Prph2 (peripherin 2) - Rat Genome Database

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Gene: Prph2 (peripherin 2) Rattus norvegicus
Analyze
Symbol: Prph2
Name: peripherin 2
RGD ID: 3549
Description: Predicted to have protein homodimerization activity. Involved in response to low light intensity stimulus. Predicted to localize to integral component of plasma membrane and photoreceptor outer segment. Biomarker of retinal disease. Human ortholog(s) of this gene implicated in Leber congenital amaurosis; eye degenerative disease (multiple); and fundus albipunctatus. Orthologous to human PRPH2 (peripherin 2); PARTICIPATES IN retinitis pigmentosa pathway; amyotrophic lateral sclerosis pathway; INTERACTS WITH 17alpha-ethynylestradiol; C60 fullerene; lead diacetate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Peripherin (retinal degradation slow); peripherin-2; Rds; retinal degeneration slow protein; retinal degeneration, slow; RSRDS
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
mRatBN7.2914,066,149 - 14,081,454 (-)NCBI
Rnor_6.0916,085,933 - 16,386,176 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0915,002,816 - 15,006,668 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.499,251,024 - 9,272,513 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.199,248,345 - 9,269,835 (-)NCBI
Celera911,815,281 - 11,829,854 (-)NCBICelera
RH 3.4 Map960.5RGD
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Ali RR, etal., Nat Genet. 2000 Jul;25(3):306-10.
2. Begy C and Bridges CD, Nucleic Acids Res 1990 May 25;18(10):3058.
3. Budu, etal., Hiroshima J Med Sci. 2005 Sep;54(3):73-6.
4. Chakraborty D, etal., PLoS One. 2013 May 1;8(5):e63321. doi: 10.1371/journal.pone.0063321. Print 2013.
5. Daiger SP, etal., Clin Genet. 2013 Aug;84(2):132-41. doi: 10.1111/cge.12203. Epub 2013 Jun 19.
6. Ekstrom U, etal., Ophthalmic Genet. 1998 Mar;19(1):27-37.
7. Fakin A, etal., Vision Res. 2012 Dec 15;75:71-6. doi: 10.1016/j.visres.2012.07.011. Epub 2012 Jul 25.
8. Felbor U, etal., Hum Mutat. 1997;10(4):301-9.
9. Fishman GA, etal., Ophthalmology. 1997 Feb;104(2):299-306.
10. Fujiki K, etal., Jpn J Ophthalmol. 1998 May-Jun;42(3):186-92.
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. Gorin MB, etal., Ophthalmology. 1995 Feb;102(2):246-55.
14. Hoyng CB, etal., Am J Ophthalmol. 1996 Jun;121(6):623-9.
15. Kajiwara K, etal., Nat Genet. 1993 Mar;3(3):208-12.
16. Kajiwara K, etal., Nature. 1991 Dec 12;354(6353):480-3.
17. Kedzierski W, etal., Invest Ophthalmol Vis Sci. 1997 Feb;38(2):498-509.
18. Keilhauer CN, etal., Arch Ophthalmol. 2006 Jul;124(7):1020-7.
19. Khoubian FJ, etal., Retina. 2005 Dec;25(8):999-1004.
20. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
21. McNally N, etal., Hum Mol Genet. 2002 May 1;11(9):1005-16.
22. MGD data from the GO Consortium
23. Nakazawa M, etal., Arch Ophthalmol. 1994 Dec;112(12):1567-73.
24. Nakazawa M, etal., Retina. 1996;16(5):405-10.
25. NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. Nichols BE, etal., Nat Genet. 1993 Mar;3(3):202-7.
27. OMIM Disease Annotation Pipeline
28. Pajic B, etal., Retina. 2006 Oct;26(8):947-53.
29. Passerini I, etal., Eur J Ophthalmol. 2007 Nov-Dec;17(6):1000-3.
30. Pipeline to import KEGG annotations from KEGG into RGD
31. Poloschek CM, etal., Invest Ophthalmol Vis Sci. 2010 Aug;51(8):4253-65. doi: 10.1167/iovs.09-4655. Epub 2010 Mar 24.
32. RGD automated data pipeline
33. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
34. RGD automated import pipeline for gene-chemical interactions
35. Saga M, etal., Hum Genet. 1993 Nov;92(5):519-21.
36. Sarra GM, etal., Hum Mol Genet 2001 Oct 1;10(21):2353-61.
37. Travis GH, etal., Nature. 1989 Mar 2;338(6210):70-3.
38. van Lith-Verhoeven JJ, etal., Arch Ophthalmol. 2003 Oct;121(10):1452-7.
39. Wang X, etal., J Med Genet. 2013 Oct;50(10):674-88. doi: 10.1136/jmedgenet-2013-101558. Epub 2013 Jul 11.
40. Yanagita T, etal., Jpn J Ophthalmol. 1993;37(1):1-8.
41. Yang H, etal., Zhonghua Yan Ke Za Zhi. 2000 Jan;36(1):52-5, 6, 7.
42. Yang Z, etal., Am J Ophthalmol. 2003 Feb;135(2):213-8.
43. Yang Z, etal., Ophthalmic Genet. 2004 Jun;25(2):133-45.
Additional References at PubMed
PMID:15964665   PMID:21052544   PMID:22183407  


Genomics

Comparative Map Data
Prph2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2914,066,149 - 14,081,454 (-)NCBI
Rnor_6.0916,085,933 - 16,386,176 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0915,002,816 - 15,006,668 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.499,251,024 - 9,272,513 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.199,248,345 - 9,269,835 (-)NCBI
Celera911,815,281 - 11,829,854 (-)NCBICelera
RH 3.4 Map960.5RGD
Cytogenetic Map9q12NCBI
PRPH2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl642,696,598 - 42,722,597 (-)EnsemblGRCh38hg38GRCh38
GRCh38642,694,509 - 42,723,039 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37642,664,336 - 42,690,335 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36642,772,314 - 42,798,287 (-)NCBINCBI36hg18NCBI36
Build 34642,772,317 - 42,798,287NCBI
Celera644,216,617 - 44,242,609 (-)NCBI
Cytogenetic Map6p21.1NCBI
HuRef642,382,731 - 42,408,581 (-)NCBIHuRef
CHM1_1642,666,888 - 42,692,860 (-)NCBICHM1_1
Prph2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391747,221,404 - 47,235,859 (+)NCBIGRCm39mm39
GRCm39 Ensembl1747,221,385 - 47,235,859 (+)Ensembl
GRCm381746,910,478 - 46,924,933 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1746,910,459 - 46,924,933 (+)EnsemblGRCm38mm10GRCm38
MGSCv371747,047,434 - 47,061,875 (+)NCBIGRCm37mm9NCBIm37
MGSCv361746,373,676 - 46,388,117 (+)NCBImm8
Celera1750,346,402 - 50,360,871 (+)NCBICelera
Cytogenetic Map17CNCBI
cM Map1722.91NCBI
Prph2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554378,782,183 - 8,795,017 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554378,784,211 - 8,794,789 (-)NCBIChiLan1.0ChiLan1.0
PRPH2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1643,582,317 - 43,608,011 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl643,582,317 - 43,608,011 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0642,284,818 - 42,316,150 (-)NCBIMhudiblu_PPA_v0panPan3
PRPH2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11211,299,236 - 11,316,175 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1211,299,236 - 11,316,175 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1211,326,457 - 11,343,396 (-)NCBI
ROS_Cfam_1.01211,780,500 - 11,797,719 (-)NCBI
UMICH_Zoey_3.11211,308,736 - 11,325,675 (-)NCBI
UNSW_CanFamBas_1.01211,393,617 - 11,410,600 (-)NCBI
UU_Cfam_GSD_1.01211,487,294 - 11,504,233 (-)NCBI
Prph2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494646,785,976 - 46,800,438 (-)NCBI
SpeTri2.0NW_00493647617,159,756 - 17,174,226 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRPH2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl737,790,178 - 37,805,142 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1737,788,547 - 37,805,142 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2743,265,462 - 43,270,328 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRPH2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11729,429,876 - 29,456,013 (+)NCBI
ChlSab1.1 Ensembl1729,430,545 - 29,453,636 (+)Ensembl
Prph2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475416,685,512 - 16,699,145 (+)NCBI

