Ap3d1 (adaptor related protein complex 3 subunit delta 1) - Rat Genome Database

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Gene: Ap3d1 (adaptor related protein complex 3 subunit delta 1) Rattus norvegicus
Analyze
Symbol: Ap3d1
Name: adaptor related protein complex 3 subunit delta 1
RGD ID: 1308659
Description: Involved in synaptic vesicle budding from endosome. Predicted to be located in axon. Predicted to be part of AP-3 adaptor complex. Predicted to be active in several cellular components, including endosome; glutamatergic synapse; and terminal bouton. Human ortholog(s) of this gene implicated in Hermansky-Pudlak syndrome. Orthologous to human AP3D1 (adaptor related protein complex 3 subunit delta 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4-amino-2,6-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: adaptor-related protein complex 3, delta 1 subunit; adaptor-related protein complex 3, delta subunit; AP-3 complex subunit delta-1; Ap3d; LOC314633
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
mRatBN7.278,970,249 - 9,005,651 (+)NCBI
Rnor_6.0 Ensembl711,838,639 - 11,873,984 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0711,838,639 - 11,873,992 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0712,006,378 - 12,041,244 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,480,810 - 10,516,163 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1710,480,817 - 10,516,163 (+)NCBI
Celera77,153,021 - 7,188,363 (+)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:11588176   PMID:12477932   PMID:14557411   PMID:15860731   PMID:16162817   PMID:17349999   PMID:17897319   PMID:19144828   PMID:19946888   PMID:20089890   PMID:20847273   PMID:21998198  
PMID:22511774   PMID:23146885   PMID:24217640  


Genomics

Comparative Map Data
Ap3d1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.278,970,249 - 9,005,651 (+)NCBI
Rnor_6.0 Ensembl711,838,639 - 11,873,984 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0711,838,639 - 11,873,992 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0712,006,378 - 12,041,244 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,480,810 - 10,516,163 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1710,480,817 - 10,516,163 (+)NCBI
Celera77,153,021 - 7,188,363 (+)NCBICelera
Cytogenetic Map7q11NCBI
AP3D1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl192,100,988 - 2,164,468 (-)EnsemblGRCh38hg38GRCh38
GRCh38192,100,988 - 2,151,566 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37192,100,987 - 2,151,565 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36192,051,993 - 2,102,556 (-)NCBINCBI36hg18NCBI36
Build 34192,051,987 - 2,102,554NCBI
Celera192,035,746 - 2,085,826 (-)NCBI
Cytogenetic Map19p13.3NCBI
HuRef191,873,271 - 1,922,400 (-)NCBIHuRef
CHM1_1192,100,857 - 2,151,100 (-)NCBICHM1_1
Ap3d1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391080,542,790 - 80,578,137 (-)NCBIGRCm39mm39
GRCm39 Ensembl1080,542,790 - 80,578,098 (-)Ensembl
GRCm381080,706,956 - 80,742,303 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1080,706,956 - 80,742,264 (-)EnsemblGRCm38mm10GRCm38
MGSCv371080,169,723 - 80,204,956 (-)NCBIGRCm37mm9NCBIm37
MGSCv361080,110,107 - 80,145,340 (-)NCBImm8
Celera1081,725,359 - 81,760,588 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Ap3d1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554955,972,433 - 6,012,433 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554955,972,177 - 6,012,525 (+)NCBIChiLan1.0ChiLan1.0
AP3D1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1192,084,349 - 2,135,058 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl192,085,540 - 2,137,593 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0191,110,419 - 1,161,826 (-)NCBIMhudiblu_PPA_v0panPan3
AP3D1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12056,893,479 - 56,932,460 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2056,893,535 - 56,931,830 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2056,688,442 - 56,727,446 (+)NCBI
ROS_Cfam_1.02057,626,251 - 57,665,286 (+)NCBI
UMICH_Zoey_3.12056,678,263 - 56,717,233 (+)NCBI
UNSW_CanFamBas_1.02057,163,351 - 57,202,395 (+)NCBI
UU_Cfam_GSD_1.02057,363,843 - 57,402,849 (+)NCBI
Ap3d1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118216,572,359 - 216,611,142 (+)NCBI
SpeTri2.0NW_0049365881,223,646 - 1,262,577 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AP3D1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl276,428,436 - 76,471,258 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1276,428,443 - 76,471,266 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2276,963,774 - 76,969,977 (-)NCBISscrofa10.2Sscrofa10.2susScr3
AP3D1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.161,901,669 - 1,951,352 (-)NCBI
ChlSab1.1 Ensembl61,901,507 - 1,951,314 (-)Ensembl
Vero_WHO_p1.0NW_0236660816,783,776 - 6,838,998 (+)NCBI
Ap3d1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248286,710,081 - 6,750,315 (+)NCBI

