Setd9-ps1 (SET domain containing, pseudogene 1) - Rat Genome Database

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Gene: Setd9-ps1 (SET domain containing, pseudogene 1) Rattus norvegicus
Analyze
Symbol: Setd9-ps1
Name: SET domain containing, pseudogene 1
RGD ID: 2318781
Description: Orthologous to human SETD9 (SET domain containing 9); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine (ortholog); acrylamide (ortholog); aflatoxin B1 (ortholog).
Type: pseudo
RefSeq Status: INFERRED
Previously known as: hypothetical LOC100362101; LOC100362101
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8245,052,682 - 45,056,085 (-)NCBIGRCr8
mRatBN7.2243,319,359 - 43,322,764 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx250,435,585 - 50,438,985 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0248,494,040 - 48,497,440 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0243,345,554 - 43,348,955 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0243,298,112 - 43,301,515 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0262,344,100 - 62,349,860 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4243,030,755 - 43,038,315 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera239,104,960 - 39,108,363 (-)NCBICelera
Cytogenetic Map2q14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Setd9-ps1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8245,052,682 - 45,056,085 (-)NCBIGRCr8
mRatBN7.2243,319,359 - 43,322,764 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx250,435,585 - 50,438,985 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0248,494,040 - 48,497,440 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0243,345,554 - 43,348,955 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0243,298,112 - 43,301,515 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0262,344,100 - 62,349,860 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4243,030,755 - 43,038,315 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera239,104,960 - 39,108,363 (-)NCBICelera
Cytogenetic Map2q14NCBI
SETD9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38556,909,260 - 56,928,900 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl556,909,260 - 56,925,532 (+)EnsemblGRCh38hg38GRCh38
GRCh37556,205,087 - 56,224,727 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36556,240,857 - 56,248,767 (+)NCBINCBI36Build 36hg18NCBI36
Celera553,159,295 - 53,175,568 (+)NCBICelera
Cytogenetic Map5q11.2NCBI
HuRef553,177,007 - 53,193,280 (+)NCBIHuRef
CHM1_1556,208,094 - 56,224,366 (+)NCBICHM1_1
T2T-CHM13v2.0557,737,511 - 57,757,157 (+)NCBIT2T-CHM13v2.0
Setd9-ps
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3913111,858,051 - 111,860,850 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl13111,858,013 - 111,860,868 (-)EnsemblGRCm39 Ensembl
GRCm3813111,721,517 - 111,724,316 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl13111,721,479 - 111,724,334 (-)EnsemblGRCm38mm10GRCm38
Cytogenetic Map13D2.2NCBI
cM Map1363.36NCBI
Setd9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544610,994,352 - 11,004,924 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544610,994,388 - 11,004,034 (-)NCBIChiLan1.0ChiLan1.0
SETD9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2457,003,568 - 57,015,000 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1555,157,199 - 55,168,680 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0557,093,340 - 57,103,500 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1558,712,170 - 58,732,480 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl558,724,521 - 58,732,478 (-)Ensemblpanpan1.1panPan2
SETD9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1244,046,549 - 44,073,781 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl244,046,605 - 44,073,536 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha241,107,851 - 41,135,469 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0244,528,554 - 44,556,172 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl244,528,574 - 44,535,729 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1241,605,367 - 41,632,981 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0242,408,810 - 42,436,429 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0243,228,779 - 43,256,229 (+)NCBIUU_Cfam_GSD_1.0
Setd9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213202,095,855 - 202,105,854 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648011,033,996 - 11,041,827 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648011,034,128 - 11,042,782 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SETD9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1635,980,201 - 35,996,722 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11635,978,960 - 35,987,161 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21638,245,927 - 38,253,081 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SETD9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1453,133,733 - 53,141,985 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl453,134,117 - 53,141,965 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660492,025,575 - 2,033,891 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Setd9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247592,326,321 - 2,337,753 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247592,326,938 - 2,337,784 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Setd9-ps1
14 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1643006Pain1Pain QTL 13.630.005mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)22699957148268661Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22715716072157160Rat
1300160Hrtrt3Heart rate QTL 33.62heart pumping trait (VT:2000009)absolute change in heart rate (CMO:0000534)22997159351729300Rat
10755434Coatc7Coat color QTL 70.04794coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23064806575648065Rat
731179Mamtr3Mammary tumor resistance QTL 30.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)23237377043665178Rat
10755436Coatc8Coat color QTL 80.02431coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23502311780023117Rat
61371Edpm1Estrogen-dependent pituitary mass QTL 140.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)23513484188029593Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)240067944102785628Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)240067944102785628Rat
12879863Bp402Blood pressure QTL 4020.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)24112578956532139Rat
1300155Bp174Blood pressure QTL 1744.09arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)24280460760653831Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607157142209Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
2293676Bmd19Bone mineral density QTL 1910.70.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)243162366111362592Rat
2293682Bmd24Bone mineral density QTL 248.90.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)243162366111362592Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243162366148478373Rat
631208Bw1Body weight QTL15.09mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)24317101783575226Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat

Markers in Region
MARC_9941-9942:996688685:2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2243,321,046 - 43,321,420 (+)MAPPERmRatBN7.2
Rnor_6.0243,299,799 - 43,300,171NCBIRnor6.0
Rnor_5.0262,346,187 - 62,346,559UniSTSRnor5.0
RGSC_v3.4243,032,535 - 43,032,907UniSTSRGSC3.4
Celera239,106,647 - 39,107,019UniSTS


Expression


Sequence



Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2318781 AgrOrtholog
BioCyc Gene G2FUF-54418 BioCyc
NCBI Gene 100362101 ENTREZGENE
PhenoGen Setd9-ps1 PhenoGen


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-11-09 Setd9-ps1  SET domain containing, pseudogene 1  LOC100362101  hypothetical LOC100362101  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100362101  hypothetical LOC100362101      Symbol and Name status set to provisional 70820 PROVISIONAL