Position Markers
RH94646  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2914,066,171 - 14,066,339 (+)MAPPER
Rnor_6.0916,085,956 - 16,086,123NCBIRnor6.0
Rnor_5.0915,002,839 - 15,003,006UniSTSRnor5.0
RGSC_v3.499,251,047 - 9,251,214UniSTSRGSC3.4
Celera911,815,304 - 11,815,471UniSTS
RH 3.4 Map960.5UniSTS
Cytogenetic Map9q12UniSTS
RH136756  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2914,066,170 - 14,066,387 (+)MAPPER
Rnor_6.0916,085,955 - 16,086,171NCBIRnor6.0
Rnor_5.0915,002,838 - 15,003,054UniSTSRnor5.0
RGSC_v3.499,251,046 - 9,251,262UniSTSRGSC3.4
Celera911,815,303 - 11,815,519UniSTS
Cytogenetic Map9q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9116520166Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9129467098Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9140383872Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9140383872Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9140383872Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9145029794Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9235572247355722Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9235572247355722Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9288097747375681Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9288097747880977Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9498609549986095Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9498609549986095Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9572425425692342Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)91221677157216771Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)91242546357425463Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)91242546357425463Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91555490147249201Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:49
Count of miRNA genes:42
Interacting mature miRNAs:46
Transcripts:ENSRNOT00000061500
Prediction methods: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


Sequence


Reference Sequences
RefSeq Acc Id: NM_013021   ⟹   NP_037153
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2914,066,149 - 14,081,454 (-)NCBI
Rnor_6.0916,085,933 - 16,386,176 (-)NCBI
Rnor_5.0915,002,816 - 15,006,668 (-)NCBI
RGSC_v3.499,251,024 - 9,272,513 (-)RGD
Celera911,815,281 - 11,829,854 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_037153 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA36603 (Get FASTA)   NCBI Sequence Viewer  
  EDM18867 (Get FASTA)   NCBI Sequence Viewer  
  P17438 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037153   ⟸   NM_013021
- UniProtKB: P17438 (UniProtKB/Swiss-Prot)
- Sequence:


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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3549 AgrOrtholog
Gene3D-CATH 1.10.1450.10 UniProtKB/Swiss-Prot
InterPro Peripherin/rom-1 UniProtKB/Swiss-Prot
  Peripherin/rom-1_CS UniProtKB/Swiss-Prot
  Peripherin_LEL UniProtKB/Swiss-Prot
  Tetraspanin/Peripherin UniProtKB/Swiss-Prot
  Tetraspanin_EC2_sf UniProtKB/Swiss-Prot
KEGG Report rno:25534 UniProtKB/Swiss-Prot
NCBI Gene 25534 ENTREZGENE
Pfam Tetraspanin UniProtKB/Swiss-Prot
PhenoGen Prph2 PhenoGen
PRINTS PERIPHERNRDS UniProtKB/Swiss-Prot
PROSITE RDS_ROM1 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48652 UniProtKB/Swiss-Prot
UniProt P17438 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-15 Prph2  peripherin 2  Rds  retinal degeneration, slow  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Rds  retinal degeneration, slow  Prph2  peripherin 2  Symbol and Name updated 1299863 APPROVED
2003-04-09 Prph2  peripherin 2  Rds  Peripherin (retinal degradation slow)  Symbol and Name updated 629477 APPROVED
2002-06-10 Rds  Peripherin (retinal degradation slow)      Symbol and Name status set to approved 70586 APPROVED