Kdm5c (lysine demethylase 5C) - Rat Genome Database

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Gene: Kdm5c (lysine demethylase 5C) Rattus norvegicus
Analyze
Symbol: Kdm5c
Name: lysine demethylase 5C
RGD ID: 1560601
Description: Predicted to enable histone demethylase activity (H3-K4 specific) and zinc ion binding activity. Involved in response to toxic substance. Predicted to be located in cytosol and nucleoplasm. Biomarker of schizophrenia. Human ortholog(s) of this gene implicated in syndromic X-linked intellectual disability Claes-Jensen type. Orthologous to human KDM5C (lysine demethylase 5C); PARTICIPATES IN histone modification pathway; renal cell carcinoma pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC102555632; LOC317432; lysine (K)-specific demethylase 5C; lysine-specific demethylase 5C; RGD1560601; similar to Jumonji/ARID domain-containing protein 1C (SmcX protein); similar to Jumonji/ARID domain-containing protein 1C (SmcX protein) (Xe169 protein); uncharacterized LOC102555632
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X21,345,459 - 21,387,045 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX21,345,481 - 21,381,870 (+)Ensembl
Rnor_6.0X22,302,664 - 22,349,298 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX22,302,485 - 22,348,627 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X64,226,119 - 64,277,476 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X41,742,803 - 41,779,479 (+)NCBIRGSC3.4rn4RGSC3.4
CeleraX21,607,558 - 21,644,634 (+)NCBICelera
Cytogenetic MapXq13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cellular_component  (ND)
cytosol  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:17320160   PMID:18078810   PMID:21960634   PMID:23246292   PMID:27214403   PMID:28262558  


Genomics

Comparative Map Data
Kdm5c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X21,345,459 - 21,387,045 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX21,345,481 - 21,381,870 (+)Ensembl
Rnor_6.0X22,302,664 - 22,349,298 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX22,302,485 - 22,348,627 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X64,226,119 - 64,277,476 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X41,742,803 - 41,779,479 (+)NCBIRGSC3.4rn4RGSC3.4
CeleraX21,607,558 - 21,644,634 (+)NCBICelera
Cytogenetic MapXq13NCBI
KDM5C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX53,191,321 - 53,225,422 (-)EnsemblGRCh38hg38GRCh38
GRCh38X53,176,277 - 53,225,207 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X53,205,459 - 53,254,389 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X53,237,378 - 53,271,329 (-)NCBINCBI36hg18NCBI36
Build 34X53,104,473 - 53,137,625NCBI
CeleraX57,049,741 - 57,083,840 (-)NCBI
Cytogenetic MapXp11.22NCBI
HuRefX50,285,660 - 50,319,741 (-)NCBIHuRef
CHM1_1X53,210,762 - 53,244,827 (-)NCBICHM1_1
Kdm5c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X151,015,698 - 151,062,098 (+)NCBIGRCm39mm39
GRCm39 EnsemblX151,016,016 - 151,057,531 (+)Ensembl
GRCm38X152,233,198 - 152,279,102 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX152,233,020 - 152,274,535 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X148,667,773 - 148,708,897 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X147,573,988 - 147,614,512 (+)NCBImm8
MGSCv36X129,241,757 - 129,282,281 (+)NCBImm8
Cytogenetic MapXF3NCBI
cM MapX68.46NCBI
Kdm5c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955475243,666 - 278,627 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955475243,666 - 278,064 (-)NCBIChiLan1.0ChiLan1.0
KDM5C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X53,486,874 - 53,548,785 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX53,515,886 - 53,548,785 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X45,377,609 - 45,440,025 (-)NCBIMhudiblu_PPA_v0panPan3
KDM5C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X44,921,271 - 44,953,338 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX44,921,816 - 44,952,616 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX36,478,724 - 36,508,722 (-)NCBI
ROS_Cfam_1.0X45,270,006 - 45,300,013 (-)NCBI
UMICH_Zoey_3.1X44,765,224 - 44,795,215 (-)NCBI
UNSW_CanFamBas_1.0X45,214,884 - 45,244,860 (-)NCBI
UU_Cfam_GSD_1.0X45,282,205 - 45,312,192 (-)NCBI
Kdm5c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X37,818,558 - 37,864,411 (-)NCBI
SpeTri2.0NW_004936751159,628 - 204,136 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM5C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX45,968,814 - 46,003,215 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X45,968,812 - 46,003,215 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X51,468,791 - 51,503,194 (-)NCBISscrofa10.2Sscrofa10.2susScr3
KDM5C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X49,306,472 - 49,356,151 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 EnsemblX49,321,173 - 49,356,100 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660863,259,499 - 3,309,984 (-)NCBIVero_WHO_p1.0
Kdm5c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624909421,033 - 455,201 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH137280  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X21,371,310 - 21,371,521 (+)MAPPERmRatBN7.2
Rnor_6.0X22,338,459 - 22,338,669NCBIRnor6.0
Rnor_6.0X22,328,450 - 22,328,660NCBIRnor6.0
Rnor_5.0X64,249,512 - 64,249,722UniSTSRnor5.0
Rnor_5.0X64,241,131 - 64,241,341UniSTSRnor5.0
RGSC_v3.4X41,768,854 - 41,769,064UniSTSRGSC3.4
RGSC_v3.41109,979,145 - 109,979,355UniSTSRGSC3.4
CeleraX21,633,283 - 21,633,493UniSTS
Cytogenetic MapXq21UniSTS
RH138851  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X21,351,028 - 21,351,193 (+)MAPPERmRatBN7.2
Rnor_6.0X22,308,246 - 22,308,410NCBIRnor6.0
Rnor_5.0X64,271,743 - 64,271,907UniSTSRnor5.0
RGSC_v3.4X41,748,357 - 41,748,521UniSTSRGSC3.4
CeleraX21,613,117 - 21,613,281UniSTS
Cytogenetic MapXq21UniSTS
Smcx  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.4X41,778,087 - 41,778,521UniSTSRGSC3.4
CeleraX21,618,170 - 21,619,375UniSTS
Cytogenetic MapXq21UniSTS
Smcx  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X21,381,268 - 21,381,703 (+)MAPPERmRatBN7.2
Rnor_6.0X22,347,905 - 22,348,339NCBIRnor6.0
Rnor_5.0X64,231,461 - 64,231,895UniSTSRnor5.0
RGSC_v3.4X41,778,087 - 41,778,521UniSTSRGSC3.4
CeleraX21,643,241 - 21,643,675UniSTS
Cytogenetic MapXq21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1529780260297802Rat
1598873Memor2Memory QTL 22.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)X2099094741052531Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2099094741203591Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:257
Count of miRNA genes:174
Interacting mature miRNAs:197
Transcripts:ENSRNOT00000004600, ENSRNOT00000067288, ENSRNOT00000067782, ENSRNOT00000071867
Prediction methods:Microtar, Miranda, Pita, 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 37 57 41 19 41 5 5 74 35 34 11 5
Low 6 3 6 7 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_001064297 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227304 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227306 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773146 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100480 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100486 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039100487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide FQ213185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GAPM01000004 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000372 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000077528   ⟹   ENSRNOP00000074157
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX22,342,308 - 22,348,627 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078617   ⟹   ENSRNOP00000075375
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX22,302,703 - 22,328,423 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079909   ⟹   ENSRNOP00000071836
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX21,345,481 - 21,381,870 (+)Ensembl
Rnor_6.0 EnsemblX22,342,308 - 22,348,233 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082725   ⟹   ENSRNOP00000074522
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX21,345,481 - 21,381,870 (+)Ensembl
Rnor_6.0 EnsemblX22,313,028 - 22,347,836 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082902   ⟹   ENSRNOP00000070936
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX22,302,485 - 22,328,423 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000086952   ⟹   ENSRNOP00000069719
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX21,345,804 - 21,371,481 (+)Ensembl
Rnor_6.0 EnsemblX22,302,714 - 22,328,423 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087945   ⟹   ENSRNOP00000072650
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX22,342,308 - 22,348,233 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090883
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX22,302,719 - 22,314,731 (+)Ensembl
RefSeq Acc Id: XM_039100480   ⟹   XP_038956408
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,345,804 - 21,387,045 (+)NCBI
RefSeq Acc Id: XM_039100481   ⟹   XP_038956409
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,345,804 - 21,381,200 (+)NCBI
RefSeq Acc Id: XM_039100482   ⟹   XP_038956410
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,345,804 - 21,381,728 (+)NCBI
RefSeq Acc Id: XM_039100483   ⟹   XP_038956411
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,345,460 - 21,381,728 (+)NCBI
RefSeq Acc Id: XM_039100484   ⟹   XP_038956412
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,345,460 - 21,387,045 (+)NCBI
RefSeq Acc Id: XM_039100485   ⟹   XP_038956413
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,345,804 - 21,381,728 (+)NCBI
RefSeq Acc Id: XM_039100486   ⟹   XP_038956414
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,345,459 - 21,387,045 (+)NCBI
RefSeq Acc Id: XM_039100487   ⟹   XP_038956415
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X21,345,460 - 21,380,566 (+)NCBI
Reference Sequences
RefSeq Acc Id: ENSRNOP00000070936   ⟸   ENSRNOT00000082902
RefSeq Acc Id: ENSRNOP00000074522   ⟸   ENSRNOT00000082725
RefSeq Acc Id: ENSRNOP00000072650   ⟸   ENSRNOT00000087945
RefSeq Acc Id: ENSRNOP00000074157   ⟸   ENSRNOT00000077528
RefSeq Acc Id: ENSRNOP00000071836   ⟸   ENSRNOT00000079909
RefSeq Acc Id: ENSRNOP00000069719   ⟸   ENSRNOT00000086952
RefSeq Acc Id: ENSRNOP00000075375   ⟸   ENSRNOT00000078617
RefSeq Acc Id: XP_038956414   ⟸   XM_039100486
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038956412   ⟸   XM_039100484
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038956411   ⟸   XM_039100483
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038956415   ⟸   XM_039100487
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038956408   ⟸   XM_039100480
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038956410   ⟸   XM_039100482
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038956413   ⟸   XM_039100485
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038956409   ⟸   XM_039100481
- Peptide Label: isoform X2
Protein Domains
ARID   JmjC   JmjN   PHD   PHD-type

