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 and hepatocellular carcinoma. 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
Previously 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 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1417,573,412 - 17,591,480 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1417,559,718 - 17,577,743 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01418,878,645 - 18,896,663 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01417,577,705 - 17,595,633 (-)NCBIRnor_WKY
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2'-Dihydroxy-4-methoxybenzophenone  (EXP)
2,3,4,5-Tetrachloro-4'-biphenylol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-tribromophenol  (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)
3,3',5,5'-tetrabromobisphenol A  (ISO)
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)
arotinoid acid  (ISO)
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 atom  (ISO)
cobalt dichloride  (EXP)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cortisol  (ISO)
coumestrol  (EXP)
Cuprizon  (EXP)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
D-glucose  (ISO)
decabromodiphenyl ether  (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-ascorbic acid  (ISO)
L-ascorbic acid 2-phosphate  (ISO)
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)
trichloroethene  (EXP)
triclosan  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
urea  (ISO)
valproic acid  (ISO)
XAV939  (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
# Reference Title Reference Citation
1. The transcription control region of the rat alpha-fetoprotein gene. DNA sequence and homology studies. Buzard G and Locker J, DNA Seq 1990;1(1):33-48.
2. Applicability of BALAD score in prognostication of hepatitis B-related hepatocellular carcinoma. Chan SL, etal., J Gastroenterol Hepatol. 2015 Oct;30(10):1529-35. doi: 10.1111/jgh.13005.
3. Hormonal modulation of alpha-fetoprotein gene expression in newborn rat livers. Chiu JF, etal., Nucleic Acids Res. 1981 Dec 21;9(24):6917-33. doi: 10.1093/nar/9.24.6917.
4. Serum biomarkers in metastatic renal cell carcinoma. Dexeus FH, etal., Urology. 1991 Jul;38(1):6-10.
5. Bone marrow derived-mesenchymal stem cells downregulate IL17A dependent IL6/STAT3 signaling pathway in CCl4-induced rat liver fibrosis. Farouk S, etal., PLoS One. 2018 Oct 22;13(10):e0206130. doi: 10.1371/journal.pone.0206130. eCollection 2018.
6. Alpha-fetoprotein, the major fetal serum protein, is not essential for embryonic development but is required for female fertility. Gabant P, etal., Proc Natl Acad Sci U S A 2002 Oct 1;99(20):12865-70. Epub 2002 Sep 24.
7. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
9. Dexamethasone inhibits alpha-fetoprotein gene transcription in neonatal rat liver and isolated nuclei. Huang DP, etal., Nucleic Acids Res. 1985 Jun 11;13(11):3873-90. doi: 10.1093/nar/13.11.3873.
10. Sequence homology between RNAs encoding rat alpha-fetoprotein and rat serum albumin. Jagodzinski LL, etal., Proc Natl Acad Sci U S A 1981 Jun;78(6):3521-5.
11. Regulation of alpha-fetoprotein expression by Nkx2.8. Kajiyama Y, etal., Mol Cell Biol 2002 Sep;22(17):6122-30.
12. The Clinical Significance of Alpha-Fetoprotein mRNAs in Patients with Hepatocellular Carcinoma. Kobayashi S, etal., Gastrointest Tumors. 2017 Mar;3(3-4):141-152. doi: 10.1159/000455955. Epub 2017 Feb 8.
13. Prognostic analysis of Japanese men with metastatic germ cell tumors showing favorable response to bleomycin, etoposide and cisplatin as first-line chemotherapy. Kumano M, etal., Hinyokika Kiyo. 2007 Dec;53(12):851-6.
14. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
15. Elevated serum alpha fetoprotein levels promote pathological progression of hepatocellular carcinoma. Li P, etal., World J Gastroenterol. 2011 Nov 7;17(41):4563-71. doi: 10.3748/wjg.v17.i41.4563.
16. Alpha-fetoprotein is dynamically expressed in rat pancreas during development. Liu L, etal., Dev Growth Differ. 2007 Oct;49(8):669-81.
17. Expression of AFP and Rev-Erb A/Rev-Erb B and N-CoR in fetal rat liver, liver injury and liver regeneration. Meier V, etal., Comp Hepatol. 2006 Jul 5;5:2.
18. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
19. Expression of liver-specific functions and secretion of a hepatocyte growth factor by a newly established rat hepatoma cell line growing in a chemically-defined serum-free medium. Miyazaki M, etal., Res Exp Med (Berl). 1991;191(5):297-307.
20. Hepatocyte nuclear factor-6 stimulates transcription of the alpha-fetoprotein gene and synergizes with the retinoic-acid-receptor-related orphan receptor alpha-4. Nacer-Cherif H, etal., Biochem J 2003 Feb 1;369(Pt 3):583-91.
21. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. Inhibitory effect of acyclic retinoid (polyprenoic acid) on the secretion of alpha-fetoprotein in CCl4-treated rats. Okuno M, etal., J Nutr Sci Vitaminol (Tokyo). 1990 Oct;36(5):437-46.
23. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
24. Assessment of 54 biomarkers for biopsy-detectable prostate cancer. Parekh DJ, etal., Cancer Epidemiol Biomarkers Prev. 2007 Oct;16(10):1966-72.
25. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
26. Pharmacokinetics of diclofenac in rats intoxicated with CCL4, and in the regenerating liver. Reyes-Gordillo K, etal., Biopharm Drug Dispos. 2007 Nov;28(8):415-22.
27. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
28. Comprehensive gene review and curation RGD comprehensive gene curation
29. Synthesis of alpha-fetoprotein and some other serum proteins in testicular tumors. Sakashita S, etal., Invest Urol. 1977 Jul;15(1):2-4.
30. Altered expression of alpha-fetoprotein and albumin in early embryonic rat liver upon heat shock. Srinivas UK and Revathi CJ, Biochem Mol Biol Int. 1994 May;33(1):21-8.
31. Gene-based anchoring of the rat genetic linkage and cytogenetic maps: new regional localizations, orientation of the linkage groups, and insights into mammalian chromosome evolution. Szpirer C, etal., Mamm Genome 1998 Sep;9(9):721-34
32. Elevation of serum alpha-fetoprotein and proliferation of oval cells in the livers of LEC rats. Takahashi H, etal., Jpn J Cancer Res. 1988 Jul;79(7):821-7. doi: 10.1111/j.1349-7006.1988.tb00043.x.
33. Direct-acting antiviral-based triple therapy on alpha-fetoprotein level in chronic hepatitis C patients. Takayama K, etal., World J Gastroenterol. 2015 Apr 21;21(15):4696-706. doi: 10.3748/wjg.v21.i15.4696.
34. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
35. Cellular analysis of alpha-fetoprotein gene activation during carbon tetrachloride and D-galactosamine-induced acute liver injury in rats. Tournier I, etal., Lab Invest. 1988 Nov;59(5):657-65.
36. Surgery in infants and children with testicular and paratesticular tumours: a single centre experience over a 25-year-period. Trobs RB, etal., Klin Padiatr. 2007 May-Jun;219(3):146-51.
37. Rat alpha 1-fetoprotein messenger RNA: 5'-end sequence and glucocorticoid-suppressed liver transcription in an improved nuclear run-off assay. Turcotte B, etal., Nucleic Acids Res 1985 Apr 11;13(7):2387-98.
38. 9-cis-retinoic acid is more effective than all-trans-retinoic acid in upregulating expression of the alpha-fetoprotein gene. Wan YJ, etal., J Mol Endocrinol. 1995 Feb;14(1):101-8. doi: 10.1677/jme.0.0140101.
39. On the mechanism of bile acid inhibition of rat sterol 12alpha-hydroxylase gene (CYP8B1) transcription: roles of alpha-fetoprotein transcription factor and hepatocyte nuclear factor 4alpha. Yang Y, etal., Biochim Biophys Acta 2002 Jun 13;1583(1):63-73.
40. Prolactin promotes hepatocellular carcinoma through Janus kinase 2. Yeh YT, etal., World J Surg. 2012 May;36(5):1128-35. doi: 10.1007/s00268-012-1505-4.
41. Development of multimarker panel for early detection of endometrial cancer. High diagnostic power of prolactin. Yurkovetsky Z, etal., Gynecol Oncol. 2007 Oct;107(1):58-65. Epub 2007 Jul 19.
42. Garlic Oil Suppressed Nitrosodiethylamine-Induced Hepatocarcinoma in Rats by Inhibiting PI3K-AKT-NF-κB Pathway. Zhang CL, etal., Int J Biol Sci. 2015 Apr 25;11(6):643-51. doi: 10.7150/ijbs.10785. eCollection 2015.
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 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1417,573,412 - 17,591,480 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1417,559,718 - 17,577,743 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01418,878,645 - 18,896,663 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01417,577,705 - 17,595,633 (-)NCBIRnor_WKY
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38473,436,221 - 73,456,174 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl473,431,138 - 73,456,174 (+)EnsemblGRCh38hg38GRCh38
GRCh37474,301,938 - 74,321,891 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36474,520,797 - 74,540,356 (+)NCBINCBI36Build 36hg18NCBI36
Build 34474,666,967 - 74,686,527NCBI
Celera471,661,745 - 71,681,240 (+)NCBICelera
Cytogenetic Map4q13.3ENTREZGENE
HuRef470,113,467 - 70,132,962 (+)NCBIHuRef
CHM1_1474,338,122 - 74,357,615 (+)NCBICHM1_1
T2T-CHM13v2.0476,779,943 - 76,799,830 (+)NCBIT2T-CHM13v2.0
Afp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39590,638,573 - 90,656,766 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl590,638,596 - 90,656,766 (+)EnsemblGRCm39 Ensembl
GRCm38590,490,714 - 90,508,907 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl590,490,737 - 90,508,907 (+)EnsemblGRCm38mm10GRCm38
MGSCv37590,919,740 - 90,937,933 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36591,565,937 - 91,584,106 (+)NCBIMGSCv36mm8
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_v0Mhudiblu_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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01362,992,405 - 63,012,932 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1362,992,405 - 63,012,932 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11362,603,973 - 62,624,508 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01362,097,020 - 62,117,581 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01363,232,901 - 63,253,687 (+)NCBIUU_Cfam_GSD_1.0
Afp
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528513,606,058 - 13,625,722 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365982,058,117 - 2,077,728 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365982,058,474 - 2,077,711 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AFP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl869,677,690 - 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
AFP
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1721,904,225 - 21,924,105 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl721,905,154 - 21,924,092 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666084873,280 - 892,444 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Afp
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473534,072,192 - 34,092,604 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473534,072,257 - 34,092,540 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Afp
290 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
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
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141757341219726296Rat
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
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat
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
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat

Markers in Region
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


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

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P02773-F1-model_v2 AlphaFold P02773 1-611 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2065 AgrOrtholog
BioCyc Gene G2FUF-16187 BioCyc
Ensembl Genes ENSRNOG00000002889 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003879 ENTREZGENE
  ENSRNOP00000003879.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003879 ENTREZGENE
  ENSRNOT00000003879.4 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