Position Markers
RH124553  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,005,266 - 9,005,574 (+)MAPPER
Rnor_6.0711,873,608 - 11,873,915NCBIRnor6.0
Rnor_5.0712,040,860 - 12,041,167UniSTSRnor5.0
RGSC_v3.4710,515,779 - 10,516,086UniSTSRGSC3.4
Celera77,187,979 - 7,188,286UniSTS
Cytogenetic Map7q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7134147172Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7134828535Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7134828535Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7137009673Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7138119654Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7265313832258115Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7591147750911477Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7595196950951969Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7975804554758045Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)71164710256647102Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:144
Count of miRNA genes:92
Interacting mature miRNAs:120
Transcripts:ENSRNOT00000025878
Prediction methods: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 7 10 74 35 41 11 7
Low 1 1 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025878   ⟹   ENSRNOP00000025878
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl711,838,639 - 11,873,984 (+)Ensembl
RefSeq Acc Id: NM_001100719   ⟹   NP_001094189
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.278,970,291 - 9,005,651 (+)NCBI
Rnor_6.0711,838,639 - 11,873,992 (+)NCBI
Rnor_5.0712,006,378 - 12,041,244 (+)NCBI
RGSC_v3.4710,480,810 - 10,516,163 (+)RGD
Celera77,153,021 - 7,188,363 (+)RGD
Sequence:
RefSeq Acc Id: XM_039079007   ⟹   XP_038934935
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.278,970,255 - 9,005,651 (+)NCBI
RefSeq Acc Id: XM_039079008   ⟹   XP_038934936
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.278,970,249 - 9,002,473 (+)NCBI
RefSeq Acc Id: XM_039079010   ⟹   XP_038934938
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.278,970,249 - 8,999,946 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001094189   ⟸   NM_001100719
- UniProtKB: B5DFK6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000025878   ⟸   ENSRNOT00000025878
RefSeq Acc Id: XP_038934936   ⟸   XM_039079008
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038934938   ⟸   XM_039079010
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038934935   ⟸   XM_039079007
- Peptide Label: isoform X1
Protein Domains
BLVR

Transcriptome

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

Promoters
RGD ID:13695007
Promoter ID:EPDNEW_R5532
Type:initiation region
Name:Ap3d1_1
Description:adaptor-related protein complex 3, delta 1 subunit
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_6.0711,838,636 - 11,838,696EPDNEW

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)
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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:1308659 AgrOrtholog
Ensembl Genes ENSRNOG00000018977 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000025878 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025878 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7112159 IMAGE-MGC_LOAD
  IMAGE:7365585 IMAGE-MGC_LOAD
InterPro AP3_complex_dsu UniProtKB/TrEMBL
  AP3D_dom_metazoa UniProtKB/TrEMBL
  ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  Clathrin/coatomer_adapt-like_N UniProtKB/TrEMBL
KEGG Report rno:314633 UniProtKB/TrEMBL
MGC_CLONE MGC:105844 IMAGE-MGC_LOAD
  MGC:116299 IMAGE-MGC_LOAD
NCBI Gene 314633 ENTREZGENE
PANTHER PTHR22781 UniProtKB/TrEMBL
Pfam Adaptin_N UniProtKB/TrEMBL
  AP3D1 UniProtKB/TrEMBL
PhenoGen Ap3d1 PhenoGen
SMART BLVR UniProtKB/TrEMBL
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
UniProt B5DFK6 ENTREZGENE, UniProtKB/TrEMBL
  Q4FZT4_RAT UniProtKB/TrEMBL
  Q5RK16_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-03 Ap3d1  adaptor related protein complex 3 subunit delta 1  Ap3d1  adaptor-related protein complex 3, delta 1 subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Ap3d1  adaptor-related protein complex 3, delta 1 subunit  Ap3d  adaptor-related protein complex 3, delta subunit  Symbol and Name updated 1299863 APPROVED
2005-12-06 Ap3d  adaptor-related protein complex 3, delta subunit  Ap3d_predicted  adaptor-related protein complex 3, delta subunit (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Ap3d_predicted  adaptor-related protein complex 3, delta subunit (predicted)      Symbol and Name status set to approved 70820 APPROVED