Setdb1 (SET domain bifurcated histone lysine methyltransferase 1) - Rat Genome Database

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Gene: Setdb1 (SET domain bifurcated histone lysine methyltransferase 1) Rattus norvegicus
Analyze
Symbol: Setdb1
Name: SET domain bifurcated histone lysine methyltransferase 1
RGD ID: 1308370
Description: Predicted to enable DNA binding activity; histone H3K9 trimethyltransferase activity; and promoter-specific chromatin binding activity. Involved in response to ethanol and response to vitamin. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in autistic disorder and lung cancer. Orthologous to human SETDB1 (SET domain bifurcated histone lysine methyltransferase 1); PARTICIPATES IN histone modification pathway; homocysteine metabolic pathway; methionine cycle/metabolic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: histone-lysine N-methyltransferase SETDB1; histone-lysine N-methyltransferase SETDB1-like; LOC100911180; LOC310668; LOC689883; SET domain, bifurcated 1; SET domain, bifurcated 1 (predicted); Setdb1_predicted; similar to Histone-lysine N-methyltransferase, H3 lysine-9 specific 4 (Histone H3-K9 methyltransferase 4) (H3-K9-HMTase 4) (SET domain bifurcated 1) (ERG-associated protein with SET domain) (ESET)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Setdb1-ps1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82185,587,722 - 185,619,084 (-)NCBIGRCr8
mRatBN7.22182,898,738 - 182,930,283 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2182,898,738 - 182,930,506 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2190,563,824 - 190,594,782 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02188,359,310 - 188,390,238 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02183,196,321 - 183,227,279 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02196,495,867 - 196,527,412 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2196,495,867 - 196,527,127 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02215,994,295 - 216,025,842 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42190,232,228 - 190,264,309 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12190,195,015 - 190,227,043 (-)NCBI
Celera2175,432,236 - 175,463,195 (-)NCBICelera
Cytogenetic Map2q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Gestational choline supplementation normalized fetal alcohol-induced alterations in histone modifications, DNA methylation, and proopiomelanocortin (POMC) gene expression in beta-endorphin-producing POMC neurons of the hypothalamus. Bekdash RA, etal., Alcohol Clin Exp Res. 2013 Jul;37(7):1133-42. doi: 10.1111/acer.12082. Epub 2013 Feb 15.
2. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Black JC, etal., Mol Cell. 2012 Nov 30;48(4):491-507. doi: 10.1016/j.molcel.2012.11.006.
3. Histone methylation at H3K9: evidence for a restrictive epigenome in schizophrenia. Chase KA, etal., Schizophr Res. 2013 Sep;149(1-3):15-20. doi: 10.1016/j.schres.2013.06.021. Epub 2013 Jun 28.
4. The expanding role of MBD genes in autism: identification of a MECP2 duplication and novel alterations in MBD5, MBD6, and SETDB1. Cukier HN, etal., Autism Res. 2012 Dec;5(6):385-97. doi: 10.1002/aur.1251. Epub 2012 Oct 10.
5. 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.
6. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
7. Setdb1-mediated histone H3K9 hypermethylation in neurons worsens the neurological phenotype of Mecp2-deficient mice. Jiang Y, etal., Neuropharmacology. 2011 Jun;60(7-8):1088-97. doi: 10.1016/j.neuropharm.2010.09.020. Epub 2010 Sep 30.
8. High-frequency p16(INK) (4A) promoter methylation is associated with histone methyltransferase SETDB1 expression in sporadic cutaneous melanoma. Kostaki M, etal., Exp Dermatol. 2014 May;23(5):332-8. doi: 10.1111/exd.12398.
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
11. GOA pipeline RGD automated data pipeline
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Comprehensive gene review and curation RGD comprehensive gene curation
14. Gene amplification of the histone methyltransferase SETDB1 contributes to human lung tumorigenesis. Rodriguez-Paredes M, etal., Oncogene. 2014 May 22;33(21):2807-13. doi: 10.1038/onc.2013.239. Epub 2013 Jun 17.
