Prom2 (prominin 2) - Rat Genome Database
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Gene: Prom2 (prominin 2) Rattus norvegicus
Analyze
Symbol: Prom2
Name: prominin 2
RGD ID: 621435
Description: Exhibits cholesterol binding activity. Predicted to be involved in several processes, including negative regulation of endocytosis; positive regulation of protein phosphorylation; and regulation of GTPase activity. Localizes to several cellular components, including microspike; microvillus; and prominosome. Colocalizes with membrane raft. Orthologous to human PROM2 (prominin 2); INTERACTS WITH 17alpha-ethynylestradiol; 6-propyl-2-thiouracil; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: PROM-2; Prom-rp; prominin-2; prominin-like protein 2; prominin-related protein; Promrp; rPROML2; testosterone-regulated prominin-related protein; Trprp
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
Rnor_6.03120,087,633 - 120,107,495 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3120,092,582 - 120,106,697 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03127,225,616 - 127,239,978 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43115,030,864 - 115,044,987 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13114,936,437 - 114,950,560 (-)NCBI
Celera3113,584,551 - 113,598,660 (-)NCBICelera
Cytogenetic Map3q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12832703   PMID:19056867   PMID:19199708   PMID:23376485   PMID:23533145   PMID:23583380   PMID:29113580  


Genomics

Comparative Map Data
Prom2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.03120,087,633 - 120,107,495 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3120,092,582 - 120,106,697 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03127,225,616 - 127,239,978 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43115,030,864 - 115,044,987 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13114,936,437 - 114,950,560 (-)NCBI
Celera3113,584,551 - 113,598,660 (-)NCBICelera
Cytogenetic Map3q36NCBI
PROM2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl295,274,449 - 95,291,308 (+)EnsemblGRCh38hg38GRCh38
GRCh38295,274,449 - 95,291,320 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37295,939,674 - 95,966,067 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36295,303,928 - 95,320,781 (+)NCBINCBI36hg18NCBI36
Build 34295,362,074 - 95,378,928NCBI
Celera290,293,346 - 90,310,195 (+)NCBI
Cytogenetic Map2q11.1NCBI
HuRef289,967,276 - 89,984,207 (+)NCBIHuRef
CHM1_1295,944,549 - 95,961,410 (+)NCBICHM1_1
Prom2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392127,368,873 - 127,383,337 (-)NCBIGRCm39mm39
GRCm382127,526,953 - 127,541,417 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2127,526,473 - 127,541,467 (-)EnsemblGRCm38mm10GRCm38
MGSCv372127,352,689 - 127,367,153 (-)NCBIGRCm37mm9NCBIm37
MGSCv362127,217,914 - 127,232,908 (-)NCBImm8
Celera2128,771,840 - 128,786,259 (-)NCBICelera
Cytogenetic Map2F1NCBI
Prom2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554703,524,805 - 3,538,935 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554703,524,900 - 3,538,882 (+)NCBIChiLan1.0ChiLan1.0
PROM2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A96,177,524 - 96,194,382 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02A104,117,086 - 104,138,298 (-)NCBIMhudiblu_PPA_v0panPan3
PROM2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1734,815,735 - 34,827,740 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11734,814,260 - 34,827,833 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Prom2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493674473,004 - 85,911 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PROM2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl346,003,238 - 46,023,405 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1346,001,949 - 46,025,425 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2348,368,831 - 48,381,710 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PROM2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.114305,442 - 323,187 (+)NCBI
ChlSab1.1 Ensembl14306,515 - 323,909 (+)Ensembl
Prom2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247492,036,335 - 2,049,434 (+)NCBI

Position Markers
RH134252  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03120,092,624 - 120,092,828NCBIRnor6.0
Rnor_5.03127,239,714 - 127,239,918UniSTSRnor5.0
RGSC_v3.43115,030,914 - 115,031,118UniSTSRGSC3.4
Celera3113,584,601 - 113,584,805UniSTS
Cytogenetic Map3q36UniSTS
RH 3.4 Map3997.3UniSTS
BM388274  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03120,100,405 - 120,100,587NCBIRnor6.0
Rnor_5.03127,231,955 - 127,232,137UniSTSRnor5.0
RGSC_v3.43115,038,696 - 115,038,878UniSTSRGSC3.4
Celera3113,592,370 - 113,592,552UniSTS
Cytogenetic Map3q36UniSTS
RH 3.4 Map3986.5UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)330114912123700444Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)394788365139788365Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)397009185142009185Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
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
7387306Bw124Body weight QTL 1243.20.0003body mass (VT:0001259)body weight (CMO:0000012)388910015133910015Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)362922868127023997Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)339248391140271184Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3117303473141971336Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3102466149147466149Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
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
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)345406058127023997Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)381136227154416635Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)378700444123700444Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3119471263164471263Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3102152812155263151Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3114376250159376250Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)351822008120917851Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)372973445127023997Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)372672290127023997Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3101058963146058963Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)351821836124513579Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:548
Count of miRNA genes:247
Interacting mature miRNAs:307
Transcripts:ENSRNOT00000020354
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

