Afp (alpha-fetoprotein) - Rat Genome Database

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Gene: Afp (alpha-fetoprotein) Rattus norvegicus
Analyze
Symbol: Afp
Name: alpha-fetoprotein
RGD ID: 2065
Description: Predicted to enable fatty acid binding activity and zinc ion binding activity. Involved in several processes, including cellular response to retinoic acid; liver regeneration; and response to dexamethasone. Located in cytosol and extracellular space. Biomarker of hepatitis. Human ortholog(s) of this gene implicated in hepatitis C. Orthologous to human AFP (alpha fetoprotein); PARTICIPATES IN forkhead class A signaling pathway; INTERACTS WITH (+)-schisandrin B; (+)-taxifolin; (S)-naringenin.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: alpha-1-fetoprotein; alpha-fetoglobulin; chloride intracellular channel 6
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: QTLs:   Scl11  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21417,573,412 - 17,591,476 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1417,573,412 - 17,591,480 (-)Ensembl
Rnor_6.01419,141,755 - 19,159,919 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1419,141,755 - 19,159,923 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01419,049,096 - 19,067,260 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41419,092,563 - 19,110,728 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11419,092,562 - 19,110,728 (-)NCBI
Celera1416,939,827 - 16,957,879 (-)NCBICelera
RH 3.4 Map14214.49RGD
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(+)-taxifolin  (EXP)
(S)-naringenin  (EXP)
1,1-dichloroethene  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
1H-1,2,4-triazole  (EXP)
2,2'-Dihydroxy-4-methoxybenzophenone  (EXP)
2,3,4,5-Tetrachloro-4'-biphenylol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-diaminotoluene  (ISO)
2,4-dinitrotoluene  (EXP)
2-acetamidofluorene  (EXP)
2-amino-2-deoxy-D-galactopyranose  (EXP)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-nitropropane  (EXP)
2-sec-butylphenol  (EXP)
3'-hydroxyflavanone  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,5,6-trichloro-2-pyridinol  (ISO)
3,5,6-trichloropyridine-2-one  (ISO)
3,5-diethoxycarbonyl-1,4-dihydrocollidine  (ISO)
4'-hydroxychalcone  (EXP)
4'-hydroxyflavanone  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxychalcone  (EXP)
4-nonylphenol  (EXP)
4-octylphenol  (EXP)
5-azacytidine  (ISO)
5-fluorouracil  (ISO)
5-hydroxytryptophan  (ISO)
7-hydroxyflavanone  (EXP)
acetic acid  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucosamine  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
all-trans-retinol  (EXP)
allyl alcohol  (EXP,ISO)
alpha-Zearalanol  (EXP)
amiodarone  (ISO)
ammonium chloride  (EXP)
apigenin  (EXP)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
Azaspiracid  (ISO)
azoxystrobin  (EXP)
baicalein  (EXP)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
Benzyl parahydroxybenzoate  (EXP)
