Phb (prohibitin) - Rat Genome Database
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Gene: Phb (prohibitin) Rattus norvegicus
Analyze
Symbol: Phb
Name: prohibitin
RGD ID: 3322
Description: Predicted to have several functions, including complement binding activity; histone deacetylase binding activity; and protein C-terminus binding activity. Involved in several processes, including female gonad development; positive regulation of protein kinase B signaling; and positive regulation of smooth muscle cell proliferation. Localizes to several cellular components, including GABA-ergic synapse; extrinsic component of presynaptic active zone membrane; and mitochondrial membrane. Biomarker of urinary bladder cancer. Human ortholog(s) of this gene implicated in breast cancer and sporadic breast cancer. Orthologous to human PHB (prohibitin); INTERACTS WITH (R)-adrenaline; 17alpha-ethynylestradiol; 17beta-hydroxy-5alpha-androstan-3-one.
Type: protein-coding
RefSeq Status: PROVISIONAL
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Phb-ps1  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21080,605,268 - 80,618,043 (+)NCBI
Rnor_6.0 Ensembl1083,476,107 - 83,488,878 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01083,476,107 - 83,488,878 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01083,284,048 - 83,296,819 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.1199,127,730 - 9,128,666 (+)NCBI
Celera1079,373,802 - 79,386,571 (+)NCBICelera
Cytogenetic Map10q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(R)-adrenaline  (EXP)
(S)-nicotine  (ISO)
(Z)-3-butylidenephthalide  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4,6-trinitrotoluene  (EXP)
2,4-dinitrotoluene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxynon-2-enal  (ISO)
7,12-dimethyltetraphene  (EXP)
7H-xanthine  (EXP)
9H-xanthine  (EXP)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bicalutamide  (ISO)
bilirubin IXalpha  (ISO)
bisphenol A  (EXP)
Brodifacoum  (EXP)
busulfan  (ISO)
cadmium dichloride  (EXP)
caffeine  (ISO)
calcitriol  (ISO)
choline  (EXP)
chromium trinitrate  (ISO)
chromium(6+)  (ISO)
clobetasol  (ISO)
clofibrate  (EXP,ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
cypermethrin  (EXP)
diarsenic trioxide  (ISO)
dichlorine  (EXP)
diuron  (EXP)
dopamine  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
eurycomanone  (ISO)
finasteride  (EXP)
flavone  (ISO)
flutamide  (EXP)
folic acid  (ISO)
genistein  (EXP)
geraniol  (EXP,ISO)
hyaluronic acid  (EXP)
hydralazine  (ISO)
hydrogen peroxide  (EXP,ISO)
ketamine  (EXP)
L-methionine  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (EXP)
lithium atom  (EXP)
lithium hydride  (EXP)
LY294002  (EXP,ISO)
malathion  (ISO)
menadione  (ISO)
methamphetamine  (EXP)
methoxychlor  (EXP)
methyl methanesulfonate  (ISO)
miconazole  (ISO)
Monobutylphthalate  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
nicotine  (ISO)
nimesulide  (EXP)
ochratoxin A  (EXP,ISO)
ozone  (EXP)
paracetamol  (ISO)
paraoxon  (ISO)
pentachlorophenol  (ISO)
perfluorododecanoic acid  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (EXP)
phenobarbital  (EXP)
PhIP  (EXP)
pirinixic acid  (EXP,ISO)
piroxicam  (ISO)
potassium chromate  (ISO)
potassium dichromate  (EXP)
progesterone  (ISO)
pyrogallol  (ISO)
quinomethionate  (ISO)
rotenone  (ISO)
sodium arsenite  (ISO)
streptozocin  (EXP)
T-2 toxin  (EXP,ISO)
tamoxifen  (ISO)
thapsigargin  (ISO)
Tributyltin oxide  (ISO)
triciribine  (EXP)
tungsten  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of phospholipase C activity  (ISO,ISS)
activation of protein kinase C activity  (ISO,ISS)
animal organ regeneration  (IEP)
antiviral innate immune response  (ISO)
B cell activation  (ISO,ISS)
CD40 signaling pathway  (ISO,ISS)
cellular response to interleukin-6  (ISO)
DNA biosynthetic process  (ISO)
histone deacetylation  (ISO)
mitochondrion organization  (IBA,ISO)
modulation by host of viral RNA genome replication  (ISO)
negative regulation of androgen receptor signaling pathway  (ISO)
negative regulation of apoptotic process  (IMP)
negative regulation of cell growth  (ISO)
negative regulation of cell population proliferation  (IMP,ISO)
negative regulation of ERK1 and ERK2 cascade  (ISO)
negative regulation of glucocorticoid receptor signaling pathway  (ISO)
negative regulation of protein catabolic process  (ISO)
negative regulation of transcription by competitive promoter binding  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
ovarian follicle atresia  (IEP)
ovarian follicle development  (IEP)
positive regulation of cell death  (ISO)
positive regulation of complement activation  (ISO)
positive regulation of ERK1 and ERK2 cascade  (ISO)
positive regulation of G protein-coupled receptor signaling pathway  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of immunoglobulin production  (ISO,ISS)
positive regulation of interleukin-17 production  (ISO,ISS)
positive regulation of NIK/NF-kappaB signaling  (ISO,ISS)
positive regulation of protein kinase B signaling  (IMP)
positive regulation of smooth muscle cell proliferation  (IMP)
positive regulation of transcription, DNA-templated  (ISO)
progesterone receptor signaling pathway  (ISO)
protein stabilization  (ISO)
regulation of transcription, DNA-templated  (ISO)
response to cytokine  (IEP)
response to drug  (IEP)
response to ethanol  (IEP)
response to immobilization stress  (IEP)
response to peptide hormone  (IEP)
RIG-I signaling pathway  (ISO)
T-helper 17 type immune response  (ISO,ISS)
viral entry into host cell  (ISO)

References

References - curated
1. Altus MS, etal., Gene 1995 Jun 9;158(2):291-4.
2. Asamoto M and Cohen SM, Cancer Lett. 1994 Aug 15;83(1-2):201-7.
3. Bailey SM, etal., Am J Physiol Gastrointest Liver Physiol. 2006 Nov;291(5):G857-67. Epub 2006 Jul 6.
4. Boyken J, etal., Neuron. 2013 Apr 24;78(2):285-97. doi: 10.1016/j.neuron.2013.02.027.
5. Byrjalsen I, etal., Mol Hum Reprod. 1999 Aug;5(8):748-56.
6. Campbell IG, etal., Cancer Epidemiol Biomarkers Prev. 2003 Nov;12(11 Pt 1):1273-4.
7. Cao YY, etal., Life Sci. 2020 Jun 1;250:117548. doi: 10.1016/j.lfs.2020.117548. Epub 2020 Mar 12.
8. Chowdhury I, etal., Endocrinology. 2007 Jan;148(1):206-17. Epub 2006 Oct 12.
9. Dixit VD, etal., Endocrinology. 2003 Apr;144(4):1496-505.
10. Dosemeci A, etal., Mol Cell Proteomics. 2007 Oct;6(10):1749-60. doi: 10.1074/mcp.M700040-MCP200. Epub 2007 Jul 9.
11. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
12. GOA data from the GO Consortium
13. Guo W, etal., Mol Cell Biochem. 2007 Jan;295(1-2):167-77. Epub 2006 Oct 17.
14. Ikonen E, etal., FEBS Lett. 1995 Jan 30;358(3):273-7.
15. Jupe ER, etal., Lancet. 2001 May 19;357(9268):1588-9.
16. Leonard JF, etal., Proteomics. 2006 Mar;6(6):1915-33.
17. Liu XH, etal., Proteomics. 2004 Oct;4(10):3167-76.
18. MGD data from the GO Consortium
19. NCBI rat LocusLink and RefSeq merged data July 26, 2002
20. Nuell MJ, etal., Mol Cell Biol 1991 Mar;11(3):1372-81.
21. OMIM Disease Annotation Pipeline
22. Opii WO, etal., J Neurotrauma. 2007 May;24(5):772-89.
23. RGD automated data pipeline
24. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
25. RGD automated import pipeline for gene-chemical interactions
26. RGD comprehensive gene curation
27. Sato T, etal., Cancer Res. 1992 Mar 15;52(6):1643-6.
28. Shan L, etal., Carcinogenesis. 2002 Oct;23(10):1561-8.
29. Spurdle AB, etal., Gynecol Oncol. 2003 Jul;90(1):145-9.
30. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
31. Tanno S, etal., Jpn J Cancer Res. 1997 Dec;88(12):1155-64.
32. Thompson WE, etal., Biol Reprod. 2004 Jul;71(1):282-90. Epub 2004 Mar 17.
33. Tsai HW, etal., Hum Pathol. 2006 Feb;37(2):198-204. Epub 2005 Dec 20.
34. Ummanni R, etal., Cancer Lett. 2008 Mar 31;.
35. Wu TF, etal., Anticancer Res. 2007 Mar-Apr;27(2):895-900.
Additional References at PubMed
PMID:11302691   PMID:11884367   PMID:12065415   PMID:12466959   PMID:12566959   PMID:12865426   PMID:14500729   PMID:14651853   PMID:15274632   PMID:15489334   PMID:16210410   PMID:16854843  
PMID:16964284   PMID:17008324   PMID:17070910   PMID:17324931   PMID:17597094   PMID:17634366   PMID:18480465   PMID:18487222   PMID:18614015   PMID:18958584   PMID:19906925   PMID:19946888  
PMID:20030709   PMID:20458337   PMID:20832420   PMID:20833797   PMID:20959514   PMID:21179762   PMID:21256116   PMID:21914039   PMID:22238093   PMID:22417827   PMID:22711522   PMID:23254195  
PMID:23376485   PMID:23921388   PMID:23992168   PMID:24096434   PMID:24185039   PMID:24204768   PMID:24625528   PMID:24732013   PMID:25031298   PMID:25463519   PMID:26048717   PMID:26310625  
PMID:26316108   PMID:26623724   PMID:27044659   PMID:27854077   PMID:28376086   PMID:29476059   PMID:29867124   PMID:30967257  


Genomics

Comparative Map Data
Phb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21080,605,268 - 80,618,043 (+)NCBI
Rnor_6.0 Ensembl1083,476,107 - 83,488,878 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01083,476,107 - 83,488,878 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01083,284,048 - 83,296,819 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.1199,127,730 - 9,128,666 (+)NCBI
Celera1079,373,802 - 79,386,571 (+)NCBICelera
Cytogenetic Map10q26NCBI
PHB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1749,404,052 - 49,414,901 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1749,404,049 - 49,414,905 (-)EnsemblGRCh38hg38GRCh38
GRCh381749,404,052 - 49,414,882 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371747,481,414 - 47,492,244 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361744,836,419 - 44,847,241 (-)NCBINCBI36hg18NCBI36
Build 341744,836,418 - 44,847,241NCBI
Celera1743,936,440 - 43,947,262 (-)NCBI
Cytogenetic Map17q21.33NCBI
HuRef1742,846,458 - 42,857,310 (-)NCBIHuRef
CHM1_11747,546,565 - 47,557,421 (-)NCBICHM1_1
Phb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391195,557,783 - 95,571,599 (+)NCBIGRCm39mm39
GRCm39 Ensembl1195,557,783 - 95,571,599 (+)Ensembl
GRCm381195,666,957 - 95,680,773 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1195,666,957 - 95,680,773 (+)EnsemblGRCm38mm10GRCm38
MGSCv371195,528,271 - 95,542,087 (+)NCBIGRCm37mm9NCBIm37
MGSCv361195,483,105 - 95,496,855 (+)NCBImm8
Celera11105,306,168 - 105,322,388 (+)NCBICelera
Cytogenetic Map11DNCBI
cM Map1159.01NCBI
Phb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545112,110,290 - 12,120,124 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495545112,110,290 - 12,119,870 (+)NCBIChiLan1.0ChiLan1.0
PHB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1178,175,912 - 8,186,790 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl178,175,968 - 8,186,790 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0178,189,555 - 8,200,491 (+)NCBIMhudiblu_PPA_v0panPan3
PHB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1925,525,711 - 25,536,722 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl925,526,649 - 25,536,722 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha924,985,397 - 24,996,403 (-)NCBI
ROS_Cfam_1.0926,321,934 - 26,332,949 (-)NCBI
UMICH_Zoey_3.1925,089,828 - 25,100,839 (-)NCBI
UNSW_CanFamBas_1.0925,349,147 - 25,360,155 (-)NCBI
UU_Cfam_GSD_1.0925,478,042 - 25,489,037 (-)NCBI
Phb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_ltri_2NW_02440560224,936,269 - 24,948,093 (-)NCBI
SpeTri2.0NW_00493649012,127,065 - 12,138,870 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1225,584,443 - 25,609,656 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11225,596,520 - 25,609,693 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21225,535,912 - 25,549,084 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PHB
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11669,805,968 - 69,816,792 (-)NCBI
ChlSab1.1 Ensembl1669,806,923 - 69,816,754 (-)Ensembl
Phb
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247955,556,728 - 5,565,969 (-)NCBI