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 15
Low 1 6 10 6 4 6 7 10 6 20 29 11 7
Below cutoff 1 20 31 19 13 19 1 1 60 8 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020354   ⟹   ENSRNOP00000020354
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3120,092,582 - 120,106,697 (-)Ensembl
RefSeq Acc Id: NM_138857   ⟹   NP_620212
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03120,092,574 - 120,106,697 (-)NCBI
Rnor_5.03127,225,616 - 127,239,978 (+)NCBI
RGSC_v3.43115,030,864 - 115,044,987 (-)RGD
Celera3113,584,551 - 113,598,660 (-)RGD
Sequence:
RefSeq Acc Id: XM_006234947   ⟹   XP_006235009
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03120,092,564 - 120,107,495 (-)NCBI
Rnor_5.03127,225,616 - 127,239,978 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017591452   ⟹   XP_017446941
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03120,087,868 - 120,107,495 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591453   ⟹   XP_017446942
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03120,094,131 - 120,106,411 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001837029
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03120,087,633 - 120,107,495 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_620212   ⟸   NM_138857
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_006235009   ⟸   XM_006234947
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017446941   ⟸   XM_017591452
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017446942   ⟸   XM_017591453
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000020354   ⟸   ENSRNOT00000020354

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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)
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
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 127232066 127232067 C T snv WKY/NCrl (KNAW), WKY/N (KNAW), WKY/NHsd (KNAW)
3 127234163 127234164 A G snv F344/Jcl (KyushuU), LH/MavRrrc (KNAW), SR/JrHsd (KNAW), BBDP/WorN (KNAW), F344/NRrrc (Illumina) (KNAW), F344/NRrrc (SOLiD) (KNAW), Crl:SD (UDEL), LEC/Tj (KyushuU), ZFDM (KyushuU), SS/JrHsdMcwi (MCW), LEW/NCrl (KNAW), LE/Stm (KyushuU), F344/Stm (KyushuU), GH/OmrMcwi (MCW), SHR/OlaIpcvPrin (KNAW), BUF/N (KNAW), LE/Stm (SOLiD) (KNAW), M520/N (KNAW), LE/OrlBarth (UDEL), F344/DuCrlCrlj (KyushuU), HWY/Slc (KyushuU), SS/Jr (KNAW), SHR/NHsd (KNAW), LEW/Crl (KNAW), MNS/Gib (KNAW), BUF/MNa (KyushuU), SHR/OlaIpcv (KNAW), WKY/Gcrc (KNAW), GK/Ox (KNAW), COP/CrCrl (MCW & UW), SS/JrHsdMcwi (KNAW), SHR/NCrlPrin (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), LE/Stm (Illumina) (KNAW), IS/Kyo (KyushuU), SDLEF7/Barth (UDEL), WAG/Rij (KNAW), KFRS3B/Kyo (KyushuU), WN/N (KNAW), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), ZF (KyushuU), SR/JrHsd (MCW), LN/MavRrrc (KNAW), SHRSP/Gcrc (KNAW), IS-Tlk/Kyo (KyushuU)
3 127238114 127238115 C T snv MNS/Gib (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 120094428 120094429 G A snv MNS/Gib (RGD)
3 120098379 120098380 T C snv SR/JrHsd (RGD), SHR/NHsd (RGD), SS/JrHsdMcwi (MCW), SS/JrHsdMcwi (RGD), WAG/Rij (RGD), WKY/Gcrc (RGD), M520/N (MCW), GK/Ox (RGD), WN/N (MCW), BBDP/Wor (RGD), F344/NCrl (RGD), LE/Stm (RGD), SR/JrHsd (MCW), LN/MavRrrc (RGD), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), CDS, Buf/N (MCW), F344/NRrrc (MCW), LH/MavRrrc (RGD), SS/Jr (RGD), SHRSP/Gcrc (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), MNS/Gib (RGD)
3 120100476 120100477 G A snv WKY/N (MCW), WKY/NHsd (RGD), WKY/NCrl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621435 AgrOrtholog
Ensembl Genes ENSRNOG00000014710 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020354 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020354 ENTREZGENE, UniProtKB/TrEMBL
InterPro Prominin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:192211 UniProtKB/Swiss-Prot
NCBI Gene 192211 ENTREZGENE
PANTHER PTHR22730 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Prominin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Prom2 PhenoGen
UniProt F1LQW5_RAT UniProtKB/TrEMBL
  PROM2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q8R4B6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Prom2  prominin 2  Promrp  prominin-related protein  Symbol and Name updated 1299863 APPROVED
2003-03-04 Promrp  prominin-related protein  Trprp  testosterone-regulated prominin-related protein  Symbol and Name updated to reflect Human and Mouse nomenclature 61478 PROVISIONAL
2002-08-07 Trprp  testosterone-regulated prominin-related protein      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization membrane protein, mainly localized in nuclear envelope and perinuclear region 628421
gene_domains contains five transmembrane segments and two glcosylated extracellular loops 633875
gene_expression not expressed in the eye in contrast to prominin-1 633875
gene_function proapoptotic membrane protein 628421
gene_process may support tumor suppression by inducing cell death in cancer cells and growth suppression in normal cells 628421
gene_process may be involved in growth suppression in prostate 628421
gene_product member of the prominin family of pentaspan membrane proteins 633875
gene_protein 886-amino acids 628421
gene_protein a transmembrane protein with five transmembrane domains; 32% homology with prominin and prominin-like protein from human 628421
gene_regulation may be associated with aggressive phenotype in prostate cancer cells 628421