Kdm4b (lysine demethylase 4B) - Rat Genome Database

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Gene: Kdm4b (lysine demethylase 4B) Rattus norvegicus
Analyze
Symbol: Kdm4b
Name: lysine demethylase 4B
RGD ID: 1588576
Description: Predicted to enable histone demethylase activity (H3-K36 specific) and histone demethylase activity (H3-K9 specific). Predicted to be involved in chromatin remodeling. Predicted to act upstream of or within histone H3-K36 demethylation; histone H3-K9 demethylation; and negative regulation of histone H3-K9 trimethylation. Located in nucleus. Human ortholog(s) of this gene implicated in autosomal dominant non-syndromic intellectual disability; breast cancer; colorectal cancer; malignant peripheral nerve sheath tumor; and stomach cancer. Orthologous to human KDM4B (lysine demethylase 4B); PARTICIPATES IN histone modification pathway; INTERACTS WITH bisphenol A; cobalt dichloride; fipronil.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC301128; lysine (K)-specific demethylase 4B; lysine-specific demethylase 4B; similar to jumonji domain containing 2B
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
mRatBN7.291,158,737 - 1,237,228 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl91,158,752 - 1,236,543 (+)Ensembl
Rnor_6.0910,656,035 - 10,734,127 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,653,216 - 10,734,073 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,647,087 - 9,725,878 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,273,613 - 7,351,363 (-)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component
cytosol  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IDA)
pericentric heterochromatin  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bjorkman M, etal., Oncogene. 2012 Jul 19;31(29):3444-56. doi: 10.1038/onc.2011.512. Epub 2011 Nov 28.
2. Black JC, etal., Mol Cell. 2012 Nov 30;48(4):491-507. doi: 10.1016/j.molcel.2012.11.006.
3. Chen L, etal., Br J Cancer. 2014 Feb 18;110(4):1014-26. doi: 10.1038/bjc.2013.808. Epub 2014 Jan 28.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Gray SG, etal., J Biol Chem. 2005 Aug 5;280(31):28507-18. Epub 2005 May 31.
6. Kawazu M, etal., PLoS One. 2011 Mar 18;6(3):e17830. doi: 10.1371/journal.pone.0017830.
7. Li W, etal., Biochem Biophys Res Commun. 2011 Dec 16;416(3-4):372-8. doi: 10.1016/j.bbrc.2011.11.045. Epub 2011 Nov 19.
8. Liu Y, etal., Gut. 2013 Apr;62(4):571-81. doi: 10.1136/gutjnl-2011-301059. Epub 2012 Feb 16.
9. Northcott PA, etal., Nat Genet. 2009 Apr;41(4):465-72. doi: 10.1038/ng.336. Epub 2009 Mar 8.
10. Pryor JG, etal., Am J Dermatopathol. 2011 Dec;33(8):780-5. doi: 10.1097/DAD.0b013e31820dfcbf.
11. RGD automated data pipeline
12. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. RGD automated import pipeline for gene-chemical interactions
14. RGD comprehensive gene curation
15. Toyokawa G, etal., Cancer Prev Res (Phila). 2011 Dec;4(12):2051-61. doi: 10.1158/1940-6207.CAPR-11-0290. Epub 2011 Sep 19.
16. Zhao L, etal., Clin Cancer Res. 2013 Dec 1;19(23):6419-29. doi: 10.1158/1078-0432.CCR-13-0254. Epub 2013 Sep 27.
17. Zhao M, etal., Br J Dermatol. 2012 Feb;166(2):226-73. doi: 10.1111/j.1365-2133.2011.10646.x. Epub 2012 Jan 9.
Additional References at PubMed
PMID:12477932   PMID:16738407   PMID:19144645   PMID:21914792   PMID:28262558   PMID:32594337  