15. ESET/SETDB1 gene expression and histone H3 (K9) trimethylation in Huntington's disease. Ryu H, etal., Proc Natl Acad Sci U S A. 2006 Dec 12;103(50):19176-81. Epub 2006 Dec 1.
16. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Schultz DC, etal., Genes Dev 2002 Apr 15;16(8):919-32.
17. Role of histone lysine methyltransferases SUV39H1 and SETDB1 in gliomagenesis: modulation of cell proliferation, migration, and colony formation. Spyropoulou A, etal., Neuromolecular Med. 2014 Mar;16(1):70-82. doi: 10.1007/s12017-013-8254-x. Epub 2013 Aug 13.
18. Histone methyltransferase SETDB1 is required for prostate cancer cell proliferation, migration and invasion. Sun Y, etal., Asian J Androl. 2014 Mar-Apr;16(2):319-24. doi: 10.4103/1008-682X.122812.
Additional References at PubMed
PMID:11791185   PMID:14536086   PMID:14993285   PMID:20164836   PMID:22079090   PMID:22495301   PMID:22876197   PMID:22939622   PMID:24623306   PMID:27029610   PMID:27732843   PMID:29728365  


Genomics

Comparative Map Data
Setdb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82185,587,722 - 185,619,084 (-)NCBIGRCr8
mRatBN7.22182,898,738 - 182,930,283 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2182,898,738 - 182,930,506 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2190,563,824 - 190,594,782 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02188,359,310 - 188,390,238 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02183,196,321 - 183,227,279 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02196,495,867 - 196,527,412 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2196,495,867 - 196,527,127 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02215,994,295 - 216,025,842 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42190,232,228 - 190,264,309 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12190,195,015 - 190,227,043 (-)NCBI
Celera2175,432,236 - 175,463,195 (-)NCBICelera
Cytogenetic Map2q34NCBI
SETDB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381150,926,263 - 150,964,737 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1150,926,263 - 150,964,744 (+)EnsemblGRCh38hg38GRCh38
GRCh371150,898,739 - 150,937,213 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361149,165,512 - 149,203,837 (+)NCBINCBI36Build 36hg18NCBI36
Build 341147,711,960 - 147,750,284NCBI
Celera1124,014,522 - 124,052,915 (+)NCBICelera
Cytogenetic Map1q21.3NCBI
HuRef1122,275,918 - 122,314,348 (+)NCBIHuRef
CHM1_11152,294,142 - 152,332,540 (+)NCBICHM1_1
T2T-CHM13v2.01150,049,948 - 150,088,436 (+)NCBIT2T-CHM13v2.0
Setdb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39395,230,836 - 95,264,513 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl395,230,836 - 95,264,513 (-)EnsemblGRCm39 Ensembl
GRCm38395,323,525 - 95,357,202 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl395,323,525 - 95,357,202 (-)EnsemblGRCm38mm10GRCm38
MGSCv37395,127,447 - 95,161,124 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36395,408,929 - 95,442,577 (-)NCBIMGSCv36mm8
Celera396,754,826 - 96,788,575 (-)NCBICelera
Cytogenetic Map3F2.1NCBI
cM Map340.74NCBI
Setdb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955588290,168 - 338,426 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955588290,497 - 338,438 (+)NCBIChiLan1.0ChiLan1.0
SETDB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2198,868,713 - 98,907,047 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1198,622,938 - 98,661,286 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01126,275,719 - 126,314,043 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11129,925,009 - 129,962,442 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1129,925,009 - 129,962,442 (+)Ensemblpanpan1.1panPan2
SETDB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11760,035,819 - 60,069,721 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1760,037,379 - 60,069,551 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1759,481,019 - 59,513,690 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01761,052,838 - 61,085,686 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1761,052,909 - 61,085,961 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11759,881,637 - 59,914,607 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01759,966,210 - 59,999,560 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01760,694,148 - 60,726,997 (+)NCBIUU_Cfam_GSD_1.0
