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: Exhibits ATP binding activity. Involved in very long-chain fatty acid catabolic process. Localizes to 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
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X151,428,334 - 151,450,115 (+)NCBI
Rnor_6.0 EnsemblX157,072,736 - 157,095,274 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X157,073,860 - 157,095,652 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01152,823,436 - 152,844,829 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,614,569 - 159,635,963 (+)NCBIRGSC3.4rn4RGSC3.4
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

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:21209459   PMID:22521832   PMID:23123468   PMID:23604518   PMID:23671276   PMID:25255441   PMID:25583114   PMID:26108493   PMID:28258215  


Genomics

Comparative Map Data
Abcd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X151,428,334 - 151,450,115 (+)NCBI
Rnor_6.0 EnsemblX157,072,736 - 157,095,274 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X157,073,860 - 157,095,652 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01152,823,436 - 152,844,829 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,614,569 - 159,635,963 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1136,439,697 - 136,461,090 (-)NCBICelera
Cytogenetic MapXq37NCBI
ABCD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX153,724,856 - 153,744,755 (+)EnsemblGRCh38hg38GRCh38
GRCh38X153,724,851 - 153,744,755 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X152,990,311 - 153,010,209 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X152,643,530 - 152,663,375 (+)NCBINCBI36hg18NCBI36
Build 34X152,511,182 - 152,531,028NCBI
CeleraX153,224,004 - 153,243,898 (+)NCBI
Cytogenetic MapXq28NCBI
HuRefX141,647,579 - 141,667,479 (+)NCBIHuRef
CHM1_1X152,864,732 - 152,884,627 (+)NCBICHM1_1
Abcd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X72,760,203 - 72,782,140 (+)NCBIGRCm39mm39
GRCm39 EnsemblX72,760,203 - 72,782,140 (+)Ensembl
GRCm38X73,716,597 - 73,738,534 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX73,716,597 - 73,738,534 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X70,961,936 - 70,983,626 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X69,969,317 - 69,991,007 (+)NCBImm8
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
PanPan1.1X153,162,412 - 153,182,424 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX153,162,412 - 153,182,424 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X143,275,165 - 143,295,283 (+)NCBIMhudiblu_PPA_v0panPan3
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 (+)NCBI
ROS_Cfam_1.0X124,687,215 - 124,707,872 (+)NCBI
UMICH_Zoey_3.1X120,456,646 - 120,477,290 (+)NCBI
UNSW_CanFamBas_1.0X122,971,670 - 122,992,305 (+)NCBI
UU_Cfam_GSD_1.0X122,733,767 - 122,754,413 (+)NCBI
Abcd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X118,877,295 - 118,896,851 (+)NCBI
SpeTri2.0NW_004936809615,133 - 634,618 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ABCD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX124,485,235 - 124,503,195 (+)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X128,152,697 - 128,171,007 (+)NCBI
Abcd1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624946421,113 - 439,961 (+)NCBI

Position Markers
GDB:376683  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,442,695 - 151,442,776 (-)MAPPER
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 (-)MAPPER
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118715462159970021Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X134627816159970021Rat


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


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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000084088   ⟹   ENSRNOP00000070359
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX157,072,736 - 157,095,274 (-)Ensembl
RefSeq Acc Id: NM_001108821   ⟹   NP_001102291
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_017602115   ⟹   XP_017457604
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X157,073,860 - 157,095,652 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099912   ⟹   XP_038955840
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,428,346 - 151,450,115 (+)NCBI
RefSeq Acc Id: XR_005498011
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,428,334 - 151,448,791 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001102291 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955840 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D3ZHR2 (Get FASTA)   NCBI Sequence Viewer  
  EDL85026 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102291   ⟸   NM_001108821
- UniProtKB: D3ZHR2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457604   ⟸   XM_017602115
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000070359   ⟸   ENSRNOT00000084088
RefSeq Acc Id: XP_038955840   ⟸   XM_039099912
- Peptide Label: isoform X1
Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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:1562128 AgrOrtholog
Ensembl Genes ENSRNOG00000056524 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000070359 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000084088 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro AAA+_ATPase UniProtKB/Swiss-Prot
  ABC1_TM_dom UniProtKB/Swiss-Prot
  ABC_transporter-like UniProtKB/Swiss-Prot
  ABC_transporter_CS UniProtKB/Swiss-Prot
  ALDP UniProtKB/Swiss-Prot
  FA_transporter UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot
KEGG Report rno:363516 UniProtKB/Swiss-Prot
NCBI Gene 363516 ENTREZGENE
PANTHER PTHR11384:SF21 UniProtKB/Swiss-Prot
Pfam ABC_membrane_2 UniProtKB/Swiss-Prot
  ABC_tran UniProtKB/Swiss-Prot
PhenoGen Abcd1 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
TIGRFAMs 3a01203 UniProtKB/Swiss-Prot
UniProt 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