Kdm6a (lysine demethylase 6A) - Rat Genome Database
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Gene: Kdm6a (lysine demethylase 6A) Rattus norvegicus
Analyze
Symbol: Kdm6a
Name: lysine demethylase 6A
RGD ID: 9275041
Description: Predicted to have DNA binding activity; histone demethylase activity (H3-K27 specific); and identical protein binding activity. Predicted to be involved in several processes, including chordate embryonic development; chromatin organization; and embryonic morphogenesis. Predicted to localize to MLL3/4 complex. Human ortholog(s) of this gene implicated in Kabuki syndrome; acute lymphoblastic leukemia; and esophagus squamous cell carcinoma. Orthologous to human KDM6A (lysine demethylase 6A); PARTICIPATES IN histone modification pathway; renal cell carcinoma pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2-acetamidofluorene; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOW QUALITY PROTEIN: lysine-specific demethylase 6A; lysine (K)-specific demethylase 6A; lysine-specific demethylase 6A; NEWGENE_1565481
Orthologs:
Homo sapiens (human) : KDM6A (lysine demethylase 6A)  HGNC  Alliance
Mus musculus (house mouse) : Kdm6a (lysine (K)-specific demethylase 6A)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Kdm6a (lysine demethylase 6A)
Pan paniscus (bonobo/pygmy chimpanzee) : KDM6A (lysine demethylase 6A)
Canis lupus familiaris (dog) : KDM6A (lysine demethylase 6A)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Kdm6a (lysine demethylase 6A)
Sus scrofa (pig) : KDM6A (lysine demethylase 6A)
Chlorocebus sabaeus (African green monkey) : KDM6A (lysine demethylase 6A)
Heterocephalus glaber (naked mole-rat) : Kdm6a (lysine demethylase 6A)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0X4,805,493 - 4,945,788 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX4,806,277 - 4,945,944 (-)EnsemblRnor6.0rn6Rnor6.0
CeleraX4,851,606 - 4,991,275 (-)NCBICelera
Cytogenetic MapXq11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:17500065   PMID:21095589   PMID:22949634   PMID:23028370   PMID:23658530   PMID:30887465  


Genomics

Comparative Map Data
Kdm6a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0X4,805,493 - 4,945,788 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX4,806,277 - 4,945,944 (-)EnsemblRnor6.0rn6Rnor6.0
CeleraX4,851,606 - 4,991,275 (-)NCBICelera
Cytogenetic MapXq11NCBI
KDM6A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX44,873,177 - 45,112,779 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 EnsemblX44,873,177 - 45,112,602 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 EnsemblX44,873,188 - 45,112,779 (+)EnsemblGRCh38hg38GRCh38
GRCh38X44,873,182 - 45,112,779 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X44,732,419 - 44,972,024 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X44,617,725 - 44,856,791 (+)NCBINCBI36hg18NCBI36
Build 34X44,489,034 - 44,728,097NCBI
CeleraX48,869,187 - 49,108,532 (+)NCBI
Cytogenetic MapXp11.3NCBI
HuRefX42,453,849 - 42,692,064 (+)NCBIHuRef
CHM1_1X44,765,275 - 45,004,750 (+)NCBICHM1_1
Kdm6a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X18,027,101 - 18,146,175 (+)NCBI
GRCm38X18,160,862 - 18,279,936 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX18,162,575 - 18,279,936 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X17,739,793 - 17,856,484 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X17,319,626 - 17,436,317 (+)NCBImm8
CeleraX15,748,215 - 15,864,723 (+)NCBICelera
Cytogenetic MapXA1.2- A1.3NCBI
cM MapX13.45NCBI
Kdm6a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555163,149,948 - 3,346,832 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555163,151,350 - 3,346,832 (-)NCBIChiLan1.0ChiLan1.0
KDM6A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X45,127,382 - 45,362,029 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX45,127,382 - 45,362,029 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X37,313,000 - 37,548,630 (+)NCBIMhudiblu_PPA_v0panPan3
KDM6A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX38,745,854 - 38,959,842 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X38,745,854 - 38,964,029 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Kdm6a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493650210,980,303 - 11,196,711 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KDM6A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX39,953,759 - 40,154,194 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X39,953,764 - 40,154,197 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X44,504,617 - 44,704,755 (+)NCBISscrofa10.2Sscrofa10.2susScr3
KDM6A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 EnsemblX42,053,336 - 42,290,526 (+)Ensembl
ChlSab1.1X42,053,272 - 42,291,013 (+)NCBI
Kdm6a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248871,065,173 - 1,279,660 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
70166Bp65Blood pressure QTL 655.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166245312370298Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X166245321592783Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X183816624331837Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat


