Sox18 (SRY-box transcription factor 18) - Rat Genome Database

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Gene: Sox18 (SRY-box transcription factor 18) Rattus norvegicus
Analyze
Symbol: Sox18
Name: SRY-box transcription factor 18
RGD ID: 1311718
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including establishment of endothelial barrier; regulation of transcription by RNA polymerase II; and vasculature development. Predicted to act upstream of or within several processes, including circulatory system development; regulation of transcription, DNA-templated; and stem cell fate specification. Predicted to be located in chromatin and nucleus. Predicted to be part of transcription regulator complex. Human ortholog(s) of this gene implicated in hypotrichosis-lymphedema-telangiectasia syndrome and hypotrichosis-lymphedema-telangiectasia-renal defect syndrome. Orthologous to human SOX18 (SRY-box transcription factor 18); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC311723; SRY (sex determining region Y)-box 18; SRY box 18; SRY-box containing gene 18; transcription factor SOX-18
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
mRatBN7.23168,785,488 - 168,787,290 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl3168,785,490 - 168,787,290 (-)Ensembl
Rnor_6.03177,177,237 - 177,179,039 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3177,177,310 - 177,179,127 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,885,768 - 180,887,570 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,820,460 - 170,822,262 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13170,726,497 - 170,728,298 (-)NCBI
Celera3163,800,470 - 163,802,272 (+)NCBICelera
Cytogenetic Map3q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (EXP)
choline  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
folic acid  (ISO)
glycidol  (EXP)
graphite  (EXP)
GW 4064  (ISO)
hesperetin  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
kenpaullone  (EXP)
L-methionine  (ISO)
lead diacetate  (EXP)
mercury atom  (ISO)
mercury(0)  (ISO)
methamphetamine  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nickel dichloride  (ISO)
nicotine  (ISO)
orphenadrine  (EXP)
oxaliplatin  (EXP)
paracetamol  (EXP,ISO)
phosgene  (ISO)
reactive oxygen species  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SCH 23390  (EXP)
silicon dioxide  (EXP)
Soman  (EXP)
temozolomide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP)
thapsigargin  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
topotecan  (EXP)
trichloroethene  (EXP,ISO)
triclosan  (ISO)
triphenyl phosphate  (EXP)
triptonide  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Mutations in the transcription factor gene SOX18 underlie recessive and dominant forms of hypotrichosis-lymphedema-telangiectasia. Irrthum A, etal., Am J Hum Genet. 2003 Jun;72(6):1470-8. Epub 2003 May 8.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:291594   PMID:7651823   PMID:10742113   PMID:11094083   PMID:11179689   PMID:11554755   PMID:12446692   PMID:12477932   PMID:14634005   PMID:16882943   PMID:16895968   PMID:16895970  
PMID:17610846   PMID:18065521   PMID:18931657   PMID:19429912   PMID:19515696   PMID:20228271   PMID:22292085   PMID:22344693  


Genomics

Comparative Map Data
Sox18
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23168,785,488 - 168,787,290 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl3168,785,490 - 168,787,290 (-)Ensembl
Rnor_6.03177,177,237 - 177,179,039 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3177,177,310 - 177,179,127 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,885,768 - 180,887,570 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,820,460 - 170,822,262 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13170,726,497 - 170,728,298 (-)NCBI
Celera3163,800,470 - 163,802,272 (+)NCBICelera
Cytogenetic Map3q43NCBI
SOX18
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382064,047,582 - 64,049,639 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2064,047,582 - 64,049,639 (-)EnsemblGRCh38hg38GRCh38
GRCh372062,678,935 - 62,680,992 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362062,149,523 - 62,151,423 (-)NCBINCBI36hg18NCBI36
Build 342062,149,524 - 62,151,423NCBI
Celera2059,365,185 - 59,367,085 (-)NCBI
Cytogenetic Map20q13.33NCBI
HuRef2059,413,178 - 59,414,764 (-)NCBIHuRef
CHM1_12062,580,086 - 62,582,001 (-)NCBICHM1_1
T2T-CHM13v2.02065,867,606 - 65,869,664 (-)NCBI
Sox18
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392181,311,630 - 181,313,433 (-)NCBIGRCm39mm39
GRCm39 Ensembl2181,311,629 - 181,313,433 (-)Ensembl
GRCm382181,669,837 - 181,671,640 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2181,669,836 - 181,671,640 (-)EnsemblGRCm38mm10GRCm38
MGSCv372181,404,542 - 181,406,345 (-)NCBIGRCm37mm9NCBIm37
MGSCv362181,599,249 - 181,601,015 (-)NCBImm8
Celera2185,752,229 - 185,754,032 (-)NCBICelera
Cytogenetic Map2H4NCBI
cM Map2103.71NCBI
Sox18
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955528204,729 - 206,772 (+)NCBIChiLan1.0ChiLan1.0
SOX18
(Pan paniscus - bonobo/pygmy chimpanzee)
No map positions available.
SOX18
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12447,494,581 - 47,496,563 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2447,494,902 - 47,496,970 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2446,628,401 - 46,630,374 (-)NCBI
ROS_Cfam_1.02448,633,494 - 48,635,467 (-)NCBI
ROS_Cfam_1.0 Ensembl2448,633,492 - 48,635,406 (-)Ensembl
UMICH_Zoey_3.12447,478,102 - 47,480,075 (-)NCBI
UNSW_CanFamBas_1.02447,602,566 - 47,604,541 (-)NCBI
UU_Cfam_GSD_1.02448,341,512 - 48,343,485 (-)NCBI
Sox18
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640195,777,684 - 195,779,662 (-)NCBI
SpeTri2.0NW_00493651411,231,327 - 11,233,292 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOX18
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1762,869,870 - 62,871,748 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11762,869,868 - 62,871,758 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SOX18
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12195,418 - 197,221 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605047,629,355 - 47,631,408 (+)NCBIVero_WHO_p1.0
Sox18
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474129,679,091 - 29,681,049 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462474129,679,274 - 29,681,069 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D3Hmgc21  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23168,787,741 - 168,787,906 (+)MAPPERmRatBN7.2
Rnor_6.03177,179,491 - 177,179,652NCBIRnor6.0
Rnor_5.03180,888,022 - 180,888,183UniSTSRnor5.0
RGSC_v3.43170,822,714 - 170,822,875UniSTSRGSC3.4
Celera3163,799,857 - 163,800,018UniSTS
Cytogenetic Map3q43UniSTS
AI385749  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23168,785,620 - 168,785,734 (+)MAPPERmRatBN7.2
Rnor_6.03177,177,370 - 177,177,483NCBIRnor6.0
Rnor_5.03180,885,901 - 180,886,014UniSTSRnor5.0
RGSC_v3.43170,820,593 - 170,820,706UniSTSRGSC3.4
Celera3163,802,026 - 163,802,139UniSTS
Cytogenetic Map3q43UniSTS
UniSTS:471103  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23168,786,412 - 168,787,008 (+)MAPPERmRatBN7.2
Rnor_6.03177,178,162 - 177,178,757NCBIRnor6.0
Rnor_5.03180,886,693 - 180,887,288UniSTSRnor5.0
RGSC_v3.43170,821,385 - 170,821,980UniSTSRGSC3.4
Celera3163,800,752 - 163,801,347UniSTS
Cytogenetic Map3q43UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3161192952169034231Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:55
Count of miRNA genes:44
Interacting mature miRNAs:51
Transcripts:ENSRNOT00000021790
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.


