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 have fatty acid binding activity and zinc ion binding activity. Involved in animal organ development and response to organic substance. Localizes to cytoplasm and extracellular space. 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
Cytogenetic Map14p22NCBI
RH 3.4 Map14214.49RGD
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)
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)
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 dichloride  (EXP)
carbon nanotube  (ISO)
carfilzomib  (EXP)
chalcone  (EXP)
CHIR 99021  (ISO)
chloroprene  (ISO)
chlorpromazine  (ISO)
chlorpyrifos  (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)
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)
hesperidin  (EXP)
hexestrol  (EXP)
hypochlorous acid  (ISO)
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)
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)
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)
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)
extracellular space  (IDA,IEA,ISO,TAS)

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. Dexeus FH, etal., Urology. 1991 Jul;38(1):6-10.
3. Gabant P, etal., Proc Natl Acad Sci U S A 2002 Oct 1;99(20):12865-70. Epub 2002 Sep 24.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Jagodzinski LL, etal., Proc Natl Acad Sci U S A 1981 Jun;78(6):3521-5.
7. Kajiyama Y, etal., Mol Cell Biol 2002 Sep;22(17):6122-30.
8. Kumano M, etal., Hinyokika Kiyo. 2007 Dec;53(12):851-6.
9. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
10. Li P, etal., World J Gastroenterol. 2011 Nov 7;17(41):4563-71. doi: 10.3748/wjg.v17.i41.4563.
11. Liu L, etal., Dev Growth Differ. 2007 Oct;49(8):669-81.
12. Meier V, etal., Comp Hepatol. 2006 Jul 5;5:2.
13. MGD data from the GO Consortium
14. Miyazaki M, etal., Res Exp Med (Berl). 1991;191(5):297-307.
15. Nacer-Cherif H, etal., Biochem J 2003 Feb 1;369(Pt 3):583-91.
16. NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. Okuno M, etal., J Nutr Sci Vitaminol (Tokyo). 1990 Oct;36(5):437-46.
18. OMIM Disease Annotation Pipeline
19. Parekh DJ, etal., Cancer Epidemiol Biomarkers Prev. 2007 Oct;16(10):1966-72.
20. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
21. Reyes-Gordillo K, etal., Biopharm Drug Dispos. 2007 Nov;28(8):415-22.
22. RGD automated import pipeline for gene-chemical interactions
23. RGD comprehensive gene curation
24. Sakashita S, etal., Invest Urol. 1977 Jul;15(1):2-4.
25. Szpirer C, etal., Mamm Genome 1998 Sep;9(9):721-34
26. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
27. Trobs RB, etal., Klin Padiatr. 2007 May-Jun;219(3):146-51.
28. Turcotte B, etal., Nucleic Acids Res 1985 Apr 11;13(7):2387-98.
29. Yang Y, etal., Biochim Biophys Acta 2002 Jun 13;1583(1):63-73.
30. 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
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
Cytogenetic Map14p22NCBI
RH 3.4 Map14214.49RGD
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
GRCh37474,301,933 - 74,321,492 (+)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_1474,338,125 - 74,357,625 (+)NCBICHM1_1
Afp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39590,638,573 - 90,656,766 (+)NCBIGRCm39mm39
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
CanFam3.1 Ensembl1362,053,814 - 62,294,709 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11362,182,876 - 62,203,414 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Afp
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1721,904,225 - 21,924,105 (+)NCBI
ChlSab1.1 Ensembl721,905,154 - 21,924,092 (+)Ensembl
Afp
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473534,072,257 - 34,092,540 (-)NCBI

Position Markers
D14Mit2  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01419,161,705 - 19,161,893NCBIRnor6.0
Cytogenetic Map14p21UniSTS
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
D14Wox8  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map14p21UniSTS
RH 3.4 Map14224.4UniSTS
RH 3.4 Map14224.4RGD
RH 2.0 Map14212.6RGD
D14Wox9  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1416,959,190 - 16,959,641UniSTS
Cytogenetic Map14p21UniSTS
RH 3.4 Map14218.8UniSTS
RH 3.4 Map14218.8RGD
PMC275467P5  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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
Cytogenetic Map14p21UniSTS
RH 3.4 Map14224.4UniSTS
RH94533  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map14p21UniSTS
RH 3.4 Map14214.49UniSTS
UniSTS:275850  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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 (Rnor_6.0)
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)14127597761Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14134403399Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14141333960Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14141333960Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14142766285Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14222782519230541Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14483323319909932Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14483323319909932Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14483323323004027Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14483323326466248Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14483323333040042Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin141053997755539977Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)141053997755539977Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141268042430155192Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141268061332593926Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141633698833163485Rat
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141915991938289187Rat

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
GenBank Nucleotide AABR07014521 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07014522 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01078391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  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
  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
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
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:
Reference Sequences
RefSeq Acc Id: NP_036625   ⟸   NM_012493
- Peptide Label: precursor
- UniProtKB: G3V6D0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003879   ⟸   ENSRNOT00000003879
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 (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)
ACI/EurMcwi (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
ACI/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
BBDP/Wor (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
BN/SsN (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
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)
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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
F344/NRrrc (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
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
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 (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 (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
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 (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 (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 (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, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003879 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003879 ENTREZGENE, 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
UniGene Rn.9174 ENTREZGENE
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