benzylpenicillin  (ISO)
beta-D-glucosamine  (ISO)
beta-Zearalanol  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromochloroacetic acid  (ISO)
brucine  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
carfilzomib  (EXP)
chalcone  (EXP)
CHIR 99021  (ISO)
chloroprene  (ISO)
chlorpromazine  (ISO)
chlorpyrifos  (EXP,ISO)
choline  (EXP,ISO)
Chorionic gonadotropin  (ISO)
chrysin  (EXP)
citral  (EXP)
clofibrate  (ISO)
cobalt dichloride  (EXP)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (EXP)
Cuprizon  (EXP)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
D-glucose  (ISO)
diarsenic trioxide  (ISO)
dicrotophos  (ISO)
dienestrol  (EXP)
diethyl maleate  (ISO)
diethyl phthalate  (EXP)
diethylstilbestrol  (EXP,ISO)
Dimethyl phthalate  (EXP)
dimethylarsinic acid  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
ebselen  (EXP)
equol  (EXP)
estra-1,3,5(10)-trien-3-ol  (EXP)
estriol  (EXP,ISO)
estrone  (EXP)
ethanol  (EXP)
fisetin  (EXP)
flavanone  (EXP)
flavonoids  (EXP)
folic acid  (EXP,ISO)
formaldehyde  (ISO)
fosinopril  (ISO)
furan  (EXP,ISO)
gemcitabine  (ISO)
geranial  (EXP)
glucose  (ISO)
glyphosate  (EXP)
hesperidin  (EXP)
hexestrol  (EXP)
hypochlorous acid  (ISO)
imidacloprid  (EXP)
isoliquiritigenin  (EXP)
isoniazide  (ISO)
kaempferol  (EXP,ISO)
ketamine  (EXP)
L-ethionine  (EXP)
L-methionine  (EXP,ISO)
levofloxacin  (EXP)
lipopolysaccharide  (ISO)
losartan  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP)
masoprocol  (EXP)
mercury dibromide  (ISO)
mestranol  (EXP)
methimazole  (ISO)
methylarsonic acid  (ISO)
methylmercury chloride  (ISO)
monobenzone  (EXP)
myricetin  (EXP)
N,N'-diphenyl-1,4-phenylenediamine  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
N-nitrosomorpholine  (EXP)
nickel atom  (ISO)
nickel dichloride  (EXP)
niclosamide  (EXP)
nitrofen  (EXP)
ochratoxin A  (ISO)
ozone  (ISO)
panaxydol  (ISO)
paracetamol  (ISO)
perindopril  (ISO)
phenobarbital  (EXP,ISO)
phenol  (ISO)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
phloretin  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
pluronic P-123  (EXP)
Poloxamer  (EXP)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
quercetin  (EXP)
rotenone  (EXP)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
saccharin  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sodium arsenite  (EXP,ISO)
sodium nitrate  (ISO)
sorafenib  (ISO)
streptozocin  (ISO)
succimer  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (EXP,ISO)
thiabendazole  (EXP)
thioacetamide  (EXP)
thymoquinone  (EXP)
titanium dioxide  (ISO)
trans-chalcone  (EXP)
tributylstannane  (ISO)
triclosan  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
urea  (ISO)
valproic acid  (ISO)
zinc dichloride  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA,IDA,IEA,ISO)
cytosol  (IDA)
extracellular space  (IDA,IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Buzard G and Locker J, DNA Seq 1990;1(1):33-48.
