Kmt5a (lysine methyltransferase 5A) - Rat Genome Database

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Gene: Kmt5a (lysine methyltransferase 5A) Rattus norvegicus
Analyze
Symbol: Kmt5a
Name: lysine methyltransferase 5A
RGD ID: 1587560
Description: Predicted to enable histone methyltransferase activity (H4-K20 specific); p53 binding activity; and transcription corepressor activity. Predicted to be involved in histone H4-K20 monomethylation; negative regulation of transcription by RNA polymerase II; and regulation of DNA damage response, signal transduction by p53 class mediator. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus and polytene chromosome. Orthologous to human KMT5A (lysine methyltransferase 5A); PARTICIPATES IN histone modification pathway; methionine cycle/metabolic pathway; p53 signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: histone methyltransferase Pr-set7/Set8; histone-lysine N-methyltransferase SETD8; LOC689820; lysine (K)-specific methyltransferase 5A; N-lysine methyltransferase KMT5A; N-lysine methyltransferase SETD8; Pr-set7; RGD1305893; SET domain containing (lysine methyltransferase) 8; SET domain-containing 8; Setd8; similar to SET domain-containing protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
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
mRatBN7.21232,139,353 - 32,167,777 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1232,139,178 - 32,162,711 (-)Ensembl
Rnor_6.01237,558,150 - 37,581,183 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1237,559,770 - 37,574,750 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01239,428,363 - 39,452,079 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41233,254,018 - 33,270,657 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1233,829,691 - 33,843,975 (-)NCBICelera
Cytogenetic Map12q15NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Targeting protein lysine methylation and demethylation in cancers. He Y, etal., Acta Biochim Biophys Sin (Shanghai). 2012 Jan;44(1):70-9. doi: 10.1093/abbs/gmr109.
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:15326124   PMID:15632090   PMID:17707234   PMID:18408754   PMID:18474616   PMID:22720056   PMID:33398850  


