,536,009 (+)NCBINCBI36Build 36hg18NCBI36
Build 34855,533,047 - 55,535,484NCBI
Celera851,361,039 - 51,364,000 (+)NCBICelera
Cytogenetic Map8q11.23NCBI
HuRef850,838,617 - 50,841,578 (+)NCBIHuRef
CHM1_1855,422,260 - 55,425,221 (+)NCBICHM1_1
T2T-CHM13v2.0854,835,189 - 54,838,146 (+)NCBIT2T-CHM13v2.0
Sox17
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914,561,154 - 4,567,624 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14,561,154 - 4,567,577 (-)EnsemblGRCm39 Ensembl
GRCm3814,490,928 - 4,497,426 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14,490,931 - 4,497,354 (-)EnsemblGRCm38mm10GRCm38
MGSCv3714,481,009 - 4,486,494 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614,481,009 - 4,486,494 (-)NCBIMGSCv36mm8
Celera14,507,797 - 4,513,282 (-)NCBICelera
Cytogenetic Map1A1NCBI
cM Map11.65NCBI
Sox17
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495545413,689,403 - 13,690,019 (+)NCBIChiLan1.0ChiLan1.0
SOX17
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2770,094,723 - 70,097,191 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1845,819,721 - 45,822,171 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0850,883,088 - 50,885,542 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1848,257,287 - 48,259,808 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl848,257,287 - 48,259,808 (+)Ensemblpanpan1.1panPan2
SOX17
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1295,979,092 - 5,981,504 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl295,979,261 - 5,981,124 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha296,289,199 - 6,291,617 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0296,057,575 - 6,059,968 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl296,057,528 - 6,059,963 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1295,992,409 - 5,994,803 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0296,198,380 - 6,200,809 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0296,377,256 - 6,379,697 (+)NCBIUU_Cfam_GSD_1.0
Sox17
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530373,534,065 - 73,536,600 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364961,248,577 - 1,251,430 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364961,248,582 - 1,251,406 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOX17
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl476,854,150 - 76,857,148 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1476,854,218 - 76,857,143 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2483,968,236 - 83,971,155 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SOX17
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1850,523,816 - 50,527,360 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl850,524,893 - 50,527,847 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603991,335,953 - 91,338,947 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sox17
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247351,276,302 - 1,279,181 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247351,276,382 - 1,278,584 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sox17
43 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:76
Count of miRNA genes:61
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000033116
Prediction methods: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
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5818750118616199Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat

Markers in Region
RH130629  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2515,021,882 - 15,022,085 (+)MAPPERmRatBN7.2
Rnor_6.0514,895,562 - 14,895,764NCBIRnor6.0
Rnor_5.0519,680,739 - 19,680,941UniSTSRnor5.0
RGSC_v3.4515,246,559 - 15,246,761UniSTSRGSC3.4
Celera514,403,246 - 14,403,448UniSTS
Cytogenetic Map5q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001107902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237809 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237812 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763537 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763538 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593323 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593325 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593326 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593327 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109751 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109752 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287521 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287522 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063287523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC166978 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473984 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000033116   ⟹   ENSRNOP00000033962
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl515,016,731 - 15,022,228 (+)Ensembl
Rnor_6.0 Ensembl514,890,408 - 14,895,907 (+)Ensembl
RefSeq Acc Id: NM_001107902   ⟹   NP_001101372
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8519,814,360 - 19,819,859 (+)NCBI
mRatBN7.2515,016,731 - 15,022,228 (+)NCBI
Rnor_6.0514,890,408 - 14,895,907 (+)NCBI
Rnor_5.0519,675,563 - 19,681,084 (+)NCBI
RGSC_v3.4515,241,405 - 15,246,904 (+)RGD
Celera514,398,084 - 14,403,591 (+)RGD
Sequence:
RefSeq Acc Id: XM_008763538   ⟹   XP_008761760
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8519,815,653 - 19,819,857 (+)NCBI
mRatBN7.2515,018,030 - 15,022,226 (+)NCBI
Rnor_6.0514,890,318 - 14,895,905 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039109751   ⟹   XP_038965679
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8519,814,347 - 19,819,857 (+)NCBI
mRatBN7.2515,016,660 - 15,022,226 (+)NCBI
RefSeq Acc Id: XM_039109752   ⟹   XP_038965680
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8519,814,345 - 19,819,857 (+)NCBI
mRatBN7.2515,016,660 - 15,022,226 (+)NCBI
RefSeq Acc Id: XM_039109753   ⟹   XP_038965681
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8519,814,345 - 19,819,857 (+)NCBI
mRatBN7.2515,016,660 - 15,022,226 (+)NCBI
RefSeq Acc Id: XM_063287521   ⟹   XP_063143591
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8519,814,345 - 19,819,857 (+)NCBI
RefSeq Acc Id: XM_063287522   ⟹   XP_063143592
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8519,814,361 - 19,819,857 (+)NCBI
RefSeq Acc Id: XM_063287523   ⟹   XP_063143593
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8519,814,345 - 19,819,857 (+)NCBI
RefSeq Acc Id: NP_001101372   ⟸   NM_001107902
- UniProtKB: G3V923 (UniProtKB/TrEMBL),   A6JFJ9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008761760   ⟸   XM_008763538
- Peptide Label: isoform X1
- UniProtKB: G3V923 (UniProtKB/TrEMBL),   A6JFJ9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000033962   ⟸   ENSRNOT00000033116
RefSeq Acc Id: XP_038965681   ⟸   XM_039109753
- Peptide Label: isoform X1
- UniProtKB: G3V923 (UniProtKB/TrEMBL),   A6JFJ9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965680   ⟸   XM_039109752
- Peptide Label: isoform X1
- UniProtKB: G3V923 (UniProtKB/TrEMBL),   A6JFJ9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965679   ⟸   XM_039109751
- Peptide Label: isoform X1
- UniProtKB: G3V923 (UniProtKB/TrEMBL),   A6JFJ9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063143591   ⟸   XM_063287521
- Peptide Label: isoform X1
- UniProtKB: A6JFJ9 (UniProtKB/TrEMBL),   G3V923 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063143593   ⟸   XM_063287523
- Peptide Label: isoform X1
- UniProtKB: A6JFJ9 (UniProtKB/TrEMBL),   G3V923 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063143592   ⟸   XM_063287522
- Peptide Label: isoform X1
- UniProtKB: A6JFJ9 (UniProtKB/TrEMBL),   G3V923 (UniProtKB/TrEMBL)
Protein Domains
HMG box   Sox C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V923-F1-model_v2 AlphaFold G3V923 1-423 view protein structure

Transcriptome

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

Promoters
RGD ID:13693545
Promoter ID:EPDNEW_R4070
Type:single initiation site
Name:Sox17_1
Description:SRY box 17
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0514,890,411 - 14,890,471EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305371 AgrOrtholog
BioCyc Gene G2FUF-42146 BioCyc
Ensembl Genes ENSRNOG00000027357 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000033116.5 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
InterPro DUF3547 UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/TrEMBL
  HMG_superfamily UniProtKB/TrEMBL
  Sox7/17/18_central UniProtKB/TrEMBL
  SRY-related_HMG-box_TFs UniProtKB/TrEMBL
KEGG Report rno:312936 UniProtKB/TrEMBL
NCBI Gene 312936 ENTREZGENE
PANTHER SOX TRANSCRIPTION FACTOR UniProtKB/TrEMBL
  TRANSCRIPTION FACTOR SOX-17 UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/TrEMBL
  Sox_C_TAD UniProtKB/TrEMBL
PhenoGen Sox17 PhenoGen
PROSITE HMG_BOX_2 UniProtKB/TrEMBL
  SOX_C UniProtKB/TrEMBL
RatGTEx ENSRNOG00000027357 RatGTEx
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP HMG-box UniProtKB/TrEMBL
UniProt A6JFJ9 ENTREZGENE, UniProtKB/TrEMBL
  B2RZ07_RAT UniProtKB/TrEMBL
  G3V923 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-05 Sox17  SRY-box transcription factor 17  Sox17  SRY box 17  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-12 Sox17  SRY box 17  Sox17  SRY (sex determining region Y)-box 17  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-18 Sox17  SRY (sex determining region Y)-box 17  Sox17  SRY-box containing gene 17   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Sox17  SRY-box containing gene 17   Sox17_predicted  SRY-box containing gene 17 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Sox17_predicted  SRY-box containing gene 17 (predicted)      Symbol and Name status set to approved 70820 APPROVED