Setdb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505822,115,903 - 22,162,583 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365801,146,277 - 1,192,842 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365801,146,286 - 1,192,842 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SETDB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl498,260,375 - 98,293,097 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1498,259,801 - 98,293,238 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24107,514,914 - 107,547,700 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SETDB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366603812,316,851 - 12,357,421 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Setdb1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477218,855,332 - 18,894,226 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477218,855,405 - 18,894,285 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Setdb1
79 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:37
Count of miRNA genes:35
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000028709
Prediction methods:Miranda, Rnahybrid
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2136445150202447032Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)218960362228801039Rat
152025245Scl81Serum cholesterol level QTL 813.49blood cholesterol amount (VT:0000180)2122609194206936711Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
12879836Kidm61Kidney mass QTL 610.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2152413072185122374Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2143657411190602963Rat
12879837Am2Aortic mass QTL 20.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2152413072185122374Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2157142209202446871Rat
12879838Cm86Cardiac mass QTL 860.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2152413072185122374Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
12879839Cm85Cardiac mass QTL 850.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2152413072185122374Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2135552573202446871Rat
1549833Bp257Blood pressure QTL 2570.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168354880185122374Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2157142078211086598Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527185876470Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
12879840Bw179Body weight QTL 1790.005body mass (VT:0001259)body weight (CMO:0000012)2152413072185122374Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2136916935189599348Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2182171407227171407Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2182171407227171407Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2157142078192625452Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150540301202447032Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2182171407227171407Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2179335906224335906Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2157142078226277316Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150341684202446871Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2168594495213594495Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2141596551202447032Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2150341585189039377Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2143157029210020885Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2133914684202447032Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2144599348189599348Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2150540301202447032Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147798556192798556Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2179946951224946951Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
631522Bp74Blood pressure QTL 740.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2172710921184114403Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2182171407227171407Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2162765032207765032Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166539266211539266Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2160564068205564068Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2164073756227146641Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
6903312Bw112Body weight QTL 1123.20.0013body mass (VT:0001259)body weight (CMO:0000012)2143657569184114274Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
2293084Iddm26Insulin dependent diabetes mellitus QTL 262.9blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2174930955213594495Rat

Markers in Region
AW535103  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22182,899,017 - 182,899,215 (+)MAPPERmRatBN7.2
Rnor_6.02196,496,147 - 196,496,344NCBIRnor6.0
Rnor_5.02215,994,575 - 215,994,772UniSTSRnor5.0
RGSC_v3.42190,232,508 - 190,232,705UniSTSRGSC3.4
Celera2175,432,516 - 175,432,713UniSTS
RH 3.4 Map21195.21UniSTS
Cytogenetic Map2q34UniSTS
UniSTS:234764  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22182,898,559 - 182,898,730 (+)MAPPERmRatBN7.2
Rnor_6.02196,495,689 - 196,495,859NCBIRnor6.0
Rnor_5.02215,994,117 - 215,994,287UniSTSRnor5.0
RGSC_v3.42190,232,050 - 190,232,220UniSTSRGSC3.4
Celera2175,432,058 - 175,432,228UniSTS
Cytogenetic Map2q34UniSTS
PMC355869P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22182,903,581 - 182,903,830 (+)MAPPERmRatBN7.2
Rnor_6.02196,500,711 - 196,500,959NCBIRnor6.0
Rnor_5.02215,999,139 - 215,999,387UniSTSRnor5.0
RGSC_v3.42190,237,072 - 190,237,320UniSTSRGSC3.4
Celera2175,437,080 - 175,437,328UniSTS
Cytogenetic Map2q34UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000028709   ⟹   ENSRNOP00000028709
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2182,898,738 - 182,929,527 (-)Ensembl
Rnor_6.0 Ensembl2196,495,867 - 196,527,127 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000077325   ⟹   ENSRNOP00000073356
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2182,898,738 - 182,930,506 (-)Ensembl
Rnor_6.0 Ensembl2196,496,189 - 196,526,886 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000111803   ⟹   ENSRNOP00000097818
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2182,898,738 - 182,930,080 (-)Ensembl
RefSeq Acc Id: NM_001271175   ⟹   NP_001258104
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82185,587,722 - 185,618,982 (-)NCBI
mRatBN7.22182,898,738 - 182,929,999 (-)NCBI
Rnor_6.02196,495,867 - 196,527,127 (-)NCBI
Rnor_5.02215,994,295 - 216,025,842 (-)NCBI
Celera2175,432,236 - 175,463,195 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006232913   ⟹   XP_006232975
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82185,587,722 - 185,619,084 (-)NCBI
mRatBN7.22182,898,738 - 182,930,283 (-)NCBI
Rnor_6.02196,495,876 - 196,527,412 (-)NCBI
Rnor_5.02215,994,295 - 216,025,842 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006232914   ⟹   XP_006232976
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82185,587,722 - 185,618,798 (-)NCBI
mRatBN7.22182,898,738 - 182,929,815 (-)NCBI
Rnor_6.02196,495,876 - 196,527,022 (-)NCBI
Rnor_5.02215,994,295 - 216,025,842 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006232917   ⟹   XP_006232979
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82185,587,722 - 185,608,165 (-)NCBI
mRatBN7.22182,898,738 - 182,919,184 (-)NCBI
Rnor_6.02196,495,876 - 196,516,299 (-)NCBI
Rnor_5.02215,994,295 - 216,025,842 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039103159   ⟹   XP_038959087
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82185,587,722 - 185,617,915 (-)NCBI
mRatBN7.22182,898,738 - 182,928,930 (-)NCBI
RefSeq Acc Id: XM_039103160   ⟹   XP_038959088
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82185,587,722 - 185,606,622 (-)NCBI
mRatBN7.22182,898,738 - 182,917,877 (-)NCBI
RefSeq Acc Id: NP_001258104   ⟸   NM_001271175
- UniProtKB: A0A8I6ASK2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006232975   ⟸   XM_006232913
- Peptide Label: isoform X1
- UniProtKB: A0A8I6ASK2 (UniProtKB/TrEMBL),   D4A081 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006232976   ⟸   XM_006232914
- Peptide Label: isoform X2
- UniProtKB: A0A8I6ASK2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006232979   ⟸   XM_006232917
- Peptide Label: isoform X4
- UniProtKB: A6K2Y7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000073356   ⟸   ENSRNOT00000077325
Ensembl Acc Id: ENSRNOP00000028709   ⟸   ENSRNOT00000028709
RefSeq Acc Id: XP_038959087   ⟸   XM_039103159
- Peptide Label: isoform X3
- UniProtKB: A6K2Y7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038959088   ⟸   XM_039103160
- Peptide Label: isoform X5
- UniProtKB: A6K2Y7 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000097818   ⟸   ENSRNOT00000111803
Protein Domains
MBD   Post-SET   Pre-SET   SET

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K5A7-F1-model_v2 AlphaFold A0A0G2K5A7 1-1322 view protein structure

Transcriptome

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

Promoters
RGD ID:13691547
Promoter ID:EPDNEW_R2072
Type:initiation region
Name:Setdb1_1
Description:SET domain, bifurcated 1
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_6.02196,527,211 - 196,527,271EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308370 AgrOrtholog
BioCyc Gene G2FUF-52097 BioCyc
Ensembl Genes ENSRNOG00000021143 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000028709.8 UniProtKB/TrEMBL
  ENSRNOT00000077325.2 UniProtKB/TrEMBL
  ENSRNOT00000111803.1 UniProtKB/TrEMBL
Gene3D-CATH 2.170.270.10 UniProtKB/TrEMBL
  2.30.30.140 UniProtKB/TrEMBL
InterPro DNA-bd_integrase-typ UniProtKB/TrEMBL
  DUF5604 UniProtKB/TrEMBL
  Hist-Lys_N-MeTrfase_SETDB1 UniProtKB/TrEMBL
  Methyl_CpG_DNA-bd UniProtKB/TrEMBL
  Post-SET_dom UniProtKB/TrEMBL
  Pre-SET_dom UniProtKB/TrEMBL
  SET_dom UniProtKB/TrEMBL
  SET_dom_sf UniProtKB/TrEMBL
  SETDB1/2-like_MBD UniProtKB/TrEMBL
  SETDB_methyltransferase UniProtKB/TrEMBL
  Tudor UniProtKB/TrEMBL
  Tudor_4 UniProtKB/TrEMBL
  TUDOR_5 UniProtKB/TrEMBL
NCBI Gene Setdb1 ENTREZGENE
PANTHER HISTONE-LYSINE N-METHYLTRANSFERASE EGGLESS UniProtKB/TrEMBL
  HISTONE-LYSINE N-METHYLTRANSFERASE SETDB1 UniProtKB/TrEMBL
Pfam DUF5604 UniProtKB/TrEMBL
  MBD UniProtKB/TrEMBL
  Pre-SET UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
  Tudor_4 UniProtKB/TrEMBL
  TUDOR_5 UniProtKB/TrEMBL
PhenoGen Setdb1 PhenoGen
PROSITE MBD UniProtKB/TrEMBL
  POST_SET UniProtKB/TrEMBL
  PRE_SET UniProtKB/TrEMBL
  SAM_MT43_SUVAR39_1 UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
RatGTEx ENSRNOG00000021143 RatGTEx
SMART MBD UniProtKB/TrEMBL
  PreSET UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
  TUDOR UniProtKB/TrEMBL
Superfamily-SCOP DNA-binding_integrase-type UniProtKB/TrEMBL
  SSF82199 UniProtKB/TrEMBL
UniProt A0A0G2K5A7_RAT UniProtKB/TrEMBL
  A0A8I6ASK2 ENTREZGENE, UniProtKB/TrEMBL
  A6K2Y7 ENTREZGENE, UniProtKB/TrEMBL
  D4A081 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Setdb1  SET domain bifurcated histone lysine methyltransferase 1  LOC100911180  histone-lysine N-methyltransferase SETDB1-like  Data merged from RGD:6494849 737654 PROVISIONAL
2019-04-02 Setdb1  SET domain bifurcated histone lysine methyltransferase 1  Setdb1  SET domain, bifurcated 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100911180  histone-lysine N-methyltransferase SETDB1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-05-20 Setdb1  SET domain, bifurcated 1  Setdb1_predicted  SET domain, bifurcated 1 (predicted)  Symbol and Name updated 1299863 APPROVED
2008-05-20 Setdb1_predicted  SET domain, bifurcated 1 (predicted)  Setdb1  SET domain, bifurcated 1  Data merged from RGD:1587497 737654 APPROVED
2008-03-06 Setdb1  SET domain, bifurcated 1  LOC689883  similar to Histone-lysine N-methyltransferase, H3 lysine-9 specific 4 (Histone H3-K9 methyltransferase 4) (H3-K9-HMTase 4) (SET domain bifurcated 1) (ERG-associated protein with SET domain) (ESET)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC689883  similar to Histone-lysine N-methyltransferase, H3 lysine-9 specific 4 (Histone H3-K9 methyltransferase 4) (H3-K9-HMTase 4) (SET domain bifurcated 1) (ERG-associated protein with SET domain) (ESET)  LOC682228  similar to Histone-lysine N-methyltransferase, H3 lysine-9 specific 4 (Histone H3-K9 methyltransferase 4) (H3-K9-HMTase 4) (SET domain bifurcated 1) (ERG-associated protein with SET domain) (ESET)  Data merged from RGD:1585761 1643240 APPROVED
2006-11-19 LOC689883  similar to Histone-lysine N-methyltransferase, H3 lysine-9 specific 4 (Histone H3-K9 methyltransferase 4) (H3-K9-HMTase 4) (SET domain bifurcated 1) (ERG-associated protein with SET domain) (ESET)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC682228  similar to Histone-lysine N-methyltransferase, H3 lysine-9 specific 4 (Histone H3-K9 methyltransferase 4) (H3-K9-HMTase 4) (SET domain bifurcated 1) (ERG-associated protein with SET domain) (ESET)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-12 Setdb1_predicted  SET domain, bifurcated 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED