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; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously 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 Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr879,620,909 - 9,656,350 (+)NCBIGRCr8
mRatBN7.278,970,249 - 9,005,651 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl78,970,291 - 9,005,643 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx711,848,541 - 11,884,095 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0713,724,050 - 13,759,604 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0711,590,505 - 11,626,054 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,838,639 - 11,873,992 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,838,639 - 11,873,984 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0712,006,378 - 12,041,244 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,480,810 - 10,516,163 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function
protein binding  (IPI,ISO)

References

References - curated
# Reference Title Reference Citation
1. Self-assembly of VPS41 promotes sorting required for biogenesis of the regulated secretory pathway. Asensio CS, etal., Dev Cell. 2013 Nov 25;27(4):425-37. doi: 10.1016/j.devcel.2013.10.007. Epub 2013 Nov 7.
2. Adaptor protein complexes 1 and 3 are essential for generation of synaptic vesicles from activity-dependent bulk endosomes. Cheung G and Cousin MA, J Neurosci. 2012 Apr 25;32(17):6014-23. doi: 10.1523/JNEUROSCI.6305-11.2012.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
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
GRCr879,620,909 - 9,656,350 (+)NCBIGRCr8
mRatBN7.278,970,249 - 9,005,651 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl78,970,291 - 9,005,643 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx711,848,541 - 11,884,095 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0713,724,050 - 13,759,604 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0711,590,505 - 11,626,054 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,838,639 - 11,873,992 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,838,639 - 11,873,984 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0712,006,378 - 12,041,244 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4710,480,810 - 10,516,163 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38192,100,988 - 2,164,616 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl192,100,988 - 2,164,468 (-)EnsemblGRCh38hg38GRCh38
GRCh37192,100,987 - 2,151,565 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36192,051,993 - 2,102,556 (-)NCBINCBI36Build 36hg18NCBI36
Build 34192,051,987 - 2,102,554NCBI
Celera192,035,746 - 2,085,826 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef191,873,271 - 1,922,400 (-)NCBIHuRef
CHM1_1192,100,857 - 2,151,100 (-)NCBICHM1_1
T2T-CHM13v2.0192,074,043 - 2,137,861 (-)NCBIT2T-CHM13v2.0
Ap3d1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391080,542,790 - 80,578,137 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1080,542,790 - 80,578,098 (-)EnsemblGRCm39 Ensembl
GRCm381080,706,956 - 80,742,303 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1080,706,956 - 80,742,264 (-)EnsemblGRCm38mm10GRCm38
MGSCv371080,169,723 - 80,204,956 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361080,110,107 - 80,145,340 (-)NCBIMGSCv36mm8
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
NHGRI_mPanPan1-v2206,482,829 - 6,534,247 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1195,713,578 - 5,765,048 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0191,110,419 - 1,161,826 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1192,084,349 - 2,135,058 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl192,085,540 - 2,137,593 (-)Ensemblpanpan1.1panPan2
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02057,626,251 - 57,665,286 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2057,626,308 - 57,665,281 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12056,678,263 - 56,717,233 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02057,163,351 - 57,202,395 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02057,363,843 - 57,402,849 (+)NCBIUU_Cfam_GSD_1.0
Ap3d1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118216,572,359 - 216,611,142 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365881,222,466 - 1,262,676 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365881,223,646 - 1,262,577 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AP3D1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl276,428,476 - 76,471,257 (+)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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl61,901,507 - 1,951,314 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660816,783,776 - 6,838,998 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ap3d1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248286,710,025 - 6,749,434 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248286,710,081 - 6,750,315 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ap3d1
146 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat

Markers in Region
RH124553  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.279,005,266 - 9,005,574 (+)MAPPERmRatBN7.2
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


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 21 141 227 147 69 147 33 42 250 115 145 57 21
Low 3 3 3
Below cutoff

Sequence


Ensembl Acc Id: ENSRNOT00000025878   ⟹   ENSRNOP00000025878
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl78,970,291 - 9,005,643 (+)Ensembl
Rnor_6.0 Ensembl711,838,639 - 11,873,984 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000095433   ⟹   ENSRNOP00000095136
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl78,970,291 - 9,005,643 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000111908   ⟹   ENSRNOP00000084637
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl78,970,291 - 9,005,643 (+)Ensembl
RefSeq Acc Id: NM_001100719   ⟹   NP_001094189
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,620,995 - 9,656,350 (+)NCBI
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_039079008   ⟹   XP_038934936
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,620,909 - 9,653,146 (+)NCBI
mRatBN7.278,970,249 - 9,002,473 (+)NCBI
RefSeq Acc Id: XM_063263422   ⟹   XP_063119492
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,620,909 - 9,656,350 (+)NCBI
RefSeq Acc Id: XM_063263423   ⟹   XP_063119493
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr879,632,983 - 9,656,350 (+)NCBI
RefSeq Acc Id: NP_001094189   ⟸   NM_001100719
- UniProtKB: B5DFK6 (UniProtKB/TrEMBL),   F7F0K5 (UniProtKB/TrEMBL),   A0A8I6AM24 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000025878   ⟸   ENSRNOT00000025878
RefSeq Acc Id: XP_038934936   ⟸   XM_039079008
- Peptide Label: isoform X3
- UniProtKB: A6K8H3 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000084637   ⟸   ENSRNOT00000111908
Ensembl Acc Id: ENSRNOP00000095136   ⟸   ENSRNOT00000095433
RefSeq Acc Id: XP_063119492   ⟸   XM_063263422
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AM24 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063119493   ⟸   XM_063263423
- Peptide Label: isoform X2
- UniProtKB: A0A8I6AM24 (UniProtKB/TrEMBL)
Protein Domains
AP-3 complex subunit delta

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B5DFK6-F1-model_v2 AlphaFold B5DFK6 1-1204 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308659 AgrOrtholog
BioCyc Gene G2FUF-34964 BioCyc
Ensembl Genes ENSRNOG00000018977 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025878.6 UniProtKB/TrEMBL
  ENSRNOT00000095433.1 UniProtKB/TrEMBL
  ENSRNOT00000111908.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
  Longin domain 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 AP-3 COMPLEX SUBUNIT DELTA-1 UniProtKB/TrEMBL
  PTHR22781 UniProtKB/TrEMBL
Pfam Adaptin_N UniProtKB/TrEMBL
  AP3D1 UniProtKB/TrEMBL
PhenoGen Ap3d1 PhenoGen
PIRSF AP3_complex_delta UniProtKB/TrEMBL
RatGTEx ENSRNOG00000018977 RatGTEx
SMART BLVR UniProtKB/TrEMBL
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
UniProt A0A8I6AM24 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GAS3_RAT UniProtKB/TrEMBL
  A6K8H3 ENTREZGENE, UniProtKB/TrEMBL
  B5DFK6 ENTREZGENE, UniProtKB/TrEMBL
  F7F0K5 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