Abcd1 (ATP binding cassette subfamily D member 1) - Rat Genome Database

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Gene: Abcd1 (ATP binding cassette subfamily D member 1) Rattus norvegicus
Analyze
Symbol: Abcd1
Name: ATP binding cassette subfamily D member 1
RGD ID: 1562128
Description: Enables ATP binding activity; protein heterodimerization activity; and protein homodimerization activity. Involved in very long-chain fatty acid catabolic process. Located in peroxisomal membrane. Human ortholog(s) of this gene implicated in adrenoleukodystrophy. Orthologous to human ABCD1 (ATP binding cassette subfamily D member 1); PARTICIPATES IN adrenoleukodystrophy pathway; carnitine-acylcarnitine translocase deficiency; fatty acid beta degradation pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ALDP; ATP-binding cassette sub-family D member 1; ATP-binding cassette, sub-family D (ALD), member 1; ATP-binding cassette, subfamily D (ALD), member 1; LOC363516; RGD1562128; similar to mALDP
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Abcd1em2Mcwi   Abcd1em4Mcwi  
Genetic Models: DA-Abcd1em4Mcwi DA-Abcd1em2Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X156,579,669 - 156,601,448 (+)NCBIGRCr8
mRatBN7.2X151,428,334 - 151,450,115 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX151,428,578 - 151,450,115 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX153,569,626 - 153,591,020 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,132,856 - 157,154,250 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X154,804,685 - 154,826,079 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X157,073,860 - 157,095,652 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX157,072,736 - 157,095,274 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,823,436 - 152,844,829 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,614,569 - 159,635,963 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1136,439,697 - 136,461,090 (-)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Topology of ATP-binding domain of adrenoleukodystrophy gene product in peroxisomes. Contreras M, etal., Arch Biochem Biophys. 1996 Oct 15;334(2):369-79.
2. 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.
3. Structure-function analysis of peroxisomal ATP-binding cassette transporters using chimeric dimers. Geillon F, etal., J Biol Chem. 2014 Aug 29;289(35):24511-20. doi: 10.1074/jbc.M114.575506. Epub 2014 Jul 20.
4. Peroxisomal ATP-binding cassette transporters form mainly tetramers. Geillon F, etal., J Biol Chem. 2017 Apr 28;292(17):6965-6977. doi: 10.1074/jbc.M116.772806. Epub 2017 Mar 3.
5. Substrate specificity overlap and interaction between adrenoleukodystrophy protein (ALDP/ABCD1) and adrenoleukodystrophy-related protein (ALDRP/ABCD2). Genin EC, etal., J Biol Chem. 2011 Mar 11;286(10):8075-8084. doi: 10.1074/jbc.M110.211912. Epub 2011 Jan 5.
6. Identification of a two base pair deletion in five unrelated families with adrenoleukodystrophy: a possible hot spot for mutations. Kemp S, etal., Biochem Biophys Res Commun. 1994 Jul 29;202(2):647-53.
7. Molecular organization of peroxisomal enzymes: protein-protein interactions in the membrane and in the matrix. Makkar RS, etal., Arch Biochem Biophys. 2006 Jul 15;451(2):128-40. Epub 2006 May 24.
8. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
9. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
10. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Intraperoxisomal localization of very-long-chain fatty acyl-CoA synthetase: implication in X-adrenoleukodystrophy. Smith BT, etal., Exp Cell Res. 2000 Feb 1;254(2):309-20.
13. ATP binding/hydrolysis by and phosphorylation of peroxisomal ATP-binding cassette proteins PMP70 (ABCD3) and adrenoleukodystrophy protein (ABCD1). Tanaka AR, etal., J Biol Chem. 2002 Oct 18;277(42):40142-7. Epub 2002 Aug 9.
Additional References at PubMed
PMID:9126326   PMID:9256488   PMID:9418970   PMID:9425230   PMID:10196381   PMID:10551832   PMID:10777694   PMID:11248239   PMID:11500517   PMID:11875044   PMID:14533738   PMID:14561759  
PMID:15489218   PMID:15682271   PMID:16213491   PMID:16946495   PMID:17542813   PMID:17609205   PMID:17761426   PMID:18344354   PMID:18614015   PMID:18723473   PMID:18757502   PMID:18854420  
PMID:19946888   PMID:20810565   PMID:21145416   PMID:22521832   PMID:23123468   PMID:23604518   PMID:23671276   PMID:25255441   PMID:25583114   PMID:26108493  