2. Chan SL, etal., J Gastroenterol Hepatol. 2015 Oct;30(10):1529-35. doi: 10.1111/jgh.13005.
3. Chiu JF, etal., Nucleic Acids Res. 1981 Dec 21;9(24):6917-33. doi: 10.1093/nar/9.24.6917.
4. Dexeus FH, etal., Urology. 1991 Jul;38(1):6-10.
5. Gabant P, etal., Proc Natl Acad Sci U S A 2002 Oct 1;99(20):12865-70. Epub 2002 Sep 24.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. GOA data from the GO Consortium
8. Huang DP, etal., Nucleic Acids Res. 1985 Jun 11;13(11):3873-90. doi: 10.1093/nar/13.11.3873.
9. Jagodzinski LL, etal., Proc Natl Acad Sci U S A 1981 Jun;78(6):3521-5.
10. Kajiyama Y, etal., Mol Cell Biol 2002 Sep;22(17):6122-30.
11. Kobayashi S, etal., Gastrointest Tumors. 2017 Mar;3(3-4):141-152. doi: 10.1159/000455955. Epub 2017 Feb 8.
12. Kumano M, etal., Hinyokika Kiyo. 2007 Dec;53(12):851-6.
13. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
14. Li P, etal., World J Gastroenterol. 2011 Nov 7;17(41):4563-71. doi: 10.3748/wjg.v17.i41.4563.
15. Liu L, etal., Dev Growth Differ. 2007 Oct;49(8):669-81.
16. Meier V, etal., Comp Hepatol. 2006 Jul 5;5:2.
17. MGD data from the GO Consortium
18. Miyazaki M, etal., Res Exp Med (Berl). 1991;191(5):297-307.
19. Nacer-Cherif H, etal., Biochem J 2003 Feb 1;369(Pt 3):583-91.
20. NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. Okuno M, etal., J Nutr Sci Vitaminol (Tokyo). 1990 Oct;36(5):437-46.
22. OMIM Disease Annotation Pipeline
23. Parekh DJ, etal., Cancer Epidemiol Biomarkers Prev. 2007 Oct;16(10):1966-72.
24. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
25. Reyes-Gordillo K, etal., Biopharm Drug Dispos. 2007 Nov;28(8):415-22.
26. RGD automated import pipeline for gene-chemical interactions
27. RGD comprehensive gene curation
28. Sakashita S, etal., Invest Urol. 1977 Jul;15(1):2-4.
29. Srinivas UK and Revathi CJ, Biochem Mol Biol Int. 1994 May;33(1):21-8.
30. Szpirer C, etal., Mamm Genome 1998 Sep;9(9):721-34
31. Takahashi H, etal., Jpn J Cancer Res. 1988 Jul;79(7):821-7. doi: 10.1111/j.1349-7006.1988.tb00043.x.
32. Takayama K, etal., World J Gastroenterol. 2015 Apr 21;21(15):4696-706. doi: 10.3748/wjg.v21.i15.4696.
33. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
34. Tournier I, etal., Lab Invest. 1988 Nov;59(5):657-65.
35. Trobs RB, etal., Klin Padiatr. 2007 May-Jun;219(3):146-51.
36. Turcotte B, etal., Nucleic Acids Res 1985 Apr 11;13(7):2387-98.
37. Wan YJ, etal., J Mol Endocrinol. 1995 Feb;14(1):101-8. doi: 10.1677/jme.0.0140101.
38. Yang Y, etal., Biochim Biophys Acta 2002 Jun 13;1583(1):63-73.
39. Yeh YT, etal., World J Surg. 2012 May;36(5):1128-35. doi: 10.1007/s00268-012-1505-4.
40. Yurkovetsky Z, etal., Gynecol Oncol. 2007 Oct;107(1):58-65. Epub 2007 Jul 19.
Additional References at PubMed
PMID:67170   PMID:1376990   PMID:2434929   PMID:2442163   PMID:2456965   PMID:2462901   PMID:6157681   PMID:6157690   PMID:8607965   PMID:9420335   PMID:12477932   PMID:16893898  
PMID:17879097   PMID:19360917   PMID:21734804   PMID:26210615   PMID:31381236  


Genomics

Comparative Map Data
Afp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21417,573,412 - 17,591,476 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1417,573,412 - 17,591,480 (-)Ensembl
Rnor_6.01419,141,755 - 19,159,919 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1419,141,755 - 19,159,923 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01419,049,096 - 19,067,260 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41419,092,563 - 19,110,728 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11419,092,562 - 19,110,728 (-)NCBI
Celera1416,939,827 - 16,957,879 (-)NCBICelera
RH 3.4 Map14214.49RGD
Cytogenetic Map14p22NCBI
AFP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl473,431,138 - 73,456,174 (+)EnsemblGRCh38hg38GRCh38
GRCh38473,436,221 - 73,456,174 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37474,301,938 - 74,321,891 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36474,520,797 - 74,540,356 (+)NCBINCBI36hg18NCBI36
Build 34474,666,967 - 74,686,527NCBI
Celera471,661,745 - 71,681,240 (+)NCBI
Cytogenetic Map4q13.3ENTREZGENE
HuRef470,113,467 - 70,132,962 (+)NCBIHuRef
CHM1_1474,338,122 - 74,357,615 (+)NCBICHM1_1
Afp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39590,638,573 - 90,656,766 (+)NCBIGRCm39mm39
GRCm39 Ensembl590,638,596 - 90,656,766 (+)Ensembl
GRCm38590,490,714 - 90,508,907 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl590,490,737 - 90,508,907 (+)EnsemblGRCm38mm10GRCm38
MGSCv37590,919,740 - 90,937,933 (+)NCBIGRCm37mm9NCBIm37
MGSCv36591,565,937 - 91,584,106 (+)NCBImm8
Celera588,652,007 - 88,670,199 (+)NCBICelera
Cytogenetic Map5E1NCBI
cM Map544.77NCBI
AFP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1456,571,519 - 56,590,391 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl456,571,519 - 56,590,391 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0450,739,197 - 50,758,459 (-)NCBIMhudiblu_PPA_v0panPan3
AFP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11362,182,876 - 62,203,414 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1362,053,814 - 62,294,709 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1361,852,491 - 61,873,033 (+)NCBI
ROS_Cfam_1.01362,992,405 - 63,012,932 (+)NCBI
UMICH_Zoey_3.11362,603,973 - 62,624,508 (+)NCBI
UNSW_CanFamBas_1.01362,097,020 - 62,117,581 (+)NCBI
UU_Cfam_GSD_1.01363,232,901 - 63,253,687 (+)NCBI
LOC101966155
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528513,606,058 - 13,625,722 (-)NCBI
SpeTri2.0NW_0049365982,058,474 - 2,077,711 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AFP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl869,677,684 - 69,698,864 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1869,677,690 - 69,698,864 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2873,777,748 - 73,798,926 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103235780
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1721,904,225 - 21,924,105 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl721,905,154 - 21,924,092 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666084873,280 - 892,444 (-)NCBIVero_WHO_p1.0
Afp
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473534,072,257 - 34,092,540 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D14Mit2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21417,593,575 - 17,593,761 (+)MAPPERmRatBN7.2
Rnor_6.01419,161,705 - 19,161,893NCBIRnor6.0
RH 3.4 Map14226.99RGD
RH 3.4 Map14226.99UniSTS
SHRSP x BN Map146.9UniSTS
SHRSP x BN Map146.9RGD
FHH x ACI Map1419.55RGD
Cytogenetic Map14p21UniSTS
D14Wox8  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map14224.4UniSTS
RH 3.4 Map14224.4RGD
RH 2.0 Map14212.6RGD
Cytogenetic Map14p21UniSTS
D14Wox9  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1416,959,190 - 16,959,641UniSTS
RH 3.4 Map14218.8UniSTS
RH 3.4 Map14218.8RGD
Cytogenetic Map14p21UniSTS
PMC275467P5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21417,575,797 - 17,576,738 (+)MAPPERmRatBN7.2
Rnor_6.01419,144,140 - 19,145,080NCBIRnor6.0
Rnor_5.01419,051,481 - 19,052,421UniSTSRnor5.0
RGSC_v3.41419,095,046 - 19,095,986UniSTSRGSC3.4
Celera1416,942,206 - 16,943,146UniSTS
Cytogenetic Map14p21UniSTS
BI285802  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21417,573,445 - 17,574,505 (+)MAPPERmRatBN7.2
Rnor_6.01419,141,789 - 19,142,847NCBIRnor6.0
Rnor_5.01419,049,130 - 19,050,188UniSTSRnor5.0
RGSC_v3.41419,092,597 - 19,093,753UniSTSRGSC3.4
Celera1416,939,861 - 16,940,913UniSTS
RH 3.4 Map14224.4UniSTS
Cytogenetic Map14p21UniSTS
RH94533  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21417,573,429 - 17,573,535 (+)MAPPERmRatBN7.2
Rnor_6.01419,141,773 - 19,141,878NCBIRnor6.0
Rnor_5.01419,049,114 - 19,049,219UniSTSRnor5.0
RGSC_v3.41419,092,581 - 19,092,686UniSTSRGSC3.4
Celera1416,939,845 - 16,939,950UniSTS
RH 3.4 Map14214.49UniSTS
Cytogenetic Map14p21UniSTS
UniSTS:275850  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21417,574,567 - 17,575,931 (+)MAPPERmRatBN7.2
Rnor_6.01419,142,910 - 19,144,273NCBIRnor6.0
Rnor_5.01419,050,251 - 19,051,614UniSTSRnor5.0
RGSC_v3.41419,093,816 - 19,095,179UniSTSRGSC3.4
Celera1416,940,976 - 16,942,339UniSTS
Cytogenetic Map14p21UniSTS
Afp  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21417,574,493 - 17,575,848 (+)MAPPERmRatBN7.2
Rnor_6.01419,142,836 - 19,144,190NCBIRnor6.0
Rnor_5.01419,050,177 - 19,051,531UniSTSRnor5.0
Celera1416,940,902 - 16,942,256UniSTS
Cytogenetic Map14p21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14381307418274691Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14381307418274691Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141757341219726296Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:153
Count of miRNA genes:125
Interacting mature miRNAs:135
Transcripts:ENSRNOT00000003879
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


