Rpn2 (ribophorin II) - Rat Genome Database

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Gene: Rpn2 (ribophorin II) Rattus norvegicus
Analyze
Symbol: Rpn2
Name: ribophorin II
RGD ID: 62075
Description: Exhibits ribosome binding activity. Involved in aging and response to drug. Localizes to autophagosome membrane and rough endoplasmic reticulum. Orthologous to human RPN2 (ribophorin II); PARTICIPATES IN Endoplasmic Reticulum-associated degradation pathway; N-linked glycan biosynthetic pathway; INTERACTS WITH 1,2,4-trimethylbenzene; 17beta-estradiol; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa subunit; dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2; ribophorin 2; ribophorin-2; RPN-II
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23145,941,787 - 145,989,271 (+)NCBI
Rnor_6.0 Ensembl3153,398,130 - 153,445,632 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03153,398,373 - 153,445,633 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03158,274,303 - 158,321,478 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43147,976,544 - 148,023,743 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13147,882,452 - 147,929,652 (+)NCBI
Celera3144,647,439 - 144,694,686 (+)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9642163   PMID:12887896   PMID:15489334   PMID:18724378   PMID:19182904   PMID:19946888   PMID:21949367   PMID:24625528  


Genomics

Comparative Map Data
Rpn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23145,941,787 - 145,989,271 (+)NCBI
Rnor_6.0 Ensembl3153,398,130 - 153,445,632 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03153,398,373 - 153,445,633 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03158,274,303 - 158,321,478 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43147,976,544 - 148,023,743 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13147,882,452 - 147,929,652 (+)NCBI
Celera3144,647,439 - 144,694,686 (+)NCBICelera
Cytogenetic Map3q42NCBI
RPN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2037,178,410 - 37,241,619 (+)EnsemblGRCh38hg38GRCh38
GRCh382037,179,161 - 37,241,623 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372035,807,733 - 35,870,022 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362035,240,888 - 35,303,440 (+)NCBINCBI36hg18NCBI36
Build 342035,240,887 - 35,303,437NCBI
Celera2032,515,047 - 32,577,306 (+)NCBI
Cytogenetic Map20q11.23NCBI
HuRef2032,542,723 - 32,605,618 (+)NCBIHuRef
CHM1_12035,710,376 - 35,772,982 (+)NCBICHM1_1
Rpn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392157,121,018 - 157,168,238 (+)NCBIGRCm39mm39
GRCm39 Ensembl2157,120,937 - 157,168,239 (+)Ensembl
GRCm382157,279,098 - 157,326,318 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2157,279,017 - 157,326,319 (+)EnsemblGRCm38mm10GRCm38
MGSCv372157,104,834 - 157,152,054 (+)NCBIGRCm37mm9NCBIm37
MGSCv362156,970,539 - 157,017,759 (+)NCBImm8
Celera2163,214,429 - 163,262,680 (+)NCBICelera
Cytogenetic Map2H1NCBI
cM Map278.2NCBI
Rpn2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542224,497,228 - 24,550,439 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542224,497,288 - 24,550,439 (-)NCBIChiLan1.0ChiLan1.0
RPN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12034,616,651 - 34,678,131 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2034,616,651 - 34,678,127 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02033,501,275 - 33,563,523 (+)NCBIMhudiblu_PPA_v0panPan3
RPN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12425,827,524 - 25,884,813 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2425,827,450 - 25,955,742 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2425,475,694 - 25,533,721 (+)NCBI
ROS_Cfam_1.02426,524,313 - 26,582,092 (+)NCBI
UMICH_Zoey_3.12425,801,956 - 25,859,617 (+)NCBI
UNSW_CanFamBas_1.02425,906,817 - 25,964,620 (+)NCBI
UU_Cfam_GSD_1.02426,396,000 - 26,453,865 (+)NCBI
Rpn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640174,728,719 - 174,788,494 (+)NCBI
SpeTri2.0NW_0049365613,960,979 - 4,020,792 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RPN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1740,322,394 - 40,378,857 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11740,322,364 - 40,378,866 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21745,858,843 - 45,874,957 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RPN2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1226,503,344 - 26,563,958 (-)NCBI
ChlSab1.1 Ensembl226,503,597 - 26,564,142 (-)Ensembl
Rpn2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248422,349,837 - 2,419,262 (-)NCBI

