Tgfa (transforming growth factor alpha) - Rat Genome Database

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Gene: Tgfa (transforming growth factor alpha) Rattus norvegicus
Analyze
Symbol: Tgfa
Name: transforming growth factor alpha
RGD ID: 3849
Description: Exhibits epidermal growth factor receptor binding activity. Involved in several processes, including hepatocyte proliferation; response to drug; and wound healing. Localizes to extracellular space and nucleus. Colocalizes with plasma membrane. Used to study pancreatic cancer. Biomarker of acute kidney failure and hepatocellular carcinoma. Human ortholog(s) of this gene implicated in gastroenteritis. Orthologous to human TGFA (transforming growth factor alpha); PARTICIPATES IN altered epidermal growth factor/neuregulin signaling pathway; epidermal growth factor/neuregulin signaling pathway; pancreatic cancer pathway; INTERACTS WITH (+)-alpha-tocopherol; 1,3-dinitrobenzene; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: protransforming growth factor alpha; RATTGFAA; TGFAA
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24118,618,043 - 118,700,897 (+)NCBI
Rnor_6.0 Ensembl4117,962,319 - 118,046,344 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04117,961,877 - 118,045,923 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04182,534,161 - 182,616,713 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44120,355,649 - 120,437,772 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14120,600,129 - 120,682,257 (+)NCBI
Celera4107,591,450 - 107,673,528 (+)NCBICelera
RH 3.4 Map4688.3RGD
Cytogenetic Map4q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-alpha-tocopherol  (EXP)
(+)-catechin  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-di-tert-butyl-4-methylphenol  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-hydroxypropanoic acid  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-nonylphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetylsalicylic acid  (EXP)
acteoside  (ISO)
aldehydo-D-glucosamine  (EXP)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beta-D-glucosamine  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bromocriptine  (EXP)
butan-1-ol  (ISO)
butanal  (ISO)
butane-2,3-dione  (ISO)
calciol  (ISO)
calcitriol  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
capsaicin  (EXP)
celecoxib  (EXP)
chlorpyrifos  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crizotinib  (ISO)
cycloheximide  (ISO)
cyproconazole  (ISO)
D-glucose  (EXP,ISO)
dexamethasone  (ISO)
dextromethorphan  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
diclofenac  (ISO)
diethylstilbestrol  (ISO)
dimethylarsinic acid  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
epoxiconazole  (ISO)
erlotinib hydrochloride  (ISO)
ethanol  (ISO)
etoposide  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
furosemide  (EXP)
gefitinib  (ISO)
genistein  (EXP,ISO)
glucose  (EXP,ISO)
hexachlorobenzene  (ISO)
hydrogen chloride  (EXP)
irinotecan  (ISO)
iron(III) nitrilotriacetate  (EXP)
isobutanol  (ISO)
kaempferol  (ISO)
lansoprazole  (ISO)
leflunomide  (ISO)
lidocaine  (ISO)
limonene  (EXP)
lipopolysaccharide  (ISO)
lycopene  (ISO)
manganese(II) chloride  (ISO)
marimastat  (ISO)
melittin  (ISO)
mercury dichloride  (EXP)
metamizole sodium  (EXP)
methapyrilene  (ISO)
methotrexate  (EXP,ISO)
mifepristone  (EXP)
N-acetyl-L-cysteine  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
nickel atom  (EXP)
nickel sulfate  (EXP,ISO)
nitrofurazone  (EXP)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
PCB138  (EXP)
PD 168393  (ISO)
PHA-665752  (ISO)
phenytoin  (ISO)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
phorone  (EXP)
pirinixic acid  (EXP,ISO)
piroxicam  (EXP)
poly(propylene imine) macromolecule  (ISO)
progesterone  (EXP,ISO)
propiconazole  (ISO)
pyrvinium  (ISO)
quercetin  (ISO)
quinomethionate  (ISO)
rac-lactic acid  (ISO)
raloxifene  (ISO)
resorcinol  (ISO)
resveratrol  (ISO)
riddelliine  (EXP)
rottlerin  (ISO)
rutin  (ISO)
serpentine asbestos  (EXP,ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
Sulpyrine  (EXP)
sunitinib  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
trans-piceid  (ISO)
tributylstannane  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
tyrphostin AG 1478  (ISO)
valproic acid  (ISO)
vemurafenib  (ISO)
vinclozolin  (EXP)
vitamin E  (EXP)
zearalenone  (ISO)

References

References - curated
1. Aihaiti X, etal., J Interferon Cytokine Res. 2006 Apr;26(4):226-34.
2. Akkoyunlu G, etal., Acta Histochem. 2003;105(4):295-301.
3. Appleton CT, etal., Arthritis Rheum. 2007 Nov;56(11):3693-705.
4. Baughman RP, etal., Sarcoidosis Vasc Diffuse Lung Dis. 1999 Mar;16(1):57-61.
5. Blasband AJ, etal., Mol Cell Biol 1990 May;10(5):2111-21.
6. Borrell-Pag├Ęs M, etal., Mol Biol Cell. 2000 Dec;11(12):4217-25.
7. Buck M, etal., Mol Cell. 1999 Dec;4(6):1087-92.
8. Dell KM, etal., Kidney Int. 2001 Oct;60(4):1240-8.
9. Dombrowski F, etal., Am J Pathol. 1997 Mar;150(3):1071-87.
10. Franklin JL, etal., Exp Cell Res. 2005 Feb 15;303(2):457-70.
11. Garrett TP, etal., Cell. 2002 Sep 20;110(6):763-73.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. Gentry LE, etal., Mol Cell Biol. 1987 May;7(5):1585-91.
14. GOA data from the GO Consortium
15. Grasl-Kraupp B, etal., Hepatology 2002 Jun;35(6):1372-80.
16. Guerra-Crespo M, etal., Neuroscience. 2009 May 5;160(2):470-83. Epub 2009 Feb 25.
17. Hardie WD, etal., Pediatr Dev Pathol. 1999 Sep-Oct;2(5):415-23.
18. Hise MK, etal., Nephron. 2001 May;88(1):71-9.
19. Jiang D, etal., J Biol Chem. 1998 Nov 20;273(47):31471-9.
20. Kim I, etal., Wound Repair Regen. 2001 Sep-Oct;9(5):386-90.
21. Kimura M, etal., J Pharmacol Sci. 2009 Apr;109(4):618-29. Epub 2009 Apr 4.
22. Kitano M, etal., Cancer Sci. 2006 Jun;97(6):478-83.
23. Korc M, etal., J Clin Invest. 1992 Oct;90(4):1352-60.
24. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
25. Le Cras TD, etal., Am J Physiol Lung Cell Mol Physiol. 2004 Oct;287(4):L718-29. Epub 2004 Apr 16.
26. Lee CS Eur J Surg Oncol. 1998 Feb;24(1):38-42.
27. Lee DC, etal., Nature 1985 Feb 7-13;313(6002):489-91.
28. Luetteke NC and Lee DC, Semin Cancer Biol. 1990 Aug;1(4):265-75.
29. Luetteke NC, etal., Cell. 1993 Apr 23;73(2):263-78.
30. Madtes DK, etal., Am J Respir Crit Care Med. 1998 Aug;158(2):424-30.
31. MGD data from the GO Consortium
32. NCBI rat LocusLink and RefSeq merged data July 26, 2002
33. Nie SN, etal., World J Gastroenterol. 2004 Dec 1;10(23):3537-41.
34. Nomura S, etal., Gastroenterology. 2005 May;128(5):1292-305.
35. Pavelic K, etal., Anticancer Res. 1996 Jul-Aug;16(4A):1707-17.
36. Petegnief V, etal., J Biol Chem 2003 Aug 8;278(32):29552-9. Epub 2003 May 27.
37. Pipeline to import KEGG annotations from KEGG into RGD
38. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
39. RGD automated data pipeline
40. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
41. RGD automated import pipeline for gene-chemical interactions
42. Rosen K, etal., J Biol Chem 2001 Oct 5;276(40):37273-9.
43. Singh AB and Harris RC, Cell Signal. 2005 Oct;17(10):1183-93.
44. Siveke JT, etal., Cancer Cell. 2007 Sep;12(3):266-79.
45. Sukhotnik I, etal., Pediatr Surg Int. 2008 Dec;24(12):1303-11.
46. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
47. Tuli SS, etal., Curr Eye Res. 2006 Sep;31(9):709-19.
48. Wang Y, etal., Biol Reprod 2002 Jun;66(6):1672-80.
49. Wong HH and Lemoine NR, Nat Rev Gastroenterol Hepatol. 2009 Jul;6(7):412-22. Epub 2009 Jun 9.
Additional References at PubMed
PMID:6320373   PMID:6605968   PMID:8702723   PMID:10331984   PMID:11278323   PMID:12743035   PMID:14998491   PMID:15064403   PMID:15353178   PMID:17031671   PMID:17553928   PMID:19237431  
PMID:24595367   PMID:26804134  


Genomics

Candidate Gene Status
Tgfa is a candidate Gene for QTL Hcar2
Tgfa is a candidate Gene for QTL Hcar8
Tgfa is a candidate Gene for QTL Ept5
Comparative Map Data
Tgfa
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24118,618,043 - 118,700,897 (+)NCBI
Rnor_6.0 Ensembl4117,962,319 - 118,046,344 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04117,961,877 - 118,045,923 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04182,534,161 - 182,616,713 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44120,355,649 - 120,437,772 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14120,600,129 - 120,682,257 (+)NCBI
Celera4107,591,450 - 107,673,528 (+)NCBICelera
RH 3.4 Map4688.3RGD
Cytogenetic Map4q34NCBI
TGFA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl270,447,284 - 70,554,193 (-)EnsemblGRCh38hg38GRCh38
GRCh38270,447,284 - 70,553,826 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37270,674,416 - 70,780,958 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36270,527,924 - 70,634,613 (-)NCBINCBI36hg18NCBI36
Build 34270,586,073 - 70,692,585NCBI
Celera270,525,095 - 70,631,786 (-)NCBI
Cytogenetic Map2p13.3NCBI
HuRef270,410,567 - 70,517,904 (-)NCBIHuRef
CHM1_1270,602,969 - 70,710,469 (-)NCBICHM1_1
Tgfa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39686,172,020 - 86,252,726 (+)NCBIGRCm39mm39
GRCm39 Ensembl686,172,205 - 86,252,701 (+)Ensembl
GRCm38686,195,038 - 86,275,744 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl686,195,223 - 86,275,719 (+)EnsemblGRCm38mm10GRCm38
MGSCv37686,145,245 - 86,225,443 (+)NCBIGRCm37mm9NCBIm37
MGSCv36686,161,050 - 86,240,791 (+)NCBImm8
Celera688,129,264 - 88,209,219 (+)NCBICelera
Cytogenetic Map6D1NCBI
cM Map637.62NCBI
Tgfa
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542414,616,259 - 14,710,183 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542414,616,390 - 14,709,723 (+)NCBIChiLan1.0ChiLan1.0
TGFA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A71,625,196 - 71,731,461 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A71,625,196 - 71,731,461 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A70,510,727 - 70,617,628 (-)NCBIMhudiblu_PPA_v0panPan3
TGFA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11068,915,671 - 68,957,027 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1068,799,798 - 68,879,353 (-)NCBI
ROS_Cfam_1.01069,935,210 - 70,012,287 (-)NCBI
UMICH_Zoey_3.11069,652,504 - 69,732,094 (-)NCBI
UNSW_CanFamBas_1.01069,914,727 - 69,994,269 (-)NCBI
UU_Cfam_GSD_1.01070,213,444 - 70,290,872 (-)NCBI
Tgfa
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629213,812,443 - 13,910,943 (+)NCBI
SpeTri2.0NW_00493649114,659,089 - 14,758,614 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TGFA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl371,948,137 - 72,050,488 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1371,948,232 - 72,054,257 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2375,409,715 - 75,437,890 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TGFA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11436,545,641 - 36,654,213 (+)NCBI
ChlSab1.1 Ensembl1436,545,875 - 36,648,237 (+)Ensembl
Vero_WHO_p1.0NW_02366604575,360,438 - 75,475,321 (-)NCBI
Tgfa
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247622,832,073 - 2,941,150 (+)NCBI