Genomics

Comparative Map Data
Kdm4b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.291,158,737 - 1,237,228 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl91,158,752 - 1,236,543 (+)Ensembl
Rnor_6.0910,656,035 - 10,734,127 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,653,216 - 10,734,073 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,647,087 - 9,725,878 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,273,613 - 7,351,363 (-)NCBICelera
Cytogenetic Map9q12NCBI
KDM4B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl194,969,113 - 5,153,598 (+)EnsemblGRCh38hg38GRCh38
GRCh38194,969,087 - 5,153,603 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37194,969,124 - 5,153,609 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,920,132 - 5,104,606 (+)NCBINCBI36hg18NCBI36
Celera194,906,316 - 5,091,160 (+)NCBI
Cytogenetic Map19p13.3NCBI
HuRef194,730,929 - 4,915,533 (+)NCBIHuRef
CHM1_1194,969,172 - 5,153,207 (+)NCBICHM1_1
Kdm4b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,632,975 - 56,710,774 (+)NCBIGRCm39mm39
GRCm39 Ensembl1756,633,062 - 56,709,870 (+)Ensembl
GRCm381756,325,970 - 56,403,774 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,326,062 - 56,402,870 (+)EnsemblGRCm38mm10GRCm38
MGSCv371756,465,473 - 56,542,296 (+)NCBIGRCm37mm9NCBIm37
MGSCv361755,959,801 - 56,036,572 (+)NCBImm8
Celera1760,697,409 - 60,748,612 (+)NCBICelera
Cytogenetic Map17DNCBI
Kdm4b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554954,018,770 - 4,114,604 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554954,019,066 - 4,101,577 (-)NCBIChiLan1.0ChiLan1.0
KDM4B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1194,977,413 - 5,116,113 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl194,977,413 - 5,116,113 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0193,986,296 - 4,172,359 (+)NCBIMhudiblu_PPA_v0panPan3
KDM4B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12054,713,900 - 54,843,991 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2054,634,121 - 54,820,816 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2054,438,687 - 54,576,517 (-)NCBI
ROS_Cfam_1.02055,368,796 - 55,506,632 (-)NCBI
UMICH_Zoey_3.12054,430,228 - 54,567,939 (-)NCBI
UNSW_CanFamBas_1.02054,910,865 - 55,048,624 (-)NCBI
UU_Cfam_GSD_1.02055,108,670 - 55,246,485 (-)NCBI
Kdm4b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118214,829,153 - 214,917,129 (-)NCBI
SpeTri2.0NW_0049365882,908,970 - 3,005,625 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM4B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl273,747,641 - 73,889,865 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1273,746,379 - 73,889,881 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2274,436,488 - 74,458,404 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KDM4B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.164,649,140 - 4,831,634 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl64,649,221 - 4,831,636 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660813,296,265 - 3,480,930 (-)NCBIVero_WHO_p1.0
Kdm4b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248284,796,306 - 4,893,093 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D9Got200  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,185,844 - 1,186,050 (-)MAPPERmRatBN7.2
Rnor_6.0910,706,528 - 10,706,733NCBIRnor6.0
Rnor_5.099,698,263 - 9,698,468UniSTSRnor5.0
Celera97,324,093 - 7,324,298UniSTS
Cytogenetic Map9q11UniSTS
RH143752  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,159,057 - 1,159,161 (-)MAPPERmRatBN7.2
Rnor_6.0910,733,691 - 10,733,794NCBIRnor6.0
Rnor_5.099,725,463 - 9,725,566UniSTSRnor5.0
Celera97,350,981 - 7,351,084UniSTS
Cytogenetic Map9q11UniSTS
AW525135  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,206,978 - 1,207,146 (-)MAPPERmRatBN7.2
Rnor_6.0910,685,433 - 10,685,600NCBIRnor6.0
Rnor_5.099,677,168 - 9,677,335UniSTSRnor5.0
Celera97,303,010 - 7,303,177UniSTS
RH 3.4 Map8180.2UniSTS
Cytogenetic Map9q11UniSTS
RH135189  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,236,318 - 1,236,505 (-)MAPPERmRatBN7.2
Rnor_6.0910,656,075 - 10,656,261NCBIRnor6.0
Rnor_5.099,647,810 - 9,647,996UniSTSRnor5.0
Celera97,273,651 - 7,273,837UniSTS
Cytogenetic Map9q11UniSTS
RH141483  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.291,235,486 - 1,235,686 (-)MAPPERmRatBN7.2
Rnor_6.0910,656,894 - 10,657,093NCBIRnor6.0
Rnor_5.099,648,629 - 9,648,828UniSTSRnor5.0
Celera97,274,470 - 7,274,669UniSTS
Cytogenetic Map9q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:556
Count of miRNA genes:256
Interacting mature miRNAs:306
Transcripts:ENSRNOT00000071199
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 29 19 4 19 4 1 2 74 23 37 11 1
Low 3 14 38 37 37 7 9 12 4 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001044236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001395633 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244316 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244317 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244318 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244319 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244320 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596321 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596322 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083143 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039083144 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC098860 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC161813 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474092 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230859 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000204 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000071199   ⟹   ENSRNOP00000066803
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,158,779 - 1,236,543 (+)Ensembl
Rnor_6.0 Ensembl910,656,037 - 10,734,073 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089374   ⟹   ENSRNOP00000070258
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,158,779 - 1,236,543 (+)Ensembl
Rnor_6.0 Ensembl910,653,216 - 10,710,648 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091450   ⟹   ENSRNOP00000073251
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl910,657,185 - 10,659,357 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095576   ⟹   ENSRNOP00000093085
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,158,779 - 1,236,543 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108055   ⟹   ENSRNOP00000083814
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl91,158,752 - 1,236,317 (+)Ensembl
RefSeq Acc Id: NM_001044236   ⟹   NP_001037701
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,158,779 - 1,236,543 (+)NCBI
Rnor_6.0910,656,037 - 10,734,073 (-)NCBI
Rnor_5.099,647,087 - 9,725,878 (-)NCBI
Celera97,273,613 - 7,351,363 (-)RGD
Sequence:
RefSeq Acc Id: XM_006244316   ⟹   XP_006244378
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,158,738 - 1,237,228 (+)NCBI
Rnor_6.0910,656,035 - 10,734,123 (-)NCBI
Rnor_5.099,647,087 - 9,725,878 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006244318   ⟹   XP_006244380
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,158,738 - 1,237,228 (+)NCBI
Rnor_6.0910,656,035 - 10,734,124 (-)NCBI
Rnor_5.099,647,087 - 9,725,878 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006244319   ⟹   XP_006244381
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,158,737 - 1,237,228 (+)NCBI
Rnor_6.0910,656,035 - 10,734,124 (-)NCBI
Rnor_5.099,647,087 - 9,725,878 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006244320   ⟹   XP_006244382
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,158,737 - 1,237,228 (+)NCBI
Rnor_6.0910,656,035 - 10,734,124 (-)NCBI
Rnor_5.099,647,087 - 9,725,878 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039083143   ⟹   XP_038939071
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,158,737 - 1,236,537 (+)NCBI
RefSeq Acc Id: XM_039083144   ⟹   XP_038939072
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.291,197,987 - 1,237,228 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001037701   ⟸   NM_001044236
- UniProtKB: M0RB75 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244382   ⟸   XM_006244320
- Peptide Label: isoform X4
- UniProtKB: A0A0G2JXG2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244381   ⟸   XM_006244319
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006244380   ⟸   XM_006244318
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006244378   ⟸   XM_006244316
- Peptide Label: isoform X1
- UniProtKB: M0RB75 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070258   ⟸   ENSRNOT00000089374
RefSeq Acc Id: ENSRNOP00000073251   ⟸   ENSRNOT00000091450
RefSeq Acc Id: ENSRNOP00000066803   ⟸   ENSRNOT00000071199
RefSeq Acc Id: XP_038939071   ⟸   XM_039083143
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038939072   ⟸   XM_039083144
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000093085   ⟸   ENSRNOT00000095576
RefSeq Acc Id: ENSRNOP00000083814   ⟸   ENSRNOT00000108055
Protein Domains
JmjC   JmjN   PHD-type

Transcriptome

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

Promoters
RGD ID:13696459
Promoter ID:EPDNEW_R6984
Type:initiation region
Name:Kdm4b_1
Description:lysine demethylase 4B
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_6.0910,734,095 - 10,734,155EPDNEW

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)
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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)
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)
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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)
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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
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)
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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
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)
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)
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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
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)
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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
M520/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
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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
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)
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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
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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)
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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
SHRSP/A3NCrl (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
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)
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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
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)
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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)
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)
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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)
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)
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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)
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 9656458 9656459 C A snv KFRS3B/Kyo (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588576 AgrOrtholog
Ensembl Genes ENSRNOG00000049221 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000066803 UniProtKB/TrEMBL
  ENSRNOP00000070258 UniProtKB/TrEMBL
  ENSRNOP00000073251 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071199 UniProtKB/TrEMBL
  ENSRNOT00000089374 UniProtKB/TrEMBL
  ENSRNOT00000091450 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8367824 IMAGE-MGC_LOAD
InterPro EPHD UniProtKB/TrEMBL
  JmjC_dom UniProtKB/TrEMBL
  KDM4_Tudor_2 UniProtKB/TrEMBL
  TF_JmjN UniProtKB/TrEMBL
  Tudor UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:301128 UniProtKB/TrEMBL
MGC_CLONE MGC:187252 IMAGE-MGC_LOAD
NCBI Gene 301128 ENTREZGENE
Pfam JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  Tudor_2 UniProtKB/TrEMBL
PhenoGen Kdm4b PhenoGen
PROSITE EPHD UniProtKB/TrEMBL
  JMJC UniProtKB/TrEMBL
  JMJN UniProtKB/TrEMBL
SMART JmjC UniProtKB/TrEMBL
  JmjN UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  TUDOR UniProtKB/TrEMBL
Superfamily-SCOP SSF57903 UniProtKB/TrEMBL
UniProt A0A0G2JXG2 ENTREZGENE, UniProtKB/TrEMBL
  M0RB75 ENTREZGENE, UniProtKB/TrEMBL
  Q4KM27_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Kdm4b  lysine demethylase 4B  Kdm4b  lysine (K)-specific demethylase 4B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-09-17 Kdm4b  lysine (K)-specific demethylase 4B  LOC301128  similar to jumonji domain containing 2B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC301128  similar to jumonji domain containing 2B      Symbol and Name status set to provisional 70820 PROVISIONAL