Position Markers
RH127963  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map19p13UniSTS
Cytogenetic MapXq14UniSTS
Cytogenetic MapXq21UniSTS
Cytogenetic Map6q31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10642907599492409Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101482789492423564Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)1020170031102897474Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102152390683549467Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)12152390690312401Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102152390690312401Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102290149793886300Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)1027237530101482600Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1027237530102427718Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103618592995845311Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)104051404485514044Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)104051404485514044Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1041260363106105607Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1043289657108540162Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104370495588704955Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104659302198939209Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104684834691848346Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104684834691848346Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104684834691848346Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)105063833795638337Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)105128920384596393Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)105128920384596393Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)105128920384596393Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)105128920384596393Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)105128920384596393Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105310471898104718Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1053621375112626471Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1053621375112626471Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105362581598939209Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105363748594807701Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)1055224855100224855Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1055678976112626471Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)1055679084102427604Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1056698730101698730Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1060450007105450007Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1060875260105875260Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1060875260105875260Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1060875260105875260Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1062096293107096293Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)106464817584601269Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)1064648175101691360Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)1064648175102149713Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1064648175102149713Rat
61402Niddm3Non-insulin dependent diabetes mellitus QTL 34.58blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)106464831185513822Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1065590122110590122Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1065992275110992275Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1065992275110992275Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1067880046112626471Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1067988218110992091Rat
2298481Eau9Experimental allergic uveoretinitis QTL 90.0169uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)106830503785514044Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1069123603101482600Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1069385595112626471Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1069385595112626471Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1070166960112626471Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1070800069112626471Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1071692298112626471Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1073008136112626471Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1073008136112626471Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1073008136112626471Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1073467158112626471Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107504539197308358Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1075544754112626471Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1075544754112626471Rat
12880053Cm104Cardiac mass QTL 1040.009heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)107598366286419171Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat
12880050Am10Aortic mass QTL 100.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)107705574186962563Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107705574198282519Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)107834302790042115Rat
2325836Bp346Blood pressure QTL 3460.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107897027986962563Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107897027998282519Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1078970279112626471Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1079927661112626471Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1080239190112626471Rat
724516Uae17Urinary albumin excretion QTL 173.6urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)108094611088200662Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)1081515116101758478Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)108164977590297007Rat
634354Rends3Renal damage susceptibility QTL 30.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)108267523388141097Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108338982894488181Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1083389828104994768Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:367
Count of miRNA genes:197
Interacting mature miRNAs:227
Transcripts:ENSRNOT00000075733
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

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

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


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000075733   ⟹   ENSRNOP00000066502
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1083,476,107 - 83,488,878 (+)Ensembl
RefSeq Acc Id: NM_031851   ⟹   NP_114039
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21080,605,268 - 80,618,042 (+)NCBI
Rnor_6.01083,476,107 - 83,488,878 (+)NCBI
Rnor_5.01083,284,048 - 83,296,819 (+)NCBI
Celera1079,373,802 - 79,386,571 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039085263   ⟹   XP_038941191
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21080,605,318 - 80,618,043 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_114039   ⟸   NM_031851
- UniProtKB: P67779 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066502   ⟸   ENSRNOT00000075733
RefSeq Acc Id: XP_038941191   ⟸   XM_039085263
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13697620
Promoter ID:EPDNEW_R8145
Type:multiple initiation site
Name:Phb_1
Description:prohibitin
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01083,476,090 - 83,476,150EPDNEW

Strain Variation

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


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 83295845 83295846 T A snv BUF/MNa (KyushuU), ZFDM (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU), NIG-III/Hok (KyushuU)


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 83487904 83487905 T A snv CDS, CDR


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3322 AgrOrtholog
Ensembl Genes ENSRNOG00000046799 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000066502 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000075733 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7105633 IMAGE-MGC_LOAD
  IMAGE:7441791 IMAGE-MGC_LOAD
InterPro Band_7 UniProtKB/Swiss-Prot
  Band_7/SPFH_dom_sf UniProtKB/Swiss-Prot
  Prohibitin UniProtKB/Swiss-Prot
KEGG Report rno:25344 UniProtKB/Swiss-Prot
MGC_CLONE MGC:114298 IMAGE-MGC_LOAD
  MGC:91613 IMAGE-MGC_LOAD
NCBI Gene 25344 ENTREZGENE
PANTHER PTHR23222 UniProtKB/Swiss-Prot
Pfam Band_7 UniProtKB/Swiss-Prot
PhenoGen Phb PhenoGen
PRINTS PROHIBITIN UniProtKB/Swiss-Prot
SMART PHB UniProtKB/Swiss-Prot
Superfamily-SCOP SSF117892 UniProtKB/Swiss-Prot
UniProt P67779 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary P24142 UniProtKB/Swiss-Prot
  Q4V8M6 UniProtKB/Swiss-Prot


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

RGD Curation Notes
Note Type Note Reference
gene_homology has homology to the Drosophila Cc gene 729436