Abcd3 (ATP binding cassette subfamily D member 3) - Rat Genome Database

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Gene: Abcd3 (ATP binding cassette subfamily D member 3) Rattus norvegicus
Analyze
Symbol: Abcd3
Name: ATP binding cassette subfamily D member 3
RGD ID: 2007
Description: Exhibits ATP binding activity and protein self-association. Involved in response to drug and response to organic cyclic compound. Localizes to mitochondrion and peroxisomal membrane. Human ortholog(s) of this gene implicated in Zellweger syndrome and congenital bile acid synthesis defect 5. Orthologous to human ABCD3 (ATP binding cassette subfamily D member 3); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 70 kDa peroxisomal membrane protein; 70-kDa peroxisomal membrane protein; ATP-binding cassette sub-family D member 3; ATP-binding cassette, sub-family D (ALD), member 3; ATP-binding cassette, subfamily D (ALD), member 3; Peroxisomal membrane protein 1; PMP70; PMP70, 70-kDa peroxisomal membrane protein; Pxmp1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22209,852,087 - 209,905,763 (-)NCBI
Rnor_6.0 Ensembl2225,335,718 - 225,389,120 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02225,335,708 - 225,389,120 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02243,374,189 - 243,409,604 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42218,396,071 - 218,432,172 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12218,359,132 - 218,395,230 (-)NCBI
Celera2202,282,471 - 202,317,962 (-)NCBICelera
RH 3.4 Map21501.0RGD
Cytogenetic Map2q41NCBI
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
(+)-alpha-tocopherol  (ISO)
(+)-catechin  (ISO)
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-hydroxypropanoic acid  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
7-ketocholesterol  (ISO)
9-cis-retinoic acid  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin M1  (ISO)
aldrin  (ISO)
all-trans-retinoic acid  (EXP,ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arachidonic acid  (ISO)
Aroclor 1254  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (EXP)
bexarotene  (EXP)
bezafibrate  (ISO)
bisphenol A  (EXP,ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloroethene  (ISO)
clofibrate  (EXP,ISO)
clofibric acid  (ISO)
clothianidin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
dibenz[a,h]anthracene  (EXP)
dibenzo[a,l]pyrene  (EXP)
dichloroacetic acid  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
enilconazole  (ISO)
fenofibrate  (ISO)
finasteride  (EXP)
fluoranthene  (EXP)
folic acid  (ISO)
fomesafen  (ISO)
formaldehyde  (ISO)
furan  (EXP)
glafenine  (EXP)
indole-3-methanol  (EXP)
leflunomide  (ISO)
MeIQx  (ISO)
methamphetamine  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
nickel atom  (ISO)
oleic acid  (ISO)
Oxyfluorfen  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium chromate  (ISO)
pravastatin  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
sarin  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sulindac  (EXP)
tamoxifen  (ISO)
Tesaglitazar  (EXP)
testosterone  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
topotecan  (ISO)
triacsin C  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
troglitazone  (EXP)
valproic acid  (ISO)
vincristine  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
zaragozic acid A  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:9425230   PMID:9765053   PMID:9922452   PMID:10527525   PMID:10704444   PMID:11248239   PMID:11453642   PMID:12865426   PMID:12915479   PMID:14651853   PMID:16344115   PMID:17542813  
PMID:17609205   PMID:18178290   PMID:18614015   PMID:18992293   PMID:19479899   PMID:19686593   PMID:19946888   PMID:20007743   PMID:21460186   PMID:21502359   PMID:21525035   PMID:22871113  
PMID:25168382   PMID:31505169  