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

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 28 28 28
Medium 3 11 9 9 1 1 6 15 19 1 1
Low 10 8 4 6 4 2 2 21 8 16 3 2
Below cutoff 11 10 9 4 4 33 8 5 4 4

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB053574 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AW141770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC097344 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DY309525 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DY310963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DY317147 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J00694 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J02816 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J02838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M18351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  V01236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  V01254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X02361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X05093 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000003879   ⟹   ENSRNOP00000003879
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1417,573,412 - 17,591,480 (-)Ensembl
Rnor_6.0 Ensembl1419,141,755 - 19,159,923 (-)Ensembl
RefSeq Acc Id: NM_012493   ⟹   NP_036625
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21417,573,412 - 17,591,476 (-)NCBI
Rnor_6.01419,141,755 - 19,159,919 (-)NCBI
Rnor_5.01419,049,096 - 19,067,260 (-)NCBI
RGSC_v3.41419,092,563 - 19,110,728 (-)RGD
Celera1416,939,827 - 16,957,879 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091614   ⟹   XP_038947542
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21417,573,412 - 17,580,901 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_036625   ⟸   NM_012493
- Peptide Label: precursor
- UniProtKB: G3V6D0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003879   ⟸   ENSRNOT00000003879
RefSeq Acc Id: XP_038947542   ⟸   XM_039091614
- Peptide Label: isoform X1
Protein Domains
Albumin

Transcriptome

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


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)
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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
PVG/Seac (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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/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:2065 AgrOrtholog
Ensembl Genes ENSRNOG00000002889 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003879 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003879 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7459964 IMAGE-MGC_LOAD
InterPro ALB/AFP/VDB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Serum_albumin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Serum_albumin/AFP/Afamin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Serum_albumin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Serum_albumin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24177 UniProtKB/TrEMBL
MGC_CLONE MGC:114356 IMAGE-MGC_LOAD
NCBI Gene 24177 ENTREZGENE
PANTHER PTHR11385 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Serum_albumin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Afp PhenoGen
PIRSF Serum_albumin_subgroup UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS AFETOPROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SERUMALBUMIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ALBUMIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ALBUMIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ALBUMIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48552 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC216588
UniProt FETA_RAT UniProtKB/Swiss-Prot
  G3V6D0 ENTREZGENE, UniProtKB/TrEMBL
  P02773 ENTREZGENE
  Q4QR90_RAT UniProtKB/TrEMBL
  Q63033_RAT UniProtKB/TrEMBL
UniProt Secondary Q63032 UniProtKB/Swiss-Prot
  Q63205 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Afp  alpha-fetoprotein      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression synthesized by the fetal liver and yolk sac 61489
gene_function binds copper, nickel, fatty acids, bilirubin, and serum albumin  
gene_process may play a role in the maintenance of osmotic pressure