Rpl5 (ribosomal protein L5) - Rat Genome Database

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Gene: Rpl5 (ribosomal protein L5) Rattus norvegicus
Analyze
Symbol: Rpl5
Name: ribosomal protein L5
RGD ID: 619825
Description: Exhibits 5S rRNA binding activity and mRNA binding activity. Involved in cellular response to inorganic substance; positive regulation of aminoacyl-tRNA ligase activity; and positive regulation of phosphatase activity. Localizes to aminoacyl-tRNA synthetase multienzyme complex; cytosolic large ribosomal subunit; and postsynaptic density. Human ortholog(s) of this gene implicated in Diamond-Blackfan anemia 6; T-cell acute lymphoblastic leukemia; and glioblastoma. Orthologous to human RPL5 (ribosomal protein L5); PARTICIPATES IN p53 signaling pathway; ribosome biogenesis pathway; translation pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 60S ribosomal protein L5
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
mRatBN7.2141,843,856 - 1,850,301 (-)NCBI
Rnor_6.0 Ensembl142,860,965 - 2,867,397 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0142,860,963 - 2,867,397 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0142,861,092 - 2,867,612 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4142,397,640 - 2,404,072 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1142,397,639 - 2,404,072 (-)NCBI
Celera141,863,797 - 1,870,229 (-)NCBICelera
Cytogenetic Map14p22NCBI
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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Anger AM, etal., Nature. 2013 May 2;497(7447):80-5. doi: 10.1038/nature12104.
2. Aoyama K, etal., J Biochem. 1984 Apr;95(4):1179-86.
3. Chan YL, etal., J Biol Chem 1987 Sep 15;262(26):12879-86.
4. Cmejla R, etal., Hum Mutat. 2009 Mar;30(3):321-7. doi: 10.1002/humu.20874.
5. De Keersmaecker K, etal., Nat Genet. 2013 Feb;45(2):186-90. doi: 10.1038/ng.2508. Epub 2012 Dec 23.
6. Delaporta P, etal., Pediatr Blood Cancer. 2014 Dec;61(12):2249-55. doi: 10.1002/pbc.25183. Epub 2014 Aug 17.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Gazda HT, etal., Am J Hum Genet. 2008 Dec;83(6):769-80. doi: 10.1016/j.ajhg.2008.11.004.
9. GOA data from the GO Consortium
10. Goudarzi KM and Lindstrom MS, Int J Oncol. 2016 Apr;48(4):1313-24. doi: 10.3892/ijo.2016.3387. Epub 2016 Feb 9.
11. Hirano K, etal., J Biol Chem. 1995 Aug 25;270(34):19786-90.
12. Huber PW and Wool IG, J Biol Chem. 1986 Mar 5;261(7):3002-5.
13. Konno Y, etal., Haematologica. 2010 Aug;95(8):1293-9. doi: 10.3324/haematol.2009.020826. Epub 2010 Apr 7.
14. MGD data from the GO Consortium
15. Miao Q, etal., Zhonghua Yu Fang Yi Xue Za Zhi. 2003 Jul;37(4):251-5.
16. NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. Ogata K, etal., Biochim Biophys Acta 1994 Aug 2;1218(3):388-400.
18. Ogata K, etal., J Biochem. 1991 Dec;110(6):1037-44.
19. Ogata K, etal., J Biochem. 1996 Nov;120(5):869-80.
20. OMIM Disease Annotation Pipeline
21. Peng J, etal., J Biol Chem. 2004 May 14;279(20):21003-11. doi: 10.1074/jbc.M400103200. Epub 2004 Mar 12.
22. Quarello P, etal., Haematologica. 2010 Feb;95(2):206-13. doi: 10.3324/haematol.2009.011783. Epub 2009 Sep 22.
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. Smetanina NS, etal., Pediatr Blood Cancer. 2015 Sep;62(9):1597-600. doi: 10.1002/pbc.25534. Epub 2015 May 6.
27. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
28. Takahashi Y and Ogata K, J Biochem. 1981 Nov;90(5):1549-52.
29. Tamura S, etal., Eur J Biochem 1987 Oct 1;168(1):83-7.
30. Uchiumi T, etal., J Biol Chem. 1985 May 10;260(9):5669-74.
31. Uchiumi T, etal., J Biol Chem. 1986 Jul 25;261(21):9663-7.
Additional References at PubMed
PMID:8626719   PMID:9687515   PMID:12962325   PMID:15314173   PMID:15469983   PMID:15489334   PMID:16213212   PMID:16635246   PMID:16648475   PMID:16791210   PMID:18560357   PMID:18697920  
PMID:18809582   PMID:19946888   PMID:20458337   PMID:21423176   PMID:22658674   PMID:22681889   PMID:24120868   PMID:24625528   PMID:30053369  


