RGD1308430 (similar to 1700123O20Rik protein) - Rat Genome Database
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Gene: RGD1308430 (similar to 1700123O20Rik protein) Rattus norvegicus
Analyze
Symbol: RGD1308430
Name: similar to 1700123O20Rik protein
RGD ID: 1308430
Description: Predicted to localize to cytosol and mitochondrion. Orthologous to human C14orf119 (chromosome 14 open reading frame 119); INTERACTS WITH bisphenol A; glafenine; leflunomide.
Type: protein-coding
RefSeq Status: PREDICTED
Also known as: hypothetical protein LOC361038; LOC361038; uncharacterized protein C14orf119 homolog; uncharacterized protein LOC361038
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_6.01533,333,009 - 33,337,677 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1533,333,420 - 33,337,674 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01537,217,882 - 37,222,473 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41532,764,912 - 32,769,169 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11532,780,673 - 32,784,876 (+)NCBI
Celera1527,725,336 - 27,729,593 (+)NCBICelera
Cytogenetic Map15p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
COVID-19  (ISO)

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

Cellular Component
cytosol  (IEA,ISO)
mitochondrion  (IEA,ISO)

Molecular Function

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932  


Genomics

Candidate Gene Status
RGD1308430 is a candidate Gene for QTL Kidm51
Comparative Map Data
RGD1308430
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01533,333,009 - 33,337,677 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1533,333,420 - 33,337,674 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01537,217,882 - 37,222,473 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41532,764,912 - 32,769,169 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11532,780,673 - 32,784,876 (+)NCBI
Celera1527,725,336 - 27,729,593 (+)NCBICelera
Cytogenetic Map15p13NCBI
C14orf119
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1423,095,505 - 23,100,456 (+)EnsemblGRCh38hg38GRCh38
GRCh381423,095,505 - 23,100,456 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371423,564,683 - 23,569,665 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361422,634,628 - 22,639,505 (+)NCBINCBI36hg18NCBI36
Build 341422,634,627 - 22,639,504NCBI
Celera143,427,493 - 3,432,371 (+)NCBI
Cytogenetic Map14q11.2NCBI
HuRef143,681,599 - 3,686,579 (+)NCBIHuRef
CHM1_11423,563,312 - 23,568,282 (+)NCBICHM1_1
1700123O20Rik
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391454,923,628 - 54,928,201 (+)NCBIGRCm39mm39
GRCm381454,686,171 - 54,690,742 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1454,686,216 - 54,690,741 (+)EnsemblGRCm38mm10GRCm38
MGSCv371455,305,008 - 55,309,579 (+)NCBIGRCm37mm9NCBIm37
MGSCv361453,640,421 - 53,644,945 (+)NCBImm8
Celera1452,474,405 - 52,478,976 (+)NCBICelera
Cytogenetic Map14C2NCBI
LOC102024654
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540937,203,604 - 37,206,426 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540937,203,604 - 37,206,853 (-)NCBIChiLan1.0ChiLan1.0
C14H14orf119
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11422,011,957 - 22,015,068 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0143,915,675 - 3,918,781 (+)NCBIMhudiblu_PPA_v0panPan3
C8H14orf119
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.183,405,418 - 3,408,966 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CUNH14orf119
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367221,219,245 - 1,226,291 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
C7H14orf119
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl775,947,769 - 75,950,956 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1775,947,765 - 75,951,047 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2781,283,562 - 81,286,796 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CUNH14orf119
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12923,464,618 - 23,467,719 (+)NCBI
CUNH14orf119
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248209,441,533 - 9,445,056 (-)NCBI

Position Markers
BI274360  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01533,337,335 - 33,337,437NCBIRnor6.0
Rnor_5.01537,222,131 - 37,222,233UniSTSRnor5.0
RGSC_v3.41532,768,827 - 32,768,929UniSTSRGSC3.4
Celera1527,729,251 - 27,729,353UniSTS
Cytogenetic Map15p13UniSTS
RH129554  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01533,337,426 - 33,337,632NCBIRnor6.0
Rnor_5.01537,222,222 - 37,222,428UniSTSRnor5.0
RGSC_v3.41532,768,918 - 32,769,124UniSTSRGSC3.4
Celera1527,729,342 - 27,729,548UniSTS
Cytogenetic Map15p13UniSTS
BE106323  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01533,337,986 - 33,338,136NCBIRnor6.0
Rnor_5.01537,222,782 - 37,222,932UniSTSRnor5.0
RGSC_v3.41532,769,478 - 32,769,628UniSTSRGSC3.4
Celera1527,729,902 - 27,730,052UniSTS
Cytogenetic Map15p13UniSTS
UniSTS:237185  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01533,336,839 - 33,337,024NCBIRnor6.0
Rnor_5.01537,221,635 - 37,221,820UniSTSRnor5.0
RGSC_v3.41532,768,331 - 32,768,516UniSTSRGSC3.4
Celera1527,728,755 - 27,728,940UniSTS
Cytogenetic Map15p13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15137708474Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15137708474Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15137708474Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15142844179Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15143521446Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15388113148881131Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
5685002Bss103Bone structure and strength QTL 1032.8tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)151582824233657761Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152102134241082727Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152102134252831189Rat
10755503Bp391Blood pressure QTL 3912.37arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)152377896946825072Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152870974173709741Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)153321910189640841Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)153321910189640841Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)153321910189640841Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:74
Count of miRNA genes:56
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000049927
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 36 57 41 19 41 6 8 74 35 41 11 6
Low 7 2 3 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000049927   ⟹   ENSRNOP00000045776
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1533,333,420 - 33,337,674 (+)Ensembl
RefSeq Acc Id: NM_001108376   ⟹   NP_001101846
RefSeq Status: PREDICTED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01533,333,420 - 33,337,677 (+)NCBI
Rnor_5.01537,217,882 - 37,222,473 (+)NCBI
RGSC_v3.41532,764,912 - 32,769,169 (+)RGD
Celera1527,725,336 - 27,729,593 (+)RGD
Sequence:
RefSeq Acc Id: XM_006251977   ⟹   XP_006252039
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01533,333,197 - 33,337,671 (+)NCBI
Rnor_5.01537,217,882 - 37,222,473 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006251978   ⟹   XP_006252040
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01533,333,009 - 33,337,671 (+)NCBI
Rnor_5.01537,217,882 - 37,222,473 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101846 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252039 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252040 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI58657 (Get FASTA)   NCBI Sequence Viewer  
  EDM14186 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101846   ⟸   NM_001108376
- UniProtKB: B0BN25 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252040   ⟸   XM_006251978
- Peptide Label: isoform X1
- UniProtKB: B0BN25 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252039   ⟸   XM_006251977
- Peptide Label: isoform X1
- UniProtKB: B0BN25 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000045776   ⟸   ENSRNOT00000049927

