Jade1 (jade family PHD finger 1) - Rat Genome Database

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Gene: Jade1 (jade family PHD finger 1) Rattus norvegicus
Analyze
Symbol: Jade1
Name: jade family PHD finger 1
RGD ID: 1306920
Description: Predicted to enable transcription coactivator activity. Predicted to be involved in several processes, including histone acetylation; negative regulation of canonical Wnt signaling pathway; and regulation of nucleobase-containing compound metabolic process. Predicted to act upstream of or within negative regulation of G1/S transition of mitotic cell cycle. Predicted to be located in several cellular components, including ciliary basal body; cytosol; and nuclear speck. Predicted to be part of histone acetyltransferase complex. Orthologous to human JADE1 (jade family PHD finger 1); INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC310352; PHD finger protein 17; Phf17; protein Jade-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22124,543,259 - 124,596,361 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2124,543,286 - 124,596,354 (+)Ensembl
Rnor_6.02128,461,147 - 128,514,298 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2128,461,224 - 128,514,291 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02148,061,324 - 148,114,469 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42128,499,983 - 128,553,050 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12128,444,210 - 128,502,196 (+)NCBI
Celera2119,445,989 - 119,498,978 (+)NCBICelera
Cytogenetic Map2q25NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-methoxyethanol  (EXP)
2-methylcholine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (EXP,ISO)
dorsomorphin  (ISO)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
indometacin  (ISO)
methapyrilene  (EXP)
methylmercury chloride  (ISO)
microcystin-LR  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nefazodone  (EXP)
nickel atom  (ISO)
p-chloromercuribenzoic acid  (ISO)
paracetamol  (EXP,ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
succimer  (ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
theophylline  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
triptonide  (ISO)
troglitazone  (ISO)
valproic acid  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12169691   PMID:16387653   PMID:22654112   PMID:23001567   PMID:24739512   PMID:30361391  


Genomics

Comparative Map Data
Jade1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22124,543,259 - 124,596,361 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2124,543,286 - 124,596,354 (+)Ensembl
Rnor_6.02128,461,147 - 128,514,298 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2128,461,224 - 128,514,291 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02148,061,324 - 148,114,469 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42128,499,983 - 128,553,050 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12128,444,210 - 128,502,196 (+)NCBI
Celera2119,445,989 - 119,498,978 (+)NCBICelera
Cytogenetic Map2q25NCBI
JADE1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384128,809,700 - 128,875,224 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl4128,809,700 - 128,875,224 (+)EnsemblGRCh38hg38GRCh38
GRCh374129,730,855 - 129,796,379 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 364129,950,229 - 130,015,829 (+)NCBINCBI36hg18NCBI36
Celera4127,112,780 - 127,178,419 (+)NCBI
Cytogenetic Map4q28.2NCBI
HuRef4125,461,152 - 125,526,511 (+)NCBIHuRef
CHM1_14129,707,281 - 129,772,873 (+)NCBICHM1_1
T2T-CHM13v2.04132,113,886 - 132,179,423 (+)NCBI
Jade1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39341,510,169 - 41,571,299 (+)NCBIGRCm39mm39
GRCm39 Ensembl341,510,166 - 41,571,299 (+)Ensembl
GRCm38341,555,734 - 41,616,864 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl341,555,731 - 41,616,864 (+)EnsemblGRCm38mm10GRCm38
MGSCv37341,359,656 - 41,420,786 (+)NCBIGRCm37mm9NCBIm37
MGSCv36341,677,744 - 41,713,406 (+)NCBImm8
Celera341,278,427 - 41,339,323 (+)NCBICelera
Cytogenetic Map3BNCBI
Jade1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542812,765,550 - 12,835,507 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542812,762,629 - 12,835,310 (-)NCBIChiLan1.0ChiLan1.0
JADE1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14132,271,559 - 132,336,620 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4132,272,642 - 132,336,620 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v04120,969,668 - 121,035,282 (+)NCBIMhudiblu_PPA_v0panPan3
JADE1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11912,187,345 - 12,250,343 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1912,189,281 - 12,250,349 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1912,375,413 - 12,438,357 (-)NCBI
ROS_Cfam_1.01912,274,017 - 12,337,297 (-)NCBI
ROS_Cfam_1.0 Ensembl1912,275,915 - 12,337,306 (-)Ensembl
UMICH_Zoey_3.11912,246,286 - 12,309,249 (-)NCBI
UNSW_CanFamBas_1.01912,535,170 - 12,598,287 (-)NCBI
UU_Cfam_GSD_1.01912,995,766 - 13,058,843 (-)NCBI
Jade1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530160,861,830 - 60,914,355 (-)NCBI
SpeTri2.0NW_0049366422,154,662 - 2,207,186 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JADE1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl896,118,610 - 96,692,407 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1896,208,217 - 96,564,132 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28102,990,692 - 103,053,784 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JADE1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1775,926,199 - 75,993,381 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl775,926,616 - 75,995,327 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603755,088,979 - 55,156,044 (+)NCBIVero_WHO_p1.0
Jade1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247779,666,762 - 9,723,381 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046247779,664,111 - 9,726,266 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
BI294258  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22124,553,416 - 124,553,666 (+)MAPPERmRatBN7.2
Rnor_6.02128,471,354 - 128,471,603NCBIRnor6.0
Rnor_5.02148,071,525 - 148,071,774UniSTSRnor5.0
RGSC_v3.42128,510,113 - 128,510,362UniSTSRGSC3.4
Celera2119,456,119 - 119,456,368UniSTS
RH 3.4 Map2661.0UniSTS
Cytogenetic Map2q26UniSTS
AW534015  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22124,594,225 - 124,594,440 (+)MAPPERmRatBN7.2
Rnor_6.02128,512,163 - 128,512,377NCBIRnor6.0
Rnor_5.02148,112,334 - 148,112,548UniSTSRnor5.0
RGSC_v3.42128,550,922 - 128,551,136UniSTSRGSC3.4
Celera2119,496,850 - 119,497,064UniSTS
RH 3.4 Map2661.0UniSTS
Cytogenetic Map2q26UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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
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
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
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243162366148478373Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1558648Smcn1Smooth muscle cell number QTL 10.039blood vessel smooth muscle cell quantity (VT:0010525)aorta smooth muscle cell count per unit vessel length (CMO:0001646)259134147127460910Rat
61438Cia7Collagen induced arthritis QTL 74.60.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)259324377141596857Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1558653Prcr1Prostate cancer resistance QTL 15prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)272532993157142209Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)276539322150540526Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
2299162Iddm32Insulin dependent diabetes mellitus QTL 322.36blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)278665616143657569Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
61392Bp6Blood pressure QTL 67arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)280270434125270434Rat
1598865Bp296Blood pressure QTL 2962.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)281018907126018907Rat
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
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
1578772Stresp14Stress response QTL 1450.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)282345893130923501Rat
7207808Bmd89Bone mineral density QTL 894.1femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)288862519133862519Rat
2300165Bmd49Bone mineral density QTL 494.80.0001lumbar vertebra mineral mass (VT:0010511)bone mineral density (CMO:0001226)288862519133862519Rat
2300170Bmd45Bone mineral density QTL 4512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)288862519133862519Rat
2300185Bmd46Bone mineral density QTL 468.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)288862519133862519Rat
1598862Glom9Glomerulus QTL 93.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)292337601137337601Rat
1598863Cm65Cardiac mass QTL 652.3heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)292337601137337601Rat
631566Bp90Blood pressure QTL 900.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2102803808147803808Rat
8662836Vetf8Vascular elastic tissue fragility QTL 80.66thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2104559726149559726Rat
1581552Pur12Proteinuria QTL 125.190.0009total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)2112103657148076632Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1354594Despr10Despair related QTL 100.00000249locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)2114654253159654253Rat
1359035Bp276Blood pressure QTL 276arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527143657569Rat
1359035Bp276Blood pressure QTL 276arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527143657569Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527185876470Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527185876470Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
5135226Leukc2Leukocyte quantity QTL 2eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)2118111229149559726Rat
1582257Gluco21Glucose level QTL 213.10.0035blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2118111229157142209Rat
738007Anxrr7Anxiety related response QTL 74.4exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2118189491163189491Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:767
Count of miRNA genes:306
Interacting mature miRNAs:412
Transcripts:ENSRNOT00000018872
Prediction methods:Microtar, Miranda, 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 26 41 25 18 25 8 9 74 35 37 11 8
Low 3 17 16 16 1 16 2 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018872   ⟹   ENSRNOP00000018872
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2124,543,286 - 124,596,354 (+)Ensembl
Rnor_6.0 Ensembl2128,461,224 - 128,514,291 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098865   ⟹   ENSRNOP00000090026
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2124,545,126 - 124,596,354 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000100298   ⟹   ENSRNOP00000088679
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2124,544,726 - 124,586,054 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000120008   ⟹   ENSRNOP00000090751
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2124,570,650 - 124,596,354 (+)Ensembl
RefSeq Acc Id: NM_001107670   ⟹   NP_001101140
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22124,543,286 - 124,596,354 (+)NCBI
Rnor_6.02128,461,224 - 128,514,291 (+)NCBI
Rnor_5.02148,061,324 - 148,114,469 (+)NCBI
RGSC_v3.42128,499,983 - 128,553,050 (+)RGD
Celera2119,445,989 - 119,498,978 (+)RGD
Sequence:
RefSeq Acc Id: XM_006232301   ⟹   XP_006232363
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22124,544,885 - 124,596,361 (+)NCBI
Rnor_6.02128,462,785 - 128,514,298 (+)NCBI
Rnor_5.02148,061,324 - 148,114,469 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006232302   ⟹   XP_006232364
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22124,543,259 - 124,596,361 (+)NCBI
Rnor_6.02128,461,147 - 128,514,298 (+)NCBI
Rnor_5.02148,061,324 - 148,114,469 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006232303   ⟹   XP_006232365
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22124,543,603 - 124,596,361 (+)NCBI
Rnor_6.02128,461,371 - 128,514,298 (+)NCBI
Rnor_5.02148,061,324 - 148,114,469 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006232304   ⟹   XP_006232366
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22124,544,685 - 124,596,361 (+)NCBI
Rnor_6.02128,462,672 - 128,514,298 (+)NCBI
Rnor_5.02148,061,324 - 148,114,469 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760928   ⟹   XP_008759150
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22124,544,706 - 124,596,361 (+)NCBI
Rnor_6.02128,462,661 - 128,514,298 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039102248   ⟹   XP_038958176
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22124,574,983 - 124,596,361 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101140   ⟸   NM_001107670
- UniProtKB: D3ZM64 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006232364   ⟸   XM_006232302
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006232365   ⟸   XM_006232303
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006232366   ⟸   XM_006232304
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006232363   ⟸   XM_006232301
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008759150   ⟸   XM_008760928
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000018872   ⟸   ENSRNOT00000018872
RefSeq Acc Id: XP_038958176   ⟸   XM_039102248
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000090026   ⟸   ENSRNOT00000098865
RefSeq Acc Id: ENSRNOP00000090751   ⟸   ENSRNOT00000120008
RefSeq Acc Id: ENSRNOP00000088679   ⟸   ENSRNOT00000100298
Protein Domains
PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZM64-F1-model_v2 AlphaFold D3ZM64 1-828 view protein structure

Transcriptome

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

Promoters
RGD ID:13691309
Promoter ID:EPDNEW_R1834
Type:initiation region
Name:Jade1_1
Description:jade family PHD finger 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_6.02128,461,171 - 128,461,231EPDNEW

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)
Visual CSV TAB Printer
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)
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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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
LE/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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (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
LEXF10A/StmMcwi (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
LEXF11/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
LEXF1A/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
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)
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
LEXF4/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
LH/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
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)
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
M520/NRrrcMcwi (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
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)
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
PVG/Seac (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
SHR/OlalpcvMcwi (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
SHRSP/A3NCrl (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
SR/JrHsd (2020)
Visual CSV TAB Printer
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)
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
WAG/RijCrl (2020)
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
WKY/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
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
2 128501734 128501735 T A snv BN/SsN (MCW)
2 128510934 128510935 C A snv MR/N (MCW), MR/N (2020)


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 148111105 148111106 C A snv MR/N (KNAW)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 128540493 128540494 T A snv BN/SsN (KNAW)
2 128549693 128549694 C A snv HCR/2Mco (UMich), LCR/1Mco (UMich), MR/N (KNAW), HCR/1Mco (UMich)


Assembly: mRatBN7.2
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 124592997 124592998 C A snv MR/N (2020)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306920 AgrOrtholog
BioCyc Gene G2FUF-53233 BioCyc
Ensembl Genes ENSRNOG00000014066 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018872 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000090026 ENTREZGENE
  ENSRNOP00000090751 ENTREZGENE
Ensembl Transcript ENSRNOT00000018872 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000098865 ENTREZGENE
  ENSRNOT00000120008 ENTREZGENE
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
InterPro Enhancer_of_polycomb-like UniProtKB/TrEMBL
  EPHD UniProtKB/TrEMBL
  Jade-1_PHD UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:310352 UniProtKB/TrEMBL
NCBI Gene 310352 ENTREZGENE
Pfam EPL1 UniProtKB/TrEMBL
PhenoGen Jade1 PhenoGen
PROSITE EPHD UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
SMART PHD UniProtKB/TrEMBL
Superfamily-SCOP FYVE_PHD_ZnF UniProtKB/TrEMBL
UniProt D3ZM64 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-22 Jade1  jade family PHD finger 1  Phf17  PHD finger protein 17  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Phf17  PHD finger protein 17   Phf17_predicted  PHD finger protein 17 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Phf17_predicted  PHD finger protein 17 (predicted)      Symbol and Name status set to approved 70820 APPROVED