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 2 33 52 36 19 36 5 5 72 32 34 11 5
Low 1 10 5 5 5 3 6 2 3 7 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_002727525 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_002727526 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_002727527 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_002727528 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_002727529 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_003754729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227257 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006227258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758349 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008758352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008773047 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07036882 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07036883 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AABR07036884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01108755 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01108756 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01108757 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01108758 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01108759 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01108760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01108761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GAPM01000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000077238   ⟹   ENSRNOP00000073763
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX4,806,847 - 4,945,944 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092829
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX4,806,277 - 4,945,725 (-)Ensembl
RefSeq Acc Id: XM_002727525   ⟹   XP_002727571
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX4,851,606 - 4,991,274 (-)NCBI
Sequence:
RefSeq Acc Id: XM_002727526   ⟹   XP_002727572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX4,851,606 - 4,991,274 (-)NCBI
Sequence:
RefSeq Acc Id: XM_002727527   ⟹   XP_002727573
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX4,851,606 - 4,991,274 (-)NCBI
Sequence:
RefSeq Acc Id: XM_002727528   ⟹   XP_002727574
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX4,851,606 - 4,991,274 (-)NCBI
Sequence:
RefSeq Acc Id: XM_002727529   ⟹   XP_002727575
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX4,851,606 - 4,991,274 (-)NCBI
Sequence:
RefSeq Acc Id: XM_003754729   ⟹   XP_003754777
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX4,851,606 - 4,991,273 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006227257   ⟹   XP_006227319
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX4,851,606 - 4,991,274 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006227258   ⟹   XP_006227320
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX4,851,606 - 4,991,273 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008758347   ⟹   XP_008756569
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX4,851,606 - 4,991,275 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008758348   ⟹   XP_008756570
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX4,851,606 - 4,991,274 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008758349   ⟹   XP_008756571
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX4,851,606 - 4,991,275 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008758352   ⟹   XP_008756574
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX4,851,606 - 4,991,274 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773047   ⟹   XP_008771269
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X4,805,493 - 4,945,788 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: XP_008756571   ⟸   XM_008758349
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_002727571   ⟸   XM_002727525
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008756569   ⟸   XM_008758347
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_002727575   ⟸   XM_002727529
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_008756574   ⟸   XM_008758352
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_002727574   ⟸   XM_002727528
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_002727572   ⟸   XM_002727526
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_002727573   ⟸   XM_002727527
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006227319   ⟸   XM_006227257
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008756570   ⟸   XM_008758348
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_003754777   ⟸   XM_003754729
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_006227320   ⟸   XM_006227258
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_008771269   ⟸   XM_008773047
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000073763   ⟸   ENSRNOT00000077238
Protein Domains
JmjC   TPR_REGION

Transcriptome

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

Promoters
RGD ID:13701706
Promoter ID:EPDNEW_R12225
Type:initiation region
Name:Kdm6a_1
Description:lysine demethylase 6A
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_6.0X4,945,749 - 4,945,809EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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 (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:9275041 AgrOrtholog
Ensembl Genes ENSRNOG00000052721 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000073763 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077238 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
InterPro JmjC_dom UniProtKB/TrEMBL
  TPR-contain_dom UniProtKB/TrEMBL
  TPR-like_helical_dom UniProtKB/TrEMBL
  TPR_repeat UniProtKB/TrEMBL
NCBI Gene Kdm6a ENTREZGENE
Pfam JmjC UniProtKB/TrEMBL
  TPR_8 UniProtKB/TrEMBL
PhenoGen Kdm6a PhenoGen
PROSITE JMJC UniProtKB/TrEMBL
  TPR UniProtKB/TrEMBL
  TPR_REGION UniProtKB/TrEMBL
SMART JmjC UniProtKB/TrEMBL
  TPR UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
UniProt A0A0G2K6D0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-10-20 Kdm6a  lysine demethylase 6A  NEWGENE_1565481  lysine (K)-specific demethylase 6A  Name and Symbol changed 629549 APPROVED