Srebf2 (sterol regulatory element binding transcription factor 2) - Rat Genome Database

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Gene: Srebf2 (sterol regulatory element binding transcription factor 2) Rattus norvegicus
Analyze
Symbol: Srebf2
Name: sterol regulatory element binding transcription factor 2
RGD ID: 1307751
Description: Enables chromatin binding activity and sequence-specific DNA binding activity. Involved in several processes, including positive regulation of transcription, DNA-templated; response to lead ion; and spermatogenesis. Located in cytoplasm; dendrite; and nucleus. Biomarker of kidney disease (multiple); lipid storage disease; obesity; and visual epilepsy. Human ortholog(s) of this gene implicated in carotid artery disease; prostate cancer; type 1 diabetes mellitus; type 2 diabetes mellitus; and vascular dementia. Orthologous to human SREBF2 (sterol regulatory element binding transcription factor 2); PARTICIPATES IN altered p53 signaling pathway; sterol regulatory element-binding protein signaling pathway; INTERACTS WITH (R)-mevalonic acid; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MGC124823; Srebf2_retired; SREBP-2; SREBP2; sterol regulatory element binding factor 2; sterol regulatory element binding protein 2; sterol regulatory element-binding protein 2; sterol regulatory element-binding transcription factor 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Srebf2_v2   Srebf2_v1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27113,663,202 - 113,720,850 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7113,663,202 - 113,720,848 (+)Ensembl
Rnor_6.07123,381,082 - 123,438,605 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7123,381,077 - 123,438,603 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07123,364,495 - 123,422,296 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47120,522,511 - 120,580,212 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17120,556,723 - 120,612,972 (+)NCBI
Celera7109,978,519 - 110,036,018 (+)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(R)-mevalonic acid  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dichloropropan-2-ol  (ISO)
1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,6-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
25-hydroxycholesterol  (ISO)
5-fluorouracil  (ISO)
acetamide  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
alliin  (ISO)
allopurinol  (EXP,ISO)
alpha-pinene  (ISO)
amitriptyline  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
aristolochic acid  (ISO)
aspartame  (ISO)
atorvastatin calcium  (EXP,ISO)
atrazine  (ISO)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (ISO)
beta-cyclodextrin  (ISO)
bezafibrate  (ISO)
bisphenol A  (EXP,ISO)
cadmium atom  (EXP)
cadmium dichloride  (EXP)
caffeine  (EXP,ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGS-21680  (ISO)
chlorpromazine  (ISO)
cholesterol  (EXP,ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
citalopram  (ISO)
clofibrate  (EXP)
clomipramine  (ISO)
clozapine  (ISO)
cobalt dichloride  (ISO)
colforsin daropate hydrochloride  (ISO)
crizotinib  (ISO)
CU-O LINKAGE  (ISO)
curcumin  (EXP,ISO)
cyclosporin A  (ISO)
D-glucose  (EXP,ISO)
DDT  (EXP)
dibutyl phthalate  (EXP)
diclofenac  (ISO)
dicrotophos  (ISO)
dinophysistoxin 1  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
ethanol  (ISO)
ezetimibe  (ISO)
fenarimol  (EXP)
fenvalerate  (EXP)
fisetin  (ISO)
Ganoderic acid A  (ISO)
geraniol  (ISO)
glafenine  (EXP)
glucose  (EXP,ISO)
glyphosate  (ISO)
haloperidol  (ISO)
herbacetin  (ISO)
hydrogen peroxide  (ISO)
imipramine  (ISO)
ketoconazole  (EXP)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP)
lead nitrate  (EXP)
linalool  (ISO)
lipopolysaccharide  (EXP,ISO)
lovastatin  (EXP,ISO)
mercury dichloride  (ISO)
metformin  (ISO)
mevastatin  (EXP,ISO)
microcystin-LR  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
Monobutylphthalate  (ISO)
monocrotophos  (EXP)
monosodium L-glutamate  (ISO)
myricetin  (EXP)
N,N-diethyl-m-toluamide  (EXP)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
obeticholic acid  (ISO)
okadaic acid  (ISO)
olanzapine  (EXP,ISO)
ozone  (EXP,ISO)
p-chloromercuribenzoic acid  (ISO)
p-menthan-3-ol  (ISO)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP)
phenylpropanolamine  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (EXP)
propiconazole  (EXP)
quercetin  (EXP,ISO)
quercetin 3-O-beta-D-glucofuranoside  (ISO)
quercetin 3-O-beta-D-glucopyranoside  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
simvastatin  (EXP,ISO)
sodium arsenate  (ISO)
Soman  (EXP)
streptozocin  (EXP,ISO)
sulindac sulfide  (ISO)
sunitinib  (ISO)
testosterone  (ISO)
thioacetamide  (EXP)
tributyl phosphate  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
tunicamycin  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Amemiya-Kudo M, etal., J Biol Chem. 2005 Oct 14;280(41):34577-89. Epub 2005 Jul 29.
2. Boizard M, etal., J Biol Chem. 1998 Oct 30;273(44):29164-71.
3. Boone LR, etal., Biochem Biophys Res Commun. 2009 May 24.
4. Chmielewski M, etal., Atherosclerosis. 2007 Apr;191(2):326-32. Epub 2006 Jun 30.
5. Cho EJ, etal., J Pharm Pharmacol. 2007 May;59(5):687-94.
6. Duan X, etal., J Lipid Res. 2005 Feb;46(2):252-7. Epub 2004 Nov 16.
7. Ettinger SL, etal., Cancer Res. 2004 Mar 15;64(6):2212-21.
8. Freed-Pastor WA and Prives C, Genes Dev. 2012 Jun 15;26(12):1268-86. doi: 10.1101/gad.190678.112.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. GOA data from the GO Consortium
11. Ishikawa M, etal., J Lipid Res. 2008 Dec;49(12):2524-34. Epub 2008 Aug 5.
12. Jiang T, etal., J Am Soc Nephrol. 2005 Aug;16(8):2385-94. Epub 2005 Jun 8.
13. Jiang T, etal., Kidney Int. 2005 Dec;68(6):2608-20.
14. Kim HJ and Vaziri ND, Am J Nephrol. 2009 Jan 16;29(6):607-614.
15. Kim JH and Ong WY, J Chem Neuroanat. 2009 Mar;37(2):71-7. Epub 2008 Dec 13.
16. Kim Y, etal., Am J Med Genet B Neuropsychiatr Genet. 2005 Nov 5;139(1):19-22.
17. Koch A, etal., J Nutr. 2007 Sep;137(9):2018-23.
18. Kojima M and Degawa M, J Appl Toxicol. 2006 Jul-Aug;26(4):381-4.
19. Lacasa D, etal., J Biol Chem. 2001 Apr 13;276(15):11512-6. Epub 2001 Jan 16.
20. MacLean PS, etal., J Clin Endocrinol Metab. 2005 Apr;90(4):2250-8. Epub 2005 Jan 11.
21. Marseille-Tremblay C, etal., Mol Reprod Dev. 2008 Jun;75(6):1054-62.
22. MGD data from the GO Consortium
23. Muller PA and Vousden KH, Nat Cell Biol. 2013 Jan;15(1):2-8. doi: 10.1038/ncb2641.
24. Muller PY and Miserez AR, J Med Genet. 2002 Apr;39(4):271-5.
25. Osborne TF and Espenshade PJ, Genes Dev. 2009 Nov 15;23(22):2578-91.
26. Pallottini V, etal., J Cell Biochem. 2006 Aug 1;98(5):1044-53.
27. Proctor G, etal., Diabetes. 2006 Sep;55(9):2502-9.
28. RGD automated data pipeline
29. RGD automated import pipeline for gene-chemical interactions
30. Robinet P, etal., Atherosclerosis. 2003 Jun;168(2):381-7.
31. Roglans N, etal., Biochem Pharmacol. 2001 Sep 15;62(6):803-9.
32. Ryan JF and Booth CM, Br J Urol. 1992 Apr;69(4):430-1.
33. Wang H, etal., Biol Reprod. 2006 Sep;75(3):318-23. Epub 2006 May 24.
34. Wang H, etal., Mol Cell Biol 2002 Dec;22(24):8478-90.
35. Wang Z, etal., Diabetes. 2005 Aug;54(8):2328-35.
36. Wu J, etal., Am J Physiol. 1999 Dec;277(6 Pt 1):E1087-94.
37. Xu G, etal., Biochim Biophys Acta. 2004 Apr 5;1688(3):274-9.
Additional References at PubMed
PMID:9242699   PMID:11090130   PMID:11739104   PMID:11829742   PMID:12202038   PMID:12242332   PMID:12421847   PMID:12477932   PMID:12488438   PMID:12941800   PMID:15358760   PMID:16100574  
PMID:16890542   PMID:16941710   PMID:17526932   PMID:17572141   PMID:17884448   PMID:19098903   PMID:19808779   PMID:20466882   PMID:21726644   PMID:23542164   PMID:23823476   PMID:24068000  
PMID:24625548   PMID:24755036   PMID:24912190   PMID:25289390   PMID:25339898   PMID:27321819   PMID:27614840   PMID:29122977   PMID:29446047   PMID:30579780  


Genomics

Comparative Map Data
Srebf2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27113,663,202 - 113,720,850 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7113,663,202 - 113,720,848 (+)Ensembl
Rnor_6.07123,381,082 - 123,438,605 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7123,381,077 - 123,438,603 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07123,364,495 - 123,422,296 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47120,522,511 - 120,580,212 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17120,556,723 - 120,612,972 (+)NCBI
Celera7109,978,519 - 110,036,018 (+)NCBICelera
Cytogenetic Map7q34NCBI
SREBF2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2241,833,079 - 41,907,307 (+)EnsemblGRCh38hg38GRCh38
GRCh382241,833,105 - 41,907,308 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372242,229,109 - 42,303,309 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362240,559,052 - 40,632,321 (+)NCBINCBI36hg18NCBI36
Build 342240,553,605 - 40,626,873NCBI
Celera2226,035,175 - 26,108,609 (+)NCBI
Cytogenetic Map22q13.2NCBI
HuRef2225,194,635 - 25,269,011 (+)NCBIHuRef
CHM1_12242,189,135 - 42,263,520 (+)NCBICHM1_1
Srebf2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391582,031,470 - 82,089,580 (+)NCBIGRCm39mm39
GRCm39 Ensembl1582,031,382 - 82,089,580 (+)Ensembl
GRCm381582,147,269 - 82,205,379 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1582,147,181 - 82,205,379 (+)EnsemblGRCm38mm10GRCm38
MGSCv371581,977,699 - 82,035,390 (+)NCBIGRCm37mm9NCBIm37
MGSCv361581,974,524 - 82,032,215 (+)NCBImm8
Celera1584,270,919 - 84,328,680 (+)NCBICelera
Cytogenetic Map15E1NCBI
Srebf2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541327,271,953 - 27,326,759 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541327,271,717 - 27,326,655 (+)NCBIChiLan1.0ChiLan1.0
SREBF2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12240,811,459 - 40,884,947 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2240,811,459 - 40,884,947 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02222,725,790 - 22,799,749 (+)NCBIMhudiblu_PPA_v0panPan3
Srebf2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049457,105,519 - 7,164,174 (-)NCBI
SpeTri2.0NW_004936492115,923 - 174,614 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SREBF2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl56,719,487 - 6,784,672 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.156,719,484 - 6,784,724 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SREBF2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11924,364,725 - 24,439,851 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1924,364,911 - 24,440,014 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666045100,972,400 - 101,047,348 (-)NCBIVero_WHO_p1.0
Srebf2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247526,815,075 - 6,871,674 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D7Rat78  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.07123,378,628 - 123,378,833UniSTSRnor5.0
RGSC_v3.47120,536,569 - 120,536,775RGDRGSC3.4
RGSC_v3.47120,536,570 - 120,536,775UniSTSRGSC3.4
RGSC_v3.17120,570,799 - 120,571,005RGD
Celera7109,992,435 - 109,992,640UniSTS
RH 2.0 Map7678.9RGD
SHRSP x BN Map765.7799RGD
FHH x ACI Map753.35RGD
Cytogenetic Map7q34UniSTS
RH128235  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27113,720,511 - 113,720,711 (+)MAPPERmRatBN7.2
Rnor_6.07123,438,267 - 123,438,466NCBIRnor6.0
Rnor_5.07123,421,958 - 123,422,157UniSTSRnor5.0
RGSC_v3.47120,579,874 - 120,580,073UniSTSRGSC3.4
Celera7110,035,680 - 110,035,879UniSTS
RH 3.4 Map7893.1UniSTS
Cytogenetic Map7q34UniSTS
AA850446  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27113,661,749 - 113,661,966 (+)MAPPERmRatBN7.2
Rnor_6.07123,379,630 - 123,379,846NCBIRnor6.0
Rnor_5.07123,363,043 - 123,363,259UniSTSRnor5.0
RGSC_v3.47120,521,059 - 120,521,275UniSTSRGSC3.4
Celera7109,977,067 - 109,977,283UniSTS
RH 3.4 Map7892.0UniSTS
Cytogenetic Map7q34UniSTS
PMC165443P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27113,720,490 - 113,720,642 (+)MAPPERmRatBN7.2
Rnor_6.07123,438,246 - 123,438,397NCBIRnor6.0
Rnor_5.07123,421,937 - 123,422,088UniSTSRnor5.0
RGSC_v3.47120,579,853 - 120,580,004UniSTSRGSC3.4
Celera7110,035,659 - 110,035,810UniSTS
Cytogenetic Map7q34UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)768938720113886318Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)768938720113886318Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)768938720113886318Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)769736226117455174Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)794811085116738842Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)794811326116294265Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7103146217116738842Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:202
Count of miRNA genes:135
Interacting mature miRNAs:164
Transcripts:ENSRNOT00000056041
Prediction methods:Miranda, 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 3 35 57 41 19 41 5 8 74 35 41 11 5
Low 8 3 3 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000056041   ⟹   ENSRNOP00000052893
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7113,663,202 - 113,720,848 (+)Ensembl
Rnor_6.0 Ensembl7123,381,082 - 123,438,603 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082603   ⟹   ENSRNOP00000071436
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7123,381,077 - 123,437,466 (+)Ensembl
RefSeq Acc Id: NM_001033694   ⟹   NP_001028866
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27113,663,202 - 113,720,850 (+)NCBI
Rnor_6.07123,381,082 - 123,438,605 (+)NCBI
Rnor_5.07123,364,495 - 123,422,296 (+)NCBI
RGSC_v3.47120,522,511 - 120,580,212 (+)RGD
Celera7109,978,519 - 110,036,018 (+)RGD
Sequence:
RefSeq Acc Id: XM_006242079   ⟹   XP_006242141
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27113,663,555 - 113,720,850 (+)NCBI
Rnor_6.07123,381,425 - 123,438,605 (+)NCBI
Rnor_5.07123,364,495 - 123,422,296 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001028866 (Get FASTA)   NCBI Sequence Viewer  
  XP_006242141 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI01903 (Get FASTA)   NCBI Sequence Viewer  
  EDM15674 (Get FASTA)   NCBI Sequence Viewer  
  Q3T1I5 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001028866   ⟸   NM_001033694
- Sequence:
RefSeq Acc Id: XP_006242141   ⟸   XM_006242079
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000071436   ⟸   ENSRNOT00000082603
RefSeq Acc Id: ENSRNOP00000052893   ⟸   ENSRNOT00000056041
Protein Domains
bHLH

Transcriptome

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

Promoters
RGD ID:13695530
Promoter ID:EPDNEW_R6053
Type:multiple initiation site