Position Markers
D4Wox18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24118,699,850 - 118,699,963 (+)MAPPER
Rnor_6.04118,044,882 - 118,044,994NCBIRnor6.0
Rnor_5.04182,615,672 - 182,615,784UniSTSRnor5.0
RGSC_v3.44120,436,732 - 120,436,845RGDRGSC3.4
RGSC_v3.44120,436,733 - 120,436,845UniSTSRGSC3.4
RGSC_v3.14120,681,213 - 120,681,326RGD
Celera4107,672,487 - 107,672,599UniSTS
RH 3.4 Map4694.3RGD
RH 3.4 Map4694.3UniSTS
Cytogenetic Map4q34UniSTS
D4Arb5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24118,699,819 - 118,700,066 (+)MAPPER
Rnor_6.04118,044,851 - 118,045,097NCBIRnor6.0
Rnor_5.04182,615,641 - 182,615,887UniSTSRnor5.0
RGSC_v3.44120,436,701 - 120,436,948RGDRGSC3.4
RGSC_v3.44120,436,702 - 120,436,948UniSTSRGSC3.4
RGSC_v3.14120,681,182 - 120,681,429RGD
Celera4107,672,456 - 107,672,702UniSTS
Cytogenetic Map4q34UniSTS
D4Got90  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24118,664,949 - 118,665,239 (+)MAPPER
Rnor_6.04118,010,289 - 118,010,578NCBIRnor6.0
Rnor_5.04182,580,930 - 182,581,219UniSTSRnor5.0
RGSC_v3.44120,402,230 - 120,402,519UniSTSRGSC3.4
RGSC_v3.44120,402,229 - 120,402,519RGDRGSC3.4
RGSC_v3.14120,646,710 - 120,647,000RGD
RH 3.4 Map4688.9UniSTS
RH 3.4 Map4688.9RGD
Cytogenetic Map4q34UniSTS
D4Cebr4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24118,686,099 - 118,686,310 (+)MAPPER
Rnor_6.04118,031,131 - 118,031,341NCBIRnor6.0
Rnor_5.04182,601,921 - 182,602,131UniSTSRnor5.0
RGSC_v3.44120,422,982 - 120,423,192UniSTSRGSC3.4
Celera4107,658,736 - 107,658,946UniSTS
Cytogenetic Map4q34UniSTS
AU047195  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24118,623,940 - 118,624,221 (+)MAPPER
Rnor_6.04117,969,355 - 117,969,635NCBIRnor6.0
Rnor_5.04182,540,023 - 182,540,303UniSTSRnor5.0
RGSC_v3.44120,361,353 - 120,361,633UniSTSRGSC3.4
Celera4107,597,112 - 107,597,392UniSTS
Cytogenetic Map4q34UniSTS
RH94516  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24118,698,966 - 118,699,136 (+)MAPPER
Rnor_6.04118,043,998 - 118,044,167NCBIRnor6.0
Rnor_5.04182,614,788 - 182,614,957UniSTSRnor5.0
RGSC_v3.44120,435,849 - 120,436,018UniSTSRGSC3.4
Celera4107,671,603 - 107,671,772UniSTS
RH 3.4 Map4688.3UniSTS
Cytogenetic Map4q34UniSTS
ABA004  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24118,696,898 - 118,697,652 (+)MAPPER
mRatBN7.24118,696,913 - 118,697,652 (+)MAPPER
Rnor_6.04118,041,930 - 118,042,683NCBIRnor6.0
Rnor_6.04118,041,945 - 118,042,683NCBIRnor6.0
Rnor_5.04182,612,735 - 182,613,473UniSTSRnor5.0
Rnor_5.04182,612,720 - 182,613,473UniSTSRnor5.0
Celera4107,669,550 - 107,670,288UniSTS
Celera4107,669,535 - 107,670,288UniSTS
Cytogenetic Map4q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)43043231145254791Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)423850384169318094Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)436615599145611886Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)443414605155469929Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)443414792146942075Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)443414792146942075Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)446898276145611886Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)449906054145611886Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)455324953148360954Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)455375865125671711Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)458640017154427984Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)458640017154427984Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)461038901127777403Rat
1641919Alc22Alcohol consumption QTL 220.0005drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)462947687125671711Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)463537179157286626Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)470773471132455556Rat
631646Stl4Serum triglyceride level QTL 46.50.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)473786419132455556Rat
724522Bp146Blood pressure QTL 1462.20.0021arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)475258970120258970Rat
2302051Pia28Pristane induced arthritis QTL 285.30.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)475258970120258970Rat
738015Pia9Pristane induced arthritis QTL 94.50.048joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)476567036121567036Rat
631662Hcar2Hepatocarcinoma resistance QTL 23.10.0003liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)479555067124555067Rat
2306899Bp338Blood pressure QTL 3380.071arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)481874073119546974Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)481959983152055009Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)484475257178931073Rat
634334Xhs3X-ray hypersensitivity QTL 310intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)485794049129615056Rat
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)486312589146942261Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)486312589147702403Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)486438317168047091Rat
61476Aia3Adjuvant induced arthritis QTL 33.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)486532519131532519Rat
1578662Bss15Bone structure and strength QTL 1519.6femur width (VT:1000666)femoral neck width (CMO:0001695)487136446132136446Rat
1578670Bss14Bone structure and strength QTL 1416.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)487136446132136446Rat
631689Scl4Serum cholesterol level QTL 41.90.008blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)494414208139414208Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)494893247168046938Rat
61434Cia3Collagen induced arthritis QTL 34.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)499066823144066823Rat
2302049Pia32Pristane induced arthritis QTL 325.10.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)4105277348150277348Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4105682594150682594Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4105971071168047091Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106347236151347236Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4108876717169215811Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109636356154636356Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109636356154636356Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110702761155702761Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110702761155702761Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4112807675157807675Rat
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4115372758150038284Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4116726724157291438Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4117926139162926139Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1086
Count of miRNA genes:339
Interacting mature miRNAs:471
Transcripts:ENSRNOT00000057441
Prediction methods:Microtar, 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 1 38 11
Low 2 29 56 41 18 41 2 2 36 35 30 11 2
Below cutoff 14 1 1 6 8 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000057441   ⟹   ENSRNOP00000054248
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4117,962,319 - 118,046,344 (+)Ensembl
RefSeq Acc Id: NM_012671   ⟹   NP_036803
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24118,618,269 - 118,700,892 (+)NCBI
Rnor_6.04117,962,178 - 118,045,923 (+)NCBI
Rnor_5.04182,534,161 - 182,616,713 (+)NCBI
RGSC_v3.44120,355,649 - 120,437,772 (+)RGD
Celera4107,591,450 - 107,673,528 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006236822   ⟹   XP_006236884
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24118,618,052 - 118,696,807 (+)NCBI
Rnor_6.04117,961,877 - 118,041,838 (+)NCBI
Rnor_5.04182,534,161 - 182,616,713 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039107070   ⟹   XP_038962998
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24118,618,043 - 118,696,807 (+)NCBI
RefSeq Acc Id: XM_039107071   ⟹   XP_038962999
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24118,618,061 - 118,700,897 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036803   ⟸   NM_012671
- Peptide Label: preproprotein
- UniProtKB: P01134 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006236884   ⟸   XM_006236822
- Peptide Label: isoform X3
- UniProtKB: U5LKN7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000054248   ⟸   ENSRNOT00000057441
RefSeq Acc Id: XP_038962998   ⟸   XM_039107070
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038962999   ⟸   XM_039107071
- Peptide Label: isoform X2
Protein Domains
EGF-like