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 27 4 4 2 4 35 21 28 11
Low 3 16 52 37 16 37 8 11 39 14 11 8
Below cutoff 1 1 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021790   ⟹   ENSRNOP00000021790
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,785,490 - 168,787,290 (-)Ensembl
Rnor_6.0 Ensembl3177,177,310 - 177,179,127 (-)Ensembl
RefSeq Acc Id: NM_001024781   ⟹   NP_001019952
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23168,785,488 - 168,787,290 (-)NCBI
Rnor_6.03177,177,237 - 177,179,039 (-)NCBI
Rnor_5.03180,885,768 - 180,887,570 (-)NCBI
RGSC_v3.43170,820,460 - 170,822,262 (-)RGD
Celera3163,800,470 - 163,802,272 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001019952 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH97973 (Get FASTA)   NCBI Sequence Viewer  
  EDL88692 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001019952   ⟸   NM_001024781
- UniProtKB: Q4V7E4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000021790   ⟸   ENSRNOT00000021790
Protein Domains
HMG box   Sox C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4V7E4-F1-model_v2 AlphaFold Q4V7E4 1-377 view protein structure

Transcriptome

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

Promoters
RGD ID:13692762
Promoter ID:EPDNEW_R3286
Type:multiple initiation site
Name:Sox18_1
Description:SRY box 18
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_6.03177,179,050 - 177,179,110EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 180886697 180886698 G A snv IS-Tlk/Kyo (KyushuU), IS/Kyo (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311718 AgrOrtholog
BioCyc Gene G2FUF-46266 BioCyc
Ensembl Genes ENSRNOG00000016248 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021790 ENTREZGENE
  ENSRNOP00000021790.3 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021790 ENTREZGENE
  ENSRNOT00000021790.6 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7442067 IMAGE-MGC_LOAD
InterPro DUF3547 UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/TrEMBL
  HMG_superfamily UniProtKB/TrEMBL
  Sox7/17/18_central UniProtKB/TrEMBL
KEGG Report rno:311723 UniProtKB/TrEMBL
MGC_CLONE MGC:116103 IMAGE-MGC_LOAD
NCBI Gene 311723 ENTREZGENE
Pfam HMG_box UniProtKB/TrEMBL
  Sox_C_TAD UniProtKB/TrEMBL
PhenoGen Sox18 PhenoGen
PROSITE HMG_BOX_2 UniProtKB/TrEMBL
  SOX_C UniProtKB/TrEMBL
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP HMG-box UniProtKB/TrEMBL
UniProt Q4V7E4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-05 Sox18  SRY-box transcription factor 18  Sox18  SRY box 18  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-12 Sox18  SRY box 18  Sox18  SRY (sex determining region Y)-box 18  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-18 Sox18  SRY (sex determining region Y)-box 18  Sox18  SRY-box containing gene 18  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Sox18  SRY-box containing gene 18  Sox18_predicted  SRY-box containing gene 18 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Sox18_predicted  SRY-box containing gene 18 (predicted)      Symbol and Name status set to approved 70820 APPROVED