Genomics

Comparative Map Data
Abcd3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22209,852,087 - 209,905,763 (-)NCBI
Rnor_6.0 Ensembl2225,335,718 - 225,389,120 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02225,335,708 - 225,389,120 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02243,374,189 - 243,409,604 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42218,396,071 - 218,432,172 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12218,359,132 - 218,395,230 (-)NCBI
Celera2202,282,471 - 202,317,962 (-)NCBICelera
RH 3.4 Map21501.0RGD
Cytogenetic Map2q41NCBI
ABCD3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl194,418,389 - 94,518,666 (+)EnsemblGRCh38hg38GRCh38
GRCh38194,418,086 - 94,518,663 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37194,883,945 - 94,984,219 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,656,599 - 94,756,672 (+)NCBINCBI36hg18NCBI36
Build 34194,596,031 - 94,696,105NCBI
Celera193,137,599 - 93,238,680 (+)NCBI
Cytogenetic Map1p21.3ENTREZGENE
HuRef193,005,619 - 93,105,917 (+)NCBIHuRef
CHM1_1194,998,783 - 95,099,070 (+)NCBICHM1_1
Abcd3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393121,552,553 - 121,609,851 (-)NCBIGRCm39mm39
GRCm39 Ensembl3121,552,423 - 121,608,951 (-)Ensembl
GRCm383121,758,904 - 121,815,302 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3121,758,774 - 121,815,302 (-)EnsemblGRCm38mm10GRCm38
MGSCv373121,461,828 - 121,518,133 (-)NCBIGRCm37mm9NCBIm37
MGSCv363121,750,933 - 121,807,238 (-)NCBImm8
Celera3128,155,294 - 128,218,276 (-)NCBICelera
Cytogenetic Map3G1NCBI
cM Map352.94NCBI
Abcd3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955423280,497 - 359,711 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955423280,497 - 359,711 (-)NCBIChiLan1.0ChiLan1.0
ABCD3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1195,808,027 - 95,907,864 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl195,808,027 - 95,907,864 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0197,079,326 - 97,179,886 (+)NCBIMhudiblu_PPA_v0panPan3
ABCD3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1654,740,704 - 54,816,854 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl654,742,111 - 54,817,235 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha657,449,009 - 57,525,742 (-)NCBI
ROS_Cfam_1.0655,116,365 - 55,193,330 (-)NCBI
UMICH_Zoey_3.1654,797,137 - 54,873,570 (-)NCBI
UNSW_CanFamBas_1.0654,781,385 - 54,858,240 (-)NCBI
UU_Cfam_GSD_1.0655,234,335 - 55,310,979 (-)NCBI
Abcd3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405058104,201,915 - 104,288,290 (+)NCBI
SpeTri2.0NW_0049365374,659,685 - 4,745,992 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABCD3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4122,837,525 - 122,953,257 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14122,847,925 - 122,929,454 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24134,491,144 - 134,572,292 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ABCD3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12038,750,147 - 38,846,011 (-)NCBI
ChlSab1.1 Ensembl2038,748,787 - 38,845,989 (-)Ensembl
Vero_WHO_p1.0NW_02366603379,200,937 - 79,302,556 (+)NCBI
Abcd3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247423,146,000 - 3,236,473 (-)NCBI

Position Markers
D2Arb23  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22209,852,836 - 209,853,134 (+)MAPPER
Rnor_6.02225,336,447 - 225,336,744NCBIRnor6.0
Rnor_5.02243,374,928 - 243,375,225UniSTSRnor5.0
RGSC_v3.42218,396,809 - 218,397,107RGDRGSC3.4
RGSC_v3.42218,396,810 - 218,397,107UniSTSRGSC3.4
RGSC_v3.12218,359,871 - 218,360,169RGD
Celera2202,283,210 - 202,283,507UniSTS
Cytogenetic Map2q41UniSTS
RH128671  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22209,852,127 - 209,852,336 (+)MAPPER
Rnor_6.02225,335,738 - 225,335,946NCBIRnor6.0
Rnor_5.02243,374,219 - 243,374,427UniSTSRnor5.0
RGSC_v3.42218,396,101 - 218,396,309UniSTSRGSC3.4
Celera2202,282,501 - 202,282,709UniSTS
RH 3.4 Map21501.4UniSTS
Cytogenetic Map2q41UniSTS
RH94667  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22209,852,706 - 209,852,860 (+)MAPPER
Rnor_6.02225,336,317 - 225,336,470NCBIRnor6.0
Rnor_5.02243,374,798 - 243,374,951UniSTSRnor5.0
RGSC_v3.42218,396,680 - 218,396,833UniSTSRGSC3.4
Celera2202,283,080 - 202,283,233UniSTS
RH 3.4 Map21501.0UniSTS
Cytogenetic Map2q41UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828236243550655Rat
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)283754907237610852Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283819608239166203Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283819608243901375Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2116075644228737869Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2116075644228737869Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2118446646227707979Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2118446793228582621Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2142053350228984665Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147122993240020001Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2147122993240020001Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2149114878225501939Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557237742948Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557254121739Rat
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)2169852670243026643Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2175403337239166203Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2177680772243901375Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2181522444226522444Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2181990297240020001Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2183984665228984665Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2184730446229730446Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2184730446229730446Rat
2293084Iddm26Insulin dependent diabetes mellitus QTL 262.9blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2188838511228984665Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2194378622239378622Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2194998627239998627Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2197253963242253963Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2197253963242253963Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2197253963242253963Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2197253963242253963Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2199380312244380312Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2200453324236318668Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2200453324236318668Rat
1298083Bp158Blood pressure QTL 1582.62arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2204003742231132207Rat
61458Bp10Blood pressure QTL 103.42arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2204003742231132207Rat
1331745Bp203Blood pressure QTL 2034.377arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2204585642235290110Rat
1581499Esta2Estrogen-induced thymic atrophy QTL 2thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2204585642243689611Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2204585642249585642Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2204585642249585642Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2205583921243562243Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2208594330263179188Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)2214870793251212353Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2217498545254132424Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2217743855262743855Rat
1302789Stl26Serum triglyceride level QTL 263.10.0035blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)2218957047240977220Rat
2299161Iddm33Insulin dependent diabetes mellitus QTL 332.98blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2221488355254121739Rat
631203Gluco14Glucose level QTL 140.0001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)2221880206235570970Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:537
Count of miRNA genes:263
Interacting mature miRNAs:318
Transcripts:ENSRNOT00000016739
Prediction methods:Microtar, 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 43 57 41 19 41 8 11 74 35 38 11 8
Low 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016739   ⟹   ENSRNOP00000016739
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2225,335,718 - 225,389,120 (-)Ensembl
RefSeq Acc Id: NM_012804   ⟹   NP_036936
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22209,852,087 - 209,905,680 (-)NCBI
Rnor_6.02225,335,708 - 225,389,120 (-)NCBI
Rnor_5.02243,374,189 - 243,409,604 (-)NCBI
RGSC_v3.42218,396,071 - 218,432,172 (-)RGD
Celera2202,282,471 - 202,317,962 (-)RGD
Sequence:
RefSeq Acc Id: XM_039101772   ⟹   XP_038957700
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22209,852,087 - 209,905,763 (-)NCBI
RefSeq Acc Id: XM_039101774   ⟹   XP_038957702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22209,852,087 - 209,905,647 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_036936   ⟸   NM_012804
- UniProtKB: P16970 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016739   ⟸   ENSRNOT00000016739
RefSeq Acc Id: XP_038957700   ⟸   XM_039101772
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038957702   ⟸   XM_039101774
- Peptide Label: isoform X2
Transcriptome

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

Promoters
RGD ID:13691720
Promoter ID:EPDNEW_R2245
Type:initiation region
Name:Abcd3_1
Description:ATP binding cassette subfamily D member 3
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_6.02225,389,173 - 225,389,233EPDNEW

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2007 AgrOrtholog
Ensembl Genes ENSRNOG00000011929 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000016739 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000016739 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro AAA+_ATPase UniProtKB/Swiss-Prot
  ABC1_TM_dom UniProtKB/Swiss-Prot
  ABC1_TM_sf UniProtKB/Swiss-Prot
  ABC_transporter-like UniProtKB/Swiss-Prot
  ABC_transporter_CS UniProtKB/Swiss-Prot
  FA_transporter UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot
KEGG Report rno:25270 UniProtKB/Swiss-Prot
NCBI Gene 25270 ENTREZGENE
Pfam ABC_membrane_2 UniProtKB/Swiss-Prot
  ABC_tran UniProtKB/Swiss-Prot
PhenoGen Abcd3 PhenoGen
PROSITE ABC_TM1F UniProtKB/Swiss-Prot
  ABC_TRANSPORTER_1 UniProtKB/Swiss-Prot
  ABC_TRANSPORTER_2 UniProtKB/Swiss-Prot
SMART AAA UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot
  SSF90123 UniProtKB/Swiss-Prot
TIGR TC229511
TIGRFAMs 3a01203 UniProtKB/Swiss-Prot
UniProt ABCD3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-09 Abcd3  ATP binding cassette subfamily D member 3  Abcd3  ATP-binding cassette, subfamily D (ALD), member 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-11-16 Abcd3  ATP-binding cassette, subfamily D (ALD), member 3  Abcd3  ATP-binding cassette, sub-family D (ALD), member 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Abcd3  ATP-binding cassette, sub-family D (ALD), member 3      Symbol and Name status set to approved 70586 APPROVED
2001-04-19 Pxmp1  Peroxisomal membrane protein 1      Symbol withdrawn, duplicate entry of Abcd3(RGD:2007) 61478 WITHDRAWN

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to the peroxisomal membrane 631711
gene_domains contains an ATP-binding domain 631711
gene_function may form an ATP-binding channel 631711
gene_homology has similarity to MalK and Mdr ATP-binding proteins 631711
gene_process may play a role in active transport in peroxisomes 631711
gene_product peroxisomal membrane protein 631711
gene_product member of the P-glycoprotein related ATP binding protein superfamily 631711
gene_protein 70-kDa 631711