Name:Srebf2_1
Description:sterol regulatory element binding transcription factor 2
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_6.07123,381,080 - 123,381,140EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
Sequenced By: MCW
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
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
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
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
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)
Visual CSV TAB Printer
Sequenced By: MCW
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
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
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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Sequenced By: MCW
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
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
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
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
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
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
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/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
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/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
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/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
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
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307751 AgrOrtholog
Ensembl Genes ENSRNOG00000007400 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000052893 UniProtKB/TrEMBL
  ENSRNOP00000071436 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000056041 UniProtKB/TrEMBL
  ENSRNOT00000082603 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7934137 IMAGE-MGC_LOAD
InterPro bHLH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig/MHC_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:300095 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124823 IMAGE-MGC_LOAD
NCBI Gene 300095 ENTREZGENE
Pfam HLH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Srebf2 PhenoGen
PROSITE BHLH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_MHC UniProtKB/TrEMBL
SMART HLH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47459 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K0G4_RAT UniProtKB/TrEMBL
  F1MA23_RAT UniProtKB/TrEMBL
  Q3T1I5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-18 Srebf2  sterol regulatory element binding transcription factor 2  Srebf2  sterol regulatory element binding factor 2   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-28 Srebf2  sterol regulatory element binding factor 2   Srebf2  sterol regulatory element binding factor 2 (predicted)  'predicted' is removed from gene name 2292626 APPROVED
2007-04-13 Srebf2  UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1  Srebf2_predicted  sterol regulatory element binding factor 2 (predicted)  Symbol updated 737654 APPROVED
2007-04-13 Srebf2_predicted  sterol regulatory element binding factor 2 (predicted)  Srebf2_retired  sterol regulatory element binding factor 2  Data Merged 737654 APPROVED
2007-04-13 Srebf2_retired  UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1  Srebf2  sterol regulatory element binding factor 2  Symbol updated 737654 APPROVED
2005-01-12 Srebf2_predicted  sterol regulatory element binding factor 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization cytoplasmic(soluble)protein 628485
gene_cellular_localization a cytoplasmic(soluble) protein 628485
gene_domains SREBP characteristic membrane-spanning and SCAP binding domains absent 628485
gene_domains contains DNA binding, dimerization, nuclear localization and N-terminal transactivation domains with characteristic membrane-spanning and SCAP binding domains absent in isoform Srebf2_v1 628485
gene_expression preferentially enriched in adult spermatogenic cells; expressed druing meitoic and early haploid spermatogenic stages 628485
gene_expression expressed in somatic tissues, testis and enriched adult spermatogenic cells 628485
gene_function transcription factor 628485
gene_physical_interaction binds to SRE-containing (ATCACCCCAC) promoter region; binds to GCP1 repeat element(CTCCAG) 628485
gene_physical_interaction binds to (Sterol Regulatory elements) SRE-containing promoters 628485
gene_process involved in regulation of cholesterol and fatty acid biosynthesis 628485
gene_process constitutively active transcriptional regulator functioning during spermatogenesis in a sterol dependent way 628485
gene_product basic helix-loop-helix zip protein 628485
gene_protein 20 amino acids absent in C-terminal compared to Srebp2 protein 628485
gene_regulation independent of regulation by SCAP 628485