Transcriptome

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

Promoters
RGD ID:13693204
Promoter ID:EPDNEW_R3729
Type:multiple initiation site
Name:Tgfa_1
Description:transforming growth factor alpha
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_6.04117,962,266 - 117,962,326EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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/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 (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
COP/CrCrl (MCW & UW)
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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)
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
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
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/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
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 (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
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
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
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
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
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 (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
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)
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
SHRSP/Gcrc (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
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/Gcrc (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
WKY/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
WKY/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
WKY/NHsd (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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3849 AgrOrtholog
Ensembl Genes ENSRNOG00000016182 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000054248 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000057441 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro EGF-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_rcpt_ligand UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24827 UniProtKB/Swiss-Prot
NCBI Gene 24827 ENTREZGENE
PANTHER PTHR10740 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tgfa PhenoGen
PROSITE EGF_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC224838
UniProt P01134 ENTREZGENE, UniProtKB/Swiss-Prot
  U5LKN7 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q63749 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Tgfa  Transforming growth factor, alpha      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in oocyte nuclei, as well as granulosa and interstitial thecal cells of developing ovarian follicles 1578551
gene_function increases in androgen production in immature Leydig cells 1578561
gene_regulation upregulates its own mRNA and protein expression as well as EGF receptor protein expression in immature Leydig cells 1578561
gene_regulation expression in gastric mucosa increases in response to water immersion and restraint stress (WRS), and continues to increase during the period of adaptation in response to repeated WRS 1578552
gene_regulation inhibition of apoptosis is c-Src-dependent 730227