Genomics

Comparative Map Data
Rpl5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2141,843,856 - 1,850,301 (-)NCBI
Rnor_6.0 Ensembl142,860,965 - 2,867,397 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0142,860,963 - 2,867,397 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0142,861,092 - 2,867,612 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4142,397,640 - 2,404,072 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1142,397,639 - 2,404,072 (-)NCBI
Celera141,863,797 - 1,870,229 (-)NCBICelera
Cytogenetic Map14p22NCBI
RPL5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl192,832,013 - 92,841,924 (+)EnsemblGRCh38hg38GRCh38
GRCh38192,831,986 - 92,841,924 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37193,297,543 - 93,307,481 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36193,070,182 - 93,080,069 (+)NCBINCBI36hg18NCBI36
Build 34193,009,630 - 93,019,501NCBI
Celera191,551,185 - 91,561,073 (+)NCBI
Cytogenetic Map1p22.1NCBI
HuRef191,418,759 - 91,428,647 (+)NCBIHuRef
CHM1_1193,412,392 - 93,422,277 (+)NCBICHM1_1
Rpl5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395108,048,388 - 108,056,871 (+)NCBIGRCm39mm39
GRCm39 Ensembl5108,048,368 - 108,056,871 (+)Ensembl
GRCm385107,900,508 - 107,909,005 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5107,900,502 - 107,909,005 (+)EnsemblGRCm38mm10GRCm38
MGSCv375108,329,547 - 108,338,024 (+)NCBIGRCm37mm9NCBIm37
MGSCv365108,329,609 - 108,337,069 (+)NCBImm8
Celera5105,013,413 - 105,021,863 (+)NCBICelera
Cytogenetic Map5FNCBI
cM Map552.23NCBI
Rpl5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554231,748,809 - 1,758,622 (-)NCBIChiLan1.0ChiLan1.0
RPL5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1194,231,605 - 94,241,522 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl194,230,451 - 94,241,522 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0195,497,047 - 95,507,006 (+)NCBIMhudiblu_PPA_v0panPan3
RPL5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1656,207,171 - 56,216,030 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl656,207,173 - 56,215,956 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha658,904,824 - 58,915,282 (-)NCBI
ROS_Cfam_1.0656,582,922 - 56,593,715 (-)NCBI
UMICH_Zoey_3.1656,262,557 - 56,272,992 (-)NCBI
UNSW_CanFamBas_1.0656,240,615 - 56,251,042 (-)NCBI
UU_Cfam_GSD_1.0656,700,600 - 56,711,209 (-)NCBI
Rpl5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405058102,602,706 - 102,606,012 (+)NCBI
SpeTri2.0NW_0049365376,341,961 - 6,344,831 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RPL5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4124,358,592 - 124,367,647 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14124,359,786 - 124,367,612 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24135,982,736 - 135,990,562 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RPL5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12040,416,553 - 40,427,027 (-)NCBI
ChlSab1.1 Ensembl2040,413,897 - 40,427,060 (-)Ensembl
Rpl5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247424,973,229 - 4,983,361 (-)NCBI

Position Markers
AI235218  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2141,843,499 - 1,843,726 (+)MAPPER
Rnor_6.0142,860,607 - 2,860,833NCBIRnor6.0
Rnor_5.0142,860,822 - 2,861,048UniSTSRnor5.0
RGSC_v3.4142,397,282 - 2,397,508UniSTSRGSC3.4
Celera141,863,439 - 1,863,665UniSTS
Cytogenetic Map14p22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14127597761Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14134403399Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14141333960Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14141333960Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14142766285Rat
71115Niddm15Non-insulin dependent diabetes mellitus QTL 154.8blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14222782512680613Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14222782519230541Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:38
Count of miRNA genes:35
Interacting mature miRNAs:36
Transcripts:ENSRNOT00000030428
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 8 14 15 14 3 14 16 18 28 2
Medium 1 29 43 27 16 27 8 11 58 17 13 9 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250585 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC060561 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214281 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215029 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215486 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219244 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219848 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219940 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220068 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220170 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220205 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229451 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229816 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230078 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230102 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230128 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230794 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232540 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M17419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X06148 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000030428   ⟹   ENSRNOP00000036514
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl142,860,965 - 2,867,397 (-)Ensembl
RefSeq Acc Id: NM_031099   ⟹   NP_112361
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,843,858 - 1,850,290 (-)NCBI
Rnor_6.0142,860,965 - 2,867,397 (-)NCBI
Rnor_5.0142,861,092 - 2,867,612 (-)NCBI
RGSC_v3.4142,397,640 - 2,404,072 (-)RGD
Celera141,863,797 - 1,870,229 (-)RGD
Sequence:
RefSeq Acc Id: XM_006250585   ⟹   XP_006250647
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2141,843,856 - 1,850,301 (-)NCBI
Rnor_6.0142,860,963 - 2,867,378 (-)NCBI
Rnor_5.0142,861,092 - 2,867,612 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_112361   ⟸   NM_031099
- UniProtKB: P09895 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006250647   ⟸   XM_006250585
- Peptide Label: isoform X1
- UniProtKB: P09895 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000036514   ⟸   ENSRNOT00000030428

Transcriptome

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

Promoters
RGD ID:13699153
Promoter ID:EPDNEW_R9678
Type:initiation region
Name:Rpl5_1
Description:ribosomal protein L5
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_6.0142,867,345 - 2,867,405EPDNEW

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)
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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)
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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: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 2401291 2401292 T C snv FHL/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619825 AgrOrtholog
Ensembl Genes ENSRNOG00000023529 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000036514 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000030428 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6918805 IMAGE-MGC_LOAD
InterPro Rbsml_L5_euk/L18_arc UniProtKB/Swiss-Prot
  Rbsml_L5e/L18P_C UniProtKB/Swiss-Prot
KEGG Report rno:81763 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72798 IMAGE-MGC_LOAD
NCBI Gene 81763 ENTREZGENE
PANTHER PTHR23410 UniProtKB/Swiss-Prot
Pfam Ribosomal_L18_c UniProtKB/Swiss-Prot
  Ribosomal_L5e UniProtKB/Swiss-Prot
PhenoGen Rpl5 PhenoGen
PRINTS RIBOSOMALL5 UniProtKB/Swiss-Prot
UniProt P09895 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Rpl5  ribosomal protein L5      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Rpl5  ribosomal protein L5      Symbol and Name status set to provisional 70820 PROVISIONAL