Position Markers
D3Rat6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23145,956,084 - 145,956,249 (+)MAPPER
Rnor_6.03153,412,455 - 153,412,619NCBIRnor6.0
Rnor_5.03158,307,259 - 158,307,423UniSTSRnor5.0
RGSC_v3.43147,990,566 - 147,990,731RGDRGSC3.4
RGSC_v3.43147,990,567 - 147,990,731UniSTSRGSC3.4
RGSC_v3.13147,896,437 - 147,896,729RGD
Celera3144,661,462 - 144,661,626UniSTS
SHRSP x BN Map370.9999RGD
SHRSP x BN Map370.9999UniSTS
FHH x ACI Map386.36RGD
Cytogenetic Map3q42UniSTS
RH128253  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23145,984,378 - 145,984,577 (+)MAPPER
Rnor_6.03153,440,741 - 153,440,939NCBIRnor6.0
Rnor_5.03158,278,997 - 158,279,195UniSTSRnor5.0
RGSC_v3.43148,018,852 - 148,019,050UniSTSRGSC3.4
Celera3144,689,795 - 144,689,993UniSTS
RH 3.4 Map31339.8UniSTS
Cytogenetic Map3q42UniSTS
RH133474  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23145,988,951 - 145,989,168 (+)MAPPER
Rnor_6.03153,445,314 - 153,445,530NCBIRnor6.0
Rnor_5.03158,274,406 - 158,274,622UniSTSRnor5.0
RGSC_v3.43148,023,425 - 148,023,641UniSTSRGSC3.4
Celera3144,694,368 - 144,694,584UniSTS
RH 3.4 Map31339.8UniSTS
Cytogenetic Map3q42UniSTS
AW530082  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23145,987,980 - 145,988,184 (+)MAPPER
Rnor_6.03153,444,343 - 153,444,546NCBIRnor6.0
Rnor_5.03158,275,390 - 158,275,593UniSTSRnor5.0
RGSC_v3.43148,022,454 - 148,022,657UniSTSRGSC3.4
Celera3144,693,397 - 144,693,600UniSTS
RH 3.4 Map31345.7UniSTS
Cytogenetic Map3q42UniSTS
AW529545  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23145,988,162 - 145,988,360 (+)MAPPER
Rnor_6.03153,444,525 - 153,444,722NCBIRnor6.0
Rnor_5.03158,275,214 - 158,275,411UniSTSRnor5.0
RGSC_v3.43148,022,636 - 148,022,833UniSTSRGSC3.4
Celera3144,693,579 - 144,693,776UniSTS
RH 3.4 Map31344.9UniSTS
Cytogenetic Map3q42UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)381136227154416635Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3102152812155263151Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3114376250159376250Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3119471263164471263Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3125848628170848628Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3126575595153412619Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3126575595165355668Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128986468173986468Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3130006659175006659Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3132875075176418101Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3136876155170935007Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3138374177177699992Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3138374177177699992Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3139578365177699992Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3146232777177699992Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3147072047154807958Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3148034701177699992Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3148348517171467264Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3148348739163640325Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3150368003177699992Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3153381237174632112Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3153381237174632112Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3153381237174632112Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3153381237174632112Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3153381237174632112Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3153381237174632112Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3153381237174632112Rat
1300113Bp176Blood pressure QTL 1763.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3153412455165355668Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)3153412455170534769Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3153412455177699992Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:43
Count of miRNA genes:39
Interacting mature miRNAs:43
Transcripts:ENSRNOT00000068135
Prediction methods: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

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: ENSRNOT00000068135   ⟹   ENSRNOP00000063207
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3153,398,130 - 153,445,632 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091273   ⟹   ENSRNOP00000074071
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3153,402,548 - 153,441,611 (+)Ensembl
RefSeq Acc Id: NM_031698   ⟹   NP_113886
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23145,942,062 - 145,989,270 (+)NCBI
Rnor_6.03153,398,432 - 153,445,632 (+)NCBI
Rnor_5.03158,274,303 - 158,321,478 (-)NCBI
RGSC_v3.43147,976,544 - 148,023,743 (+)RGD
Celera3144,647,439 - 144,694,686 (+)RGD
Sequence:
RefSeq Acc Id: XM_006235379   ⟹   XP_006235441
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23145,941,787 - 145,989,271 (+)NCBI
Rnor_6.03153,398,373 - 153,445,633 (+)NCBI
Rnor_5.03158,274,303 - 158,321,478 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039105815   ⟹   XP_038961743
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23145,943,094 - 145,989,271 (+)NCBI
RefSeq Acc Id: XM_039105816   ⟹   XP_038961744
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23145,943,334 - 145,989,271 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_113886   ⟸   NM_031698
- Peptide Label: precursor
- UniProtKB: P25235 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006235441   ⟸   XM_006235379
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000074071   ⟸   ENSRNOT00000091273
RefSeq Acc Id: ENSRNOP00000063207   ⟸   ENSRNOT00000068135
RefSeq Acc Id: XP_038961743   ⟸   XM_039105815
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038961744   ⟸   XM_039105816
- Peptide Label: isoform X2

Transcriptome

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

Promoters
RGD ID:13692609
Promoter ID:EPDNEW_R3134
Type:initiation region
Name:Rpn2_1
Description:ribophorin II
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_6.03153,398,429 - 153,398,489EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
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)
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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)
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)
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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)
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)
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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:62075 AgrOrtholog
Ensembl Genes ENSRNOG00000007492 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000063207 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000074071 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068135 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000091273 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6919638 IMAGE-MGC_LOAD
InterPro Swp1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:64701 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72765 IMAGE-MGC_LOAD
NCBI Gene 64701 ENTREZGENE
PANTHER PTHR12640 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ribophorin_II UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rpn2 PhenoGen
TIGR TC216621
UniProt A0A0G2K757_RAT UniProtKB/TrEMBL
  P25235 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q6P9X0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Rpn2  ribophorin II    ribophorin 2  Name updated 1299863 APPROVED
2002-06-10 Rpn2  ribophorin 2      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference