Kmt2c (lysine methyltransferase 2C) - Rat Genome Database

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Gene: Kmt2c (lysine methyltransferase 2C) Rattus norvegicus
Analyze
Symbol: Kmt2c
Name: lysine methyltransferase 2C
RGD ID: 1587205
Description: Predicted to enable histone methyltransferase activity (H3-K4 specific). Predicted to be involved in histone H3-K4 monomethylation. Predicted to act upstream of or within several processes, including eyelid development in camera-type eye; positive regulation of fibroblast proliferation; and single fertilization. Predicted to be located in nucleus. Predicted to be part of MLL3/4 complex. Human ortholog(s) of this gene implicated in Klatskin's tumor; Kleefstra syndrome 2; esophagus squamous cell carcinoma; and squamous cell carcinoma. Orthologous to human KMT2C (lysine methyltransferase 2C); PARTICIPATES IN DNA modification pathway; histone modification pathway; INTERACTS WITH amphetamine; bisphenol A; dibutyl phthalate.
Type: protein-coding
RefSeq Status: MODEL
Also known as: histone-lysine N-methyltransferase 2C; LOC502710; LOW QUALITY PROTEIN: histone-lysine N-methyltransferase 2C; lysine (K)-specific methyltransferase 2C; myeloid/lymphoid or mixed-lineage leukemia 3-like; similar to Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog (Histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3)
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
mRatBN7.249,620,638 - 9,834,787 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl49,609,627 - 9,833,539 (+)Ensembl
Rnor_6.0482,506 - 109,986 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.046,083,650 - 6,294,413 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl46,083,736 - 6,292,516 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.046,104,240 - 6,315,339 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0482,826 - 109,979 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.445,020,018 - 5,239,019 (+)NCBIRGSC3.4rn4RGSC3.4
Celera4484,949 - 698,981 (-)NCBICelera
Cytogenetic Map4q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:17021013   PMID:17500065   PMID:18172164   PMID:22266653   PMID:22658674   PMID:26324722  


Genomics

Comparative Map Data
Kmt2c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.249,620,638 - 9,834,787 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl49,609,627 - 9,833,539 (+)Ensembl
Rnor_6.0482,506 - 109,986 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.046,083,650 - 6,294,413 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl46,083,736 - 6,292,516 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.046,104,240 - 6,315,339 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0482,826 - 109,979 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.445,020,018 - 5,239,019 (+)NCBIRGSC3.4rn4RGSC3.4
Celera4484,949 - 698,981 (-)NCBICelera
Cytogenetic Map4q11NCBI
KMT2C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl7152,134,922 - 152,436,644 (-)EnsemblGRCh38hg38GRCh38
GRCh387152,134,925 - 152,436,642 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh377151,832,010 - 152,133,088 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 367151,462,943 - 151,764,023 (-)NCBINCBI36hg18NCBI36
Build 347151,271,503 - 151,570,699NCBI
Celera7146,389,572 - 146,690,258 (-)NCBI
Cytogenetic Map7q36.1NCBI
HuRef7145,643,457 - 145,868,582 (-)NCBIHuRef
CHM1_17151,840,538 - 152,142,092 (-)NCBICHM1_1
CRA_TCAGchr7v27151,159,181 - 151,460,261 (-)NCBI
Kmt2c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39525,476,793 - 25,703,853 (-)NCBIGRCm39mm39
GRCm39 Ensembl525,476,796 - 25,703,781 (-)Ensembl
GRCm38525,271,795 - 25,498,855 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl525,271,798 - 25,498,783 (-)EnsemblGRCm38mm10GRCm38
MGSCv37524,777,612 - 25,004,601 (-)NCBIGRCm37mm9NCBIm37
MGSCv36524,781,859 - 25,008,848 (-)NCBImm8
Celera522,207,830 - 22,380,620 (-)NCBICelera
Cytogenetic Map5B1NCBI
Kmt2c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554916,247,249 - 6,402,470 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554916,245,408 - 6,420,535 (-)NCBIChiLan1.0ChiLan1.0
KMT2C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.17155,860,699 - 156,081,038 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl7155,862,610 - 156,081,043 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v07143,714,716 - 144,016,188 (-)NCBIMhudiblu_PPA_v0panPan3
KMT2C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11615,962,045 - 16,117,601 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1615,963,901 - 16,158,408 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1616,575,056 - 16,858,922 (-)NCBI
ROS_Cfam_1.01617,685,626 - 17,972,552 (-)NCBI
UMICH_Zoey_3.11616,062,320 - 16,346,556 (-)NCBI
UNSW_CanFamBas_1.01616,643,550 - 16,927,359 (-)NCBI
UU_Cfam_GSD_1.01616,694,819 - 16,978,785 (-)NCBI
Kmt2c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244051185,323,045 - 5,592,544 (+)NCBI
SpeTri2.0NW_0049365277,310,885 - 7,508,032 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KMT2C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl184,993,196 - 5,279,042 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1184,993,213 - 5,279,668 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2185,538,409 - 5,587,967 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KMT2C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.121120,299,295 - 120,587,843 (-)NCBI
ChlSab1.1 Ensembl21120,301,188 - 120,587,137 (-)Ensembl
Vero_WHO_p1.0NW_02366607216,283,079 - 16,504,530 (-)NCBI
Kmt2c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248004,510,669 - 4,785,909 (+)NCBI

Position Markers
RH133147  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.249,833,857 - 9,834,042 (+)MAPPERmRatBN7.2
Rnor_6.046,293,484 - 6,293,668NCBIRnor6.0
Rnor_5.046,314,410 - 6,314,594UniSTSRnor5.0
RGSC_v3.445,238,090 - 5,238,274UniSTSRGSC3.4
Celera4485,694 - 485,878UniSTS
Cytogenetic Map4q11UniSTS
RH139525  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.249,834,444 - 9,834,641 (+)MAPPERmRatBN7.2
Rnor_6.046,294,071 - 6,294,267NCBIRnor6.0
Rnor_5.046,314,997 - 6,315,193UniSTSRnor5.0
RGSC_v3.445,238,677 - 5,238,873UniSTSRGSC3.4
Celera4485,095 - 485,291UniSTS
Cytogenetic Map4q11UniSTS
RH137632  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map4q11UniSTS
D7S3202  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.249,834,309 - 9,834,727 (+)MAPPERmRatBN7.2
Rnor_6.046,293,936 - 6,294,353NCBIRnor6.0
Rnor_5.046,314,862 - 6,315,279UniSTSRnor5.0
RGSC_v3.445,238,542 - 5,238,959UniSTSRGSC3.4
Celera4485,009 - 485,426UniSTS
Cytogenetic Map4q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61351Bp33Blood pressure QTL 330.0018arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4127716890Rat
61408Scl23Serum cholesterol level QTL 230.0005blood HDL phospholipid amount (VT:0010504)serum high density lipoprotein phospholipid level (CMO:0001567)4127716890Rat
724557Plsm1Polydactyly-luxate syndrome (PLS) morphotypes QTL 10.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)4127716890Rat
1641905Colcr1Colorectal carcinoma resistance QTL 14.30.0003intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)4129494328Rat
61333Gluco16Glucose level QTL 164.30.00001adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)4130372989Rat
9589097Slep11Serum leptin concentration QTL 115.090.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)4131934116Rat
8552903Pigfal2Plasma insulin-like growth factor 1 level QTL 27.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)4131934116Rat
9589046Scfw2Subcutaneous fat weight QTL 25.540.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)4131934116Rat
9590100Sffal4Serum free fatty acids level QTL 47.360.05blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)4131934116Rat
738021Hcar13Hepatocarcinoma resistance QTL 134.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)4132584199Rat
1357341Gluco5Glucose level QTL 56.4adipocyte free fatty acid secretion trait (VT:0010465)absolute change in adipocyte free fatty acid secretion per unit volume (CMO:0001446)4133250345Rat
1357343Gluco4Glucose level QTL 40.00002adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake to basal glucose uptake ratio (CMO:0000874)4133250345Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4139505420Rat
634323Hc2Hypercalciuria QTL 22.15urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)421079645210796Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829457114705Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
1358201Gluco12Glucose level QTL121.6adipocyte glucose uptake trait (VT:0004185)adipocyte maximal glucose uptake (CMO:0000870)4521839229593287Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521917856647776Rat


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 12 26 10 17 10 8 8 71 28 33 8 8
Low 3 31 30 30 2 30 3 3 7 8 3
Below cutoff 1 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_006224786 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224788 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224790 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224791 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224792 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224793 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224794 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224795 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224796 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224798 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006224801 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006235840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762670 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775646 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108965 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108966 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108967 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108971 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108972 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108974 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108976 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108978 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039108982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005504104 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005504105 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005504106 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide FQ219148 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233094 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000139 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000010349   ⟹   ENSRNOP00000010349
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl46,282,278 - 6,292,487 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077289   ⟹   ENSRNOP00000072878
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl46,159,006 - 6,201,526 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093625
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl49,620,538 - 9,833,539 (+)Ensembl
Rnor_6.0 Ensembl46,083,736 - 6,292,516 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101551   ⟹   ENSRNOP00000089164
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl49,609,627 - 9,833,539 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000103015   ⟹   ENSRNOP00000078989
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl49,620,487 - 9,833,539 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108916   ⟹   ENSRNOP00000086031
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl49,620,634 - 9,833,539 (+)Ensembl
RefSeq Acc Id: XM_008762670   ⟹   XP_008760892
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,833,088 (+)NCBI
Rnor_6.046,083,650 - 6,294,413 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039108963   ⟹   XP_038964891
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,834,787 (+)NCBI
RefSeq Acc Id: XM_039108964   ⟹   XP_038964892
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108965   ⟹   XP_038964893
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108966   ⟹   XP_038964894
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108967   ⟹   XP_038964895
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108968   ⟹   XP_038964896
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,654,534 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108969   ⟹   XP_038964897
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108970   ⟹   XP_038964898
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,654,535 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108971   ⟹   XP_038964899
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108972   ⟹   XP_038964900
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108973   ⟹   XP_038964901
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108974   ⟹   XP_038964902
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108975   ⟹   XP_038964903
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108976   ⟹   XP_038964904
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,909 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108977   ⟹   XP_038964905
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,909 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108978   ⟹   XP_038964906
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108979   ⟹   XP_038964907
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,640 - 9,833,088 (+)NCBI
RefSeq Acc Id: XM_039108981   ⟹   XP_038964909
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,638 - 9,812,490 (+)NCBI
RefSeq Acc Id: XM_039108982   ⟹   XP_038964910
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,638 - 9,807,803 (+)NCBI
RefSeq Acc Id: XR_005504104
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,638 - 9,814,979 (+)NCBI
RefSeq Acc Id: XR_005504105
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,638 - 9,814,980 (+)NCBI
RefSeq Acc Id: XR_005504106
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.249,620,638 - 9,814,955 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_008760892   ⟸   XM_008762670
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: ENSRNOP00000072878   ⟸   ENSRNOT00000077289
RefSeq Acc Id: ENSRNOP00000010349   ⟸   ENSRNOT00000010349
RefSeq Acc Id: XP_038964909   ⟸   XM_039108981
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038964910   ⟸   XM_039108982
- Peptide Label: isoform X20
RefSeq Acc Id: XP_038964891   ⟸   XM_039108963
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038964897   ⟸   XM_039108969
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038964894   ⟸   XM_039108966
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038964899   ⟸   XM_039108971
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038964893   ⟸   XM_039108965
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038964902   ⟸   XM_039108974
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038964906   ⟸   XM_039108978
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038964907   ⟸   XM_039108979
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038964903   ⟸   XM_039108975
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038964901   ⟸   XM_039108973
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038964900   ⟸   XM_039108972
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038964895   ⟸   XM_039108967
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038964892   ⟸   XM_039108964
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038964904   ⟸   XM_039108976
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038964905   ⟸   XM_039108977
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038964896   ⟸   XM_039108968
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038964898   ⟸   XM_039108970
- Peptide Label: isoform X8
RefSeq Acc Id: ENSRNOP00000078989   ⟸   ENSRNOT00000103015
RefSeq Acc Id: ENSRNOP00000086031   ⟸   ENSRNOT00000108916
RefSeq Acc Id: ENSRNOP00000089164   ⟸   ENSRNOT00000101551
Protein Domains
FYR C-terminal   FYR N-terminal   PHD-type   Post-SET   RING-type   SET

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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
ACI/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)
ACI/EurMcwi (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
ACI/N (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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
BN/SsN (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BUF/N (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (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
BXH3/CubMcwi (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
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/NRrrc (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
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)
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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)
FHH/EurMcwi (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
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)
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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
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)
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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)
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)
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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
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)
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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
HXB20/IpcvMcwi (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
HXB31/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
HXB4/IpcvMcwi (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
LE/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
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)
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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: 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)
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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
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)
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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
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)
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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
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)
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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
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
LH/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
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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)
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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/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)
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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 (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
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
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1587205 AgrOrtholog
Ensembl Genes ENSRNOG00000061080 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000010349 UniProtKB/TrEMBL
  ENSRNOP00000072878 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010349 UniProtKB/TrEMBL
  ENSRNOT00000077289 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
InterPro EPHD UniProtKB/TrEMBL
  FYrich_C UniProtKB/TrEMBL
  FYrich_N UniProtKB/TrEMBL
  KMT2C UniProtKB/TrEMBL
  Post-SET_dom UniProtKB/TrEMBL
  SET_dom UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
NCBI Gene 502710 ENTREZGENE
PANTHER PTHR45888:SF1 UniProtKB/TrEMBL
Pfam FYRC UniProtKB/TrEMBL
  FYRN UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
PhenoGen Kmt2c PhenoGen
PROSITE EPHD UniProtKB/TrEMBL
  FYRC UniProtKB/TrEMBL
  FYRN UniProtKB/TrEMBL
  POST_SET UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/TrEMBL
SMART FYRC UniProtKB/TrEMBL
  FYRN UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  PostSET UniProtKB/TrEMBL
  RING UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
Superfamily-SCOP SSF57903 UniProtKB/TrEMBL
UniProt A0A0G2K426_RAT UniProtKB/TrEMBL
  F1LXW1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Kmt2c  lysine methyltransferase 2C  Kmt2c  lysine (K)-specific methyltransferase 2C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-09 Kmt2c  lysine (K)-specific methyltransferase 2C  LOC502710  similar to Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog (Histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 LOC502710  similar to Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog (Histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3)  LOC100364718  myeloid/lymphoid or mixed-lineage leukemia 3-like  Data Merged 1643240 APPROVED
2010-05-05 LOC100364718  myeloid/lymphoid or mixed-lineage leukemia 3-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-01-09 LOC502710  similar to Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog (Histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3)  LOC679252  similar to Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog (Histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3)  Data Merged 1643240 APPROVED
2006-11-20 LOC679252  similar to Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog (Histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC502710  similar to Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog (Histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3)      Symbol and Name status set to provisional 70820 PROVISIONAL