Transcriptome

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

Promoters
RGD ID:13701777
Promoter ID:EPDNEW_R12296
Type:multiple initiation site
Name:Kdm5c_1
Description:Lysine-specific demethylase 5C
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_6.0X22,302,711 - 22,302,771EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NHsd (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
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560601 AgrOrtholog
Ensembl Genes ENSRNOG00000057706 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000069719 UniProtKB/TrEMBL
  ENSRNOP00000070936 UniProtKB/TrEMBL
  ENSRNOP00000071836 UniProtKB/TrEMBL
  ENSRNOP00000072650 UniProtKB/TrEMBL
  ENSRNOP00000074157 UniProtKB/TrEMBL
  ENSRNOP00000074522 UniProtKB/TrEMBL
  ENSRNOP00000075375 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077528 UniProtKB/TrEMBL
  ENSRNOT00000078617 UniProtKB/TrEMBL
  ENSRNOT00000079909 UniProtKB/TrEMBL
  ENSRNOT00000082725 UniProtKB/TrEMBL
  ENSRNOT00000082902 UniProtKB/TrEMBL
  ENSRNOT00000086952 UniProtKB/TrEMBL
  ENSRNOT00000087945 UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.60 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
InterPro ARID/BRIGHT_DNA-bd UniProtKB/TrEMBL
  ARID_dom_sf UniProtKB/TrEMBL
  JmjC_dom UniProtKB/TrEMBL
  Lys_sp_deMease_like_dom UniProtKB/TrEMBL
  TF_JmjN UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/TrEMBL
  Znf_C5HC2 UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
NCBI Gene 317432 ENTREZGENE
Pfam ARID UniProtKB/TrEMBL
  JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  PLU-1 UniProtKB/TrEMBL
  zf-C5HC2 UniProtKB/TrEMBL
PhenoGen Kdm5c PhenoGen
PROSITE ARID UniProtKB/TrEMBL
  JMJC UniProtKB/TrEMBL
  JMJN UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
SMART BRIGHT UniProtKB/TrEMBL
  JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
Superfamily-SCOP FYVE_PHD_ZnF UniProtKB/TrEMBL
  SSF46774 UniProtKB/TrEMBL
UniProt A0A0G2JW30_RAT UniProtKB/TrEMBL
  A0A0G2JZ72_RAT UniProtKB/TrEMBL
  A0A0G2K3I4_RAT UniProtKB/TrEMBL
  A0A0G2K897_RAT UniProtKB/TrEMBL
  A0A0G2KAF1_RAT UniProtKB/TrEMBL
  V9GW19_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Kdm5c  lysine demethylase 5C  Kdm5c  lysine (K)-specific demethylase 5C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-29 Kdm5c  lysine (K)-specific demethylase 5C  LOC102555632  uncharacterized LOC102555632  Data Merged 737654 PROVISIONAL
2013-12-18 LOC102555632  uncharacterized LOC102555632      Symbol and Name status set to provisional 70820 PROVISIONAL
2013-11-25 Kdm5c  lysine (K)-specific demethylase 5C  RGD1560601  similar to Jumonji/ARID domain-containing protein 1C (SmcX protein)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1560601  similar to Jumonji/ARID domain-containing protein 1C (SmcX protein)   RGD1560601_predicted  similar to Jumonji/ARID domain-containing protein 1C (SmcX protein) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-10 RGD1560601_predicted  similar to Jumonji/ARID domain-containing protein 1C (SmcX protein) (predicted)    similar to Jumonji/ARID domain-containing protein 1C (SmcX protein) (Xe169 protein) (predicted)  Name updated 1299863 APPROVED
2006-03-07 RGD1560601_predicted  similar to Jumonji/ARID domain-containing protein 1C (SmcX protein) (Xe169 protein) (predicted)  LOC317432  similar to Jumonji/ARID domain-containing protein 1C (SmcX protein) (Xe169 protein)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317432  similar to Jumonji/ARID domain-containing protein 1C (SmcX protein) (Xe169 protein)      Symbol and Name status set to provisional 70820 PROVISIONAL