Genomics

Comparative Map Data
Abcd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X156,579,669 - 156,601,448 (+)NCBIGRCr8
mRatBN7.2X151,428,334 - 151,450,115 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX151,428,578 - 151,450,115 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX153,569,626 - 153,591,020 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,132,856 - 157,154,250 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X154,804,685 - 154,826,079 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X157,073,860 - 157,095,652 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX157,072,736 - 157,095,274 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,823,436 - 152,844,829 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,614,569 - 159,635,963 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1136,439,697 - 136,461,090 (-)NCBICelera
Cytogenetic MapXq37NCBI
ABCD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X153,724,856 - 153,744,755 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX153,724,856 - 153,744,755 (+)EnsemblGRCh38hg38GRCh38
GRCh37X152,990,311 - 153,010,209 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X152,643,530 - 152,663,375 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X152,511,182 - 152,531,028NCBI
CeleraX153,224,004 - 153,243,898 (+)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX141,647,579 - 141,667,479 (+)NCBIHuRef
CHM1_1X152,864,732 - 152,884,627 (+)NCBICHM1_1
T2T-CHM13v2.0X151,998,519 - 152,018,419 (+)NCBIT2T-CHM13v2.0
Abcd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X72,760,203 - 72,782,140 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX72,760,203 - 72,782,140 (+)EnsemblGRCm39 Ensembl
GRCm38X73,716,597 - 73,738,534 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX73,716,597 - 73,738,534 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X70,961,936 - 70,983,626 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X69,969,317 - 69,991,007 (+)NCBIMGSCv36mm8
CeleraX64,970,295 - 64,991,971 (+)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX37.39NCBI
Abcd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955580459,715 - 475,774 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955580459,715 - 475,363 (+)NCBIChiLan1.0ChiLan1.0
ABCD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X153,764,997 - 153,785,252 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X153,768,686 - 153,788,864 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X143,275,165 - 143,295,283 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X153,162,412 - 153,182,424 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX153,162,412 - 153,182,424 (+)Ensemblpanpan1.1panPan2
ABCD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X121,545,690 - 121,564,117 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX121,545,586 - 121,563,186 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX106,875,063 - 106,895,708 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X124,687,215 - 124,707,872 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX124,687,201 - 124,705,644 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X120,456,646 - 120,477,290 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X122,971,670 - 122,992,305 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X122,733,767 - 122,754,413 (+)NCBIUU_Cfam_GSD_1.0
Abcd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X118,877,295 - 118,896,851 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936809615,139 - 635,990 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936809615,133 - 634,618 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABCD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX124,485,076 - 124,501,741 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X124,485,076 - 124,501,742 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X142,049,646 - 142,066,321 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ABCD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X128,152,697 - 128,171,007 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606566,018,682 - 66,038,332 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Abcd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624946421,132 - 440,075 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624946421,113 - 439,961 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Abcd1
15 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:381
Count of miRNA genes:192
Interacting mature miRNAs:226
Transcripts:ENSRNOT00000025863
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat

Markers in Region
GDB:376683  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,442,695 - 151,442,776 (-)MAPPERmRatBN7.2
Rnor_6.0X157,081,197 - 157,081,277NCBIRnor6.0
Rnor_5.01152,830,516 - 152,830,596UniSTSRnor5.0
RGSC_v3.4X159,628,803 - 159,628,883UniSTSRGSC3.4
Celera1136,446,781 - 136,446,861UniSTS
Cytogenetic MapXq37UniSTS
UniSTS:238038  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,449,689 - 151,449,871 (-)MAPPERmRatBN7.2
Rnor_6.0X157,074,104 - 157,074,285NCBIRnor6.0
Rnor_5.01152,823,423 - 152,823,604UniSTSRnor5.0
RGSC_v3.4X159,635,795 - 159,635,976UniSTSRGSC3.4
Celera1136,439,684 - 136,439,865UniSTS
Cytogenetic MapXq37UniSTS


Genetic Models
This gene Abcd1 is modified in the following models/strains:


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 2 9 23 15 11 15 1 4 20 29 11
Low 1 34 34 26 8 26 8 10 70 15 12 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000084088   ⟹   ENSRNOP00000070359
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,428,578 - 151,450,115 (+)Ensembl
Rnor_6.0 EnsemblX157,072,736 - 157,095,274 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107613   ⟹   ENSRNOP00000083864
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,428,578 - 151,450,115 (+)Ensembl
RefSeq Acc Id: NM_001108821   ⟹   NP_001102291
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,579,797 - 156,601,191 (+)NCBI
mRatBN7.2X151,428,461 - 151,449,858 (+)NCBI
Rnor_6.0X157,074,117 - 157,095,511 (-)NCBI
Rnor_5.01152,823,436 - 152,844,829 (-)NCBI
RGSC_v3.4X159,614,569 - 159,635,963 (+)RGD
Celera1136,439,697 - 136,461,090 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099912   ⟹   XP_038955840
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,579,694 - 156,601,448 (+)NCBI
mRatBN7.2X151,428,346 - 151,450,115 (+)NCBI
RefSeq Acc Id: XR_005498011
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X156,579,669 - 156,600,124 (+)NCBI
mRatBN7.2X151,428,334 - 151,448,791 (+)NCBI
RefSeq Acc Id: NP_001102291   ⟸   NM_001108821
- UniProtKB: D3ZHR2 (UniProtKB/TrEMBL),   A0A8I5ZWT6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070359   ⟸   ENSRNOT00000084088
RefSeq Acc Id: XP_038955840   ⟸   XM_039099912
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000083864   ⟸   ENSRNOT00000107613
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZHR2-F1-model_v2 AlphaFold D3ZHR2 1-737 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562128 AgrOrtholog
BioCyc Gene G2FUF-666 BioCyc
Ensembl Genes ENSRNOG00000056524 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055024378 UniProtKB/Swiss-Prot
  ENSRNOG00060006225 UniProtKB/Swiss-Prot
  ENSRNOG00065014619 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000084088 ENTREZGENE
  ENSRNOT00000084088.2 UniProtKB/Swiss-Prot
  ENSRNOT00000107613.1 UniProtKB/TrEMBL
  ENSRNOT00055041904 UniProtKB/Swiss-Prot
  ENSRNOT00060010244 UniProtKB/Swiss-Prot
  ENSRNOT00065024160 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro AAA+_ATPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC1_TM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_transporter-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_transporter_CS UniProtKB/Swiss-Prot
  FA_transporter UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:363516 UniProtKB/Swiss-Prot
NCBI Gene 363516 ENTREZGENE
PANTHER ATP-BINDING CASSETTE, SUB-FAMILY D MEMBER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11384:SF21 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam ABC_membrane_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_tran UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Abcd1 PhenoGen
PROSITE ABC_TM1F UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ABC_TRANSPORTER_1 UniProtKB/Swiss-Prot
  ABC_TRANSPORTER_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000056524 RatGTEx
  ENSRNOG00055024378 RatGTEx
  ENSRNOG00060006225 RatGTEx
  ENSRNOG00065014619 RatGTEx
SMART AAA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5ZWT6 ENTREZGENE, UniProtKB/TrEMBL
  ABCD1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-09 Abcd1  ATP binding cassette subfamily D member 1  Abcd1  ATP-binding cassette, subfamily D (ALD), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-11-16 Abcd1  ATP-binding cassette, subfamily D (ALD), member 1  Abcd1  ATP-binding cassette, sub-family D (ALD), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Abcd1  ATP-binding cassette, sub-family D (ALD), member 1   Abcd1_predicted  ATP-binding cassette, sub-family D (ALD), member 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Abcd1_predicted  ATP-binding cassette, sub-family D (ALD), member 1 (predicted)  RGD1562128_predicted  similar to mALDP (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1562128_predicted  similar to mALDP (predicted)  LOC363516  similar to mALDP  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC363516  similar to mALDP      Symbol and Name status set to provisional 70820 PROVISIONAL