Genomics

Comparative Map Data
Kmt5a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21232,139,353 - 32,167,777 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1232,139,178 - 32,162,711 (-)Ensembl
Rnor_6.01237,558,150 - 37,581,183 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1237,559,770 - 37,574,750 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01239,428,363 - 39,452,079 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41233,254,018 - 33,270,657 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1233,829,691 - 33,843,975 (-)NCBICelera
Cytogenetic Map12q15NCBI
KMT5A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812123,384,132 - 123,409,353 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl12123,384,132 - 123,409,353 (+)EnsemblGRCh38hg38GRCh38
GRCh3712123,868,679 - 123,893,900 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3612122,434,657 - 122,459,853 (+)NCBINCBI36hg18NCBI36
Celera12123,461,215 - 123,486,597 (+)NCBI
Cytogenetic Map12q24.31NCBI
HuRef12120,829,632 - 120,854,730 (+)NCBIHuRef
CHM1_112123,683,455 - 123,708,653 (+)NCBICHM1_1
T2T-CHM13v2.012123,380,646 - 123,405,922 (+)NCBI
Kmt5a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395124,577,993 - 124,600,374 (+)NCBIGRCm39mm39
GRCm39 Ensembl5124,577,993 - 124,600,371 (+)Ensembl
GRCm385124,439,930 - 124,462,311 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5124,439,930 - 124,462,308 (+)EnsemblGRCm38mm10GRCm38
MGSCv375124,889,939 - 124,912,316 (+)NCBIGRCm37mm9NCBIm37
MGSCv365124,700,548 - 124,722,925 (+)NCBImm8
Celera5121,513,480 - 121,535,737 (+)NCBICelera
Cytogenetic Map5FNCBI
Kmt5a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554825,485,649 - 5,501,636 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554825,488,151 - 5,500,764 (-)NCBIChiLan1.0ChiLan1.0
KMT5A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112125,211,201 - 125,234,986 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v012120,982,059 - 121,007,360 (+)NCBIMhudiblu_PPA_v0panPan3
Kmt5a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118158,125,115 - 158,134,261 (+)NCBI
SpeTri2.0NW_0049365581,346,040 - 1,366,601 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
KMT5A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1429,523,105 - 29,543,493 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11429,523,102 - 29,543,522 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21431,215,887 - 31,234,841 (-)NCBISscrofa10.2Sscrofa10.2susScr3
KMT5A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111118,712,964 - 118,743,322 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl11118,723,029 - 118,743,325 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037126,539,281 - 126,565,296 (-)NCBIVero_WHO_p1.0
Kmt5a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474723,289,119 - 23,308,682 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462474723,289,118 - 23,309,465 (+)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12134851688Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)12142110980Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12142110980Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)12142110980Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12142450532Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12144465750Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12144503507Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12144503507Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12117200546172005Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6556449546669029Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12556449546669029Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449846669029Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12610757946669029Rat
1302792Scl21Serum cholesterol level QTL 213.80.0011blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)12719673046669029Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121047413746669029Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121047413746669029Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121107382545055165Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121235161946669029Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121281238546669029Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121281238546669029Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121318273646669029Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101318273646669029Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121319815746669029Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121363552335682913Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121555082638478808Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121587265332974238Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)121961087040218516Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961087042828880Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)121961087046669029Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121961088935682913Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121983578938193007Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122032881946669029Rat
70169Eae13Experimental allergic encephalomyelitis QTL 130.032nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)122413920236638073Rat
1556747Calcic1Intracellular calcium level QTL 13.6platelet calcium amount (VT:0010500)platelet intracellular calcium level (CMO:0000922)122806443340130419Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)122806443345899022Rat
1600386Calcic2Intracellular calcium level QTL 20.001platelet physiology trait (VT:0005464)platelet intracellular calcium level (CMO:0000922)122806443346669029Rat
1331787Rf41Renal function QTL 412.998kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)122806455740218380Rat
631829Alc6Alcohol consumption QTL 64.7consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)122860752637691617Rat
1300162Bp188Blood pressure QTL 1883.19arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123210317445899022Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:32
Count of miRNA genes:30
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000066253
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 36 45 29 19 29 1 3 67 34 36 11 1
Low 7 12 12 12 7 8 7 1 5 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001246665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249328 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006249330 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598457 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017598458 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089771 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089772 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089773 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039089774 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB606422 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DV214760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DY311222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JN896763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000066253   ⟹   ENSRNOP00000062763
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1232,139,470 - 32,162,711 (-)Ensembl
Rnor_6.0 Ensembl1237,559,770 - 37,574,750 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106064   ⟹   ENSRNOP00000095821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1232,139,178 - 32,156,245 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106166   ⟹   ENSRNOP00000084143
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1232,139,470 - 32,161,830 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108981   ⟹   ENSRNOP00000092997
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1232,139,178 - 32,161,830 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111843   ⟹   ENSRNOP00000088749
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1232,139,178 - 32,161,830 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114055   ⟹   ENSRNOP00000080894
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1232,139,178 - 32,162,646 (-)Ensembl
RefSeq Acc Id: NM_001246665   ⟹   NP_001233594
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21232,140,973 - 32,156,509 (-)NCBI
Rnor_6.01237,559,770 - 37,574,750 (-)NCBI
Rnor_5.01239,428,363 - 39,452,079 (-)NCBI
Celera1233,829,691 - 33,843,975 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249328   ⟹   XP_006249390
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21232,139,353 - 32,162,728 (-)NCBI
Rnor_6.01237,558,150 - 37,581,183 (-)NCBI
Rnor_5.01239,428,363 - 39,452,079 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006249330   ⟹   XP_006249392
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21232,139,353 - 32,155,853 (-)NCBI
Rnor_6.01237,558,150 - 37,574,027 (-)NCBI
Rnor_5.01239,428,363 - 39,452,079 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598458   ⟹   XP_017453947
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21232,139,353 - 32,162,703 (-)NCBI
Rnor_6.01237,558,152 - 37,581,176 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039089770   ⟹   XP_038945698
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21232,139,353 - 32,157,410 (-)NCBI
RefSeq Acc Id: XM_039089771   ⟹   XP_038945699
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21232,139,353 - 32,162,626 (-)NCBI
RefSeq Acc Id: XM_039089772   ⟹   XP_038945700
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21232,139,353 - 32,156,949 (-)NCBI
RefSeq Acc Id: XM_039089773   ⟹   XP_038945701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21232,139,353 - 32,157,614 (-)NCBI
RefSeq Acc Id: XM_039089774   ⟹   XP_038945702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21232,139,353 - 32,167,777 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001233594   ⟸   NM_001246665
- UniProtKB: D3ZEB9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006249390   ⟸   XM_006249328
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006249392   ⟸   XM_006249330
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017453947   ⟸   XM_017598458
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000062763   ⟸   ENSRNOT00000066253
RefSeq Acc Id: XP_038945702   ⟸   XM_039089774
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038945699   ⟸   XM_039089771
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038945701   ⟸   XM_039089773
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038945698   ⟸   XM_039089770
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038945700   ⟸   XM_039089772
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000080894   ⟸   ENSRNOT00000114055
RefSeq Acc Id: ENSRNOP00000088749   ⟸   ENSRNOT00000111843
RefSeq Acc Id: ENSRNOP00000084143   ⟸   ENSRNOT00000106166
RefSeq Acc Id: ENSRNOP00000095821   ⟸   ENSRNOT00000106064
RefSeq Acc Id: ENSRNOP00000092997   ⟸   ENSRNOT00000108981

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZEB9-F1-model_v2 AlphaFold D3ZEB9 1-322 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
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
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
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
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
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/Stm (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
GK/FarMcwi (2019)
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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
HXB10/IpcvMcwi (2019)
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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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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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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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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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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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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
LEW/Crl (2019)
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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
LEXF10A/StmMcwi (2020)
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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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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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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
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
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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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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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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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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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/NRrrcMcwi (2019)
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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
MR/N (2020)
Visual CSV TAB Printer
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
MWF/Hsd (2019)
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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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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
SHR/OlalpcvMcwi (2019)
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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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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
SR/JrHsd (2020)
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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
SS/JrHsdMcwi (2019)
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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
WAG/RijCrl (2020)
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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/N (2020)
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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/NCrl (2019)
Visual CSV TAB Printer
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
WN/N (2020)
Visual CSV TAB Printer
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 37559951 37559952 A G snv SS/JrHsdMcwi (MCW), SBH/Ygl (MCW), ACI/EurMcwi (MCW), CDS


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 39430164 39430165 A G snv ACI/EurMcwi (MCW), SDLEF7/Barth (UDEL), SS/JrHsdMcwi (MCW), SBH/Ygl (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1587560 AgrOrtholog
BioCyc Gene G2FUF-19354 BioCyc
Ensembl Genes ENSRNOG00000001062 Ensembl
  ENSRNOG00000064318 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000062763 ENTREZGENE
  ENSRNOP00000062763.3 UniProtKB/TrEMBL
  ENSRNOP00000080894 ENTREZGENE
  ENSRNOP00000080894.1 UniProtKB/TrEMBL
  ENSRNOP00000084143 ENTREZGENE
  ENSRNOP00000084143.1 UniProtKB/TrEMBL
  ENSRNOP00000088749.1 UniProtKB/TrEMBL
  ENSRNOP00000092997 ENTREZGENE
  ENSRNOP00000092997.1 UniProtKB/TrEMBL
  ENSRNOP00000095821.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066253 ENTREZGENE
  ENSRNOT00000066253.3 UniProtKB/TrEMBL
  ENSRNOT00000106064.1 UniProtKB/TrEMBL
  ENSRNOT00000106166 ENTREZGENE
  ENSRNOT00000106166.1 UniProtKB/TrEMBL
  ENSRNOT00000108981 ENTREZGENE
  ENSRNOT00000108981.1 UniProtKB/TrEMBL
  ENSRNOT00000111843.1 UniProtKB/TrEMBL
  ENSRNOT00000114055 ENTREZGENE
  ENSRNOT00000114055.1 UniProtKB/TrEMBL
Gene3D-CATH 2.170.270.10 UniProtKB/TrEMBL
InterPro Hist_H4-K20_MeTrfase UniProtKB/TrEMBL
  SET_dom UniProtKB/TrEMBL
  SET_dom_sf UniProtKB/TrEMBL
KEGG Report rno:689820 UniProtKB/TrEMBL
NCBI Gene 689820 ENTREZGENE
Pfam SET UniProtKB/TrEMBL
PhenoGen Kmt5a PhenoGen
PIRSF Histone_H4-K20_mtfrase UniProtKB/TrEMBL
PROSITE SAM_MT43_7 UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
SMART SET UniProtKB/TrEMBL
Superfamily-SCOP SSF82199 UniProtKB/TrEMBL
UniProt A0A8I5ZQS7_RAT UniProtKB/TrEMBL
  A0A8I5ZY89_RAT UniProtKB/TrEMBL
  A0A8I6A5Q1_RAT UniProtKB/TrEMBL
  A0A8I6ANW6_RAT UniProtKB/TrEMBL
  A0A8I6GKG3_RAT UniProtKB/TrEMBL
  A0A8J8XFN9_RAT UniProtKB/TrEMBL
  D3ZEB9 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F7J138 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Kmt5a  lysine methyltransferase 5A  Kmt5a  lysine (K)-specific methyltransferase 5A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-13 Kmt5a  lysine (K)-specific methyltransferase 5A  Setd8  SET domain containing (lysine methyltransferase) 8  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-06-15 Setd8  SET domain containing (lysine methyltransferase) 8  LOC687538  similar to SET domain-containing protein  Data Merged 1643240 APPROVED
2009-01-26 Setd8  SET domain containing (lysine methyltransferase) 8  LOC689820  similar to SET domain-containing protein  Symbol and Name updated 1299863 APPROVED
2006-11-19 LOC689820  similar to SET domain-containing protein      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC687538  similar to SET domain-containing protein      Symbol and Name status set to provisional 70820 PROVISIONAL