Transcriptome

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

Promoters
RGD ID:13699658
Promoter ID:EPDNEW_R10181
Type:initiation region
Name:RGD1308430_1
Description:similar to 1700123O20Rik protein
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_6.01533,333,474 - 33,333,534EPDNEW

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)
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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: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 37221677 37221678 G C snv DOB/Oda (KyushuU), F344/NSlc (KyushuU), LEC/Tj (KyushuU), LE/OrlBarth (UDEL), HWY/Slc (KyushuU), F344/DuCrlCrlj (KyushuU), BUF/MNa (KyushuU), BN/SsNSlc (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), HTX/Kyo (KyushuU), NIG-III/Hok (KyushuU), ZFDM (KyushuU), LE/Stm (KyushuU), SDLEF7/Barth (UDEL), KFRS3B/Kyo (KyushuU), Crl:SD (UDEL)
15 37221709 37221710 G A snv Crl:SD (UDEL), HTX/Kyo (KyushuU), IS/Kyo (KyushuU), BUF/MNa (KyushuU), ZFDM (KyushuU), LE/Stm (KyushuU), DOB/Oda (KyushuU), KFRS3B/Kyo (KyushuU), F344/DuCrlCrlj (KyushuU), BN/SsNSlc (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), LEC/Tj (KyushuU), NIG-III/Hok (KyushuU), LE/OrlBarth (UDEL), HWY/Slc (KyushuU), SDLEF7/Barth (UDEL)
15 37221760 37221761 T G snv NIG-III/Hok (KyushuU), LEC/Tj (KyushuU), KFRS3B/Kyo (KyushuU), BUF/MNa (KyushuU)
15 37221831 37221832 C T snv NIG-III/Hok (KyushuU), F344/NSlc (KyushuU), HWY/Slc (KyushuU)
15 37221840 37221841 G T snv HWY/Slc (KyushuU), NIG-III/Hok (KyushuU)
15 37221943 37221944 C A snv BN/SsNSlc (KyushuU), SDLEF7/Barth (UDEL), IS/Kyo (KyushuU), LE/OrlBarth (UDEL), RCS/Kyo (KyushuU), Crl:SD (UDEL)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 33336881 33336882 G C snv ACI/EurMcwi (MCW), SS/JrHsdMcwi (MCW), SBH/Ygl (MCW), CDS, CDR, SR/JrHsd (MCW), FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), SBN/Ygl (MCW)
15 33336913 33336914 G A snv ACI/EurMcwi (MCW), SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW), FHH/EurMcwi (MCW), GH/OmrMcwi (MCW), SR/JrHsd (MCW), COP/CrCrl (MCW & UW), SBH/Ygl (MCW), SBN/Ygl (MCW)
15 33337044 33337045 G T snv FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW), SS/JrHsdMcwi (MCW), SBH/Ygl (MCW), SR/JrHsd (MCW), SBN/Ygl (MCW), FHH/EurMcwi (MCW), ACI/EurMcwi (MCW), MNS/Gib (RGD)
15 33337147 33337148 C A snv FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), CDS, CDR, SBH/Ygl (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
15 32768373 32768374 G C snv SS/JrHsdMcwi (MDC), SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308430 AgrOrtholog
Ensembl Genes ENSRNOG00000029146 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000045776 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000049927 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8369089 IMAGE-MGC_LOAD
InterPro DUF4508 UniProtKB/TrEMBL
KEGG Report rno:361038 UniProtKB/TrEMBL
MGC_CLONE MGC:187641 IMAGE-MGC_LOAD
NCBI Gene 361038 ENTREZGENE
PANTHER PTHR16260 UniProtKB/TrEMBL
Pfam DUF4508 UniProtKB/TrEMBL
PhenoGen RGD1308430 PhenoGen
UniGene Rn.2583 ENTREZGENE
UniProt B0BN25 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 RGD1308430  similar to 1700123O20Rik protein   RGD1308430_predicted  similar to 1700123O20Rik protein (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1308430_predicted  similar to 1700123O20Rik protein (predicted)  LOC361038_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361038_predicted  similar to 1700123O20Rik protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL