Human Gene AP3M1 (uc001jwh.3) Description and Page Index
  Description: Homo sapiens adaptor-related protein complex 3, mu 1 subunit (AP3M1), transcript variant 2, mRNA.
RefSeq Summary (NM_012095): The protein encoded by this gene is the medium subunit of AP-3, which is an adaptor-related protein complex associated with the Golgi region as well as more peripheral intracellular structures. AP-3 facilitates the budding of vesicles from the Golgi membrane, and it may directly function in protein sorting to the endosomal/lysosomal system. AP-3 is a heterotetrameric protein complex composed of two large subunits (delta and beta3), a medium subunit (mu3), and a small subunit (sigma 3). Mutations in one of the large subunits of AP-3 have been associated with the Hermansky-Pudlak syndrome, a genetic disorder characterized by defective lysosome-related organelles. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2016].
Transcript (Including UTRs)
   Position: hg19 chr10:75,880,015-75,910,826 Size: 30,812 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr10:75,883,568-75,898,137 Size: 14,570 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr10:75,880,015-75,910,826)mRNA (may differ from genome)Protein (418 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=AP-3 complex subunit mu-1; AltName: Full=AP-3 adapter complex mu3A subunit; AltName: Full=Adapter-related protein complex 3 mu-1 subunit; AltName: Full=Mu-adaptin 3A; AltName: Full=Mu3A-adaptin;
FUNCTION: Part of the AP-3 complex, an adaptor-related complex which is not clathrin-associated. The complex is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. In concert with the BLOC-1 complex, AP-3 is required to target cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals.
SUBUNIT: Adaptor protein complex 3 (AP-3) is an heterotetramer composed of two large adaptins (delta-type subunit AP3D1 and beta- type subunit AP3B1 or AP3B2), a medium adaptin (mu-type subunit AP3M1 or AP3M2) and a small adaptin (sigma-type subunit APS1 or AP3S2). Interacts with AGAP1. AP-3 associates with the BLOC-1 complex (By similarity).
SIMILARITY: Belongs to the adaptor complexes medium subunit family.
SIMILARITY: Contains 1 MHD (mu homology) domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): AP3M1
CDC HuGE Published Literature: AP3M1

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 24.07 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 465.90 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -101.42317-0.320 Picture PostScript Text
3' UTR -974.513553-0.274 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR022775 - AP_mu_sigma_su
IPR001392 - Clathrin_mu
IPR008968 - Clathrin_mu_C
IPR018240 - Clathrin_mu_CS
IPR011012 - Longin-like_dom

Pfam Domains:
PF00928 - Adaptor complexes medium subunit family
PF01217 - Clathrin adaptor complex small chain

SCOP Domains:
49447 - Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor
64356 - SNARE-like

ModBase Predicted Comparative 3D Structure on Q9Y2T2
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGD  WormBase 
 Protein Sequence  Protein Sequence 
 Alignment  Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0017137 Rab GTPase binding

Biological Process:
GO:0006622 protein targeting to lysosome
GO:0006886 intracellular protein transport
GO:0008089 anterograde axonal transport
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0048490 anterograde synaptic vesicle transport

Cellular Component:
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0030131 clathrin adaptor complex
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:1904115 axon cytoplasm

-  Descriptions from all associated GenBank mRNAs
  LF209954 - JP 2014500723-A/17457: Polycomb-Associated Non-Coding RNAs.
LF209955 - JP 2014500723-A/17458: Polycomb-Associated Non-Coding RNAs.
BC067127 - Homo sapiens adaptor-related protein complex 3, mu 1 subunit, mRNA (cDNA clone MGC:75195 IMAGE:6169822), complete cds.
AK026983 - Homo sapiens cDNA: FLJ23330 fis, clone HEP12654.
AL833820 - Homo sapiens mRNA; cDNA DKFZp586G1518 (from clone DKFZp586G1518).
BC026232 - Homo sapiens adaptor-related protein complex 3, mu 1 subunit, mRNA (cDNA clone MGC:22164 IMAGE:4807259), complete cds.
AK299352 - Homo sapiens cDNA FLJ51284 complete cds, highly similar to Adapter-relatedprotein complex 3 mu-1 subunit.
AF092092 - Homo sapiens AP-3 adaptor complex mu3A subunit mRNA, complete cds.
AK315597 - Homo sapiens cDNA, FLJ96676.
KJ893584 - Synthetic construct Homo sapiens clone ccsbBroadEn_02978 AP3M1 gene, encodes complete protein.
DQ893112 - Synthetic construct clone IMAGE:100005742; FLH193850.01X; RZPDo839C0979D adaptor-related protein complex 3, mu 1 subunit (AP3M1) gene, encodes complete protein.
DQ896386 - Synthetic construct Homo sapiens clone IMAGE:100010846; FLH193846.01L; RZPDo839C0969D adaptor-related protein complex 3, mu 1 subunit (AP3M1) gene, encodes complete protein.
EU176768 - Synthetic construct Homo sapiens clone IMAGE:100011584; FLH263630.01L; RZPDo839H02256D adaptor-related protein complex 3, mu 1 subunit (AP3M1) gene, encodes complete protein.
AB529047 - Synthetic construct DNA, clone: pF1KB3614, Homo sapiens AP3M1 gene for adaptor-related protein complex 3, mu 1 subunit, without stop codon, in Flexi system.
CU688256 - Synthetic construct Homo sapiens gateway clone IMAGE:100021759 5' read AP3M1 mRNA.
MA445531 - JP 2018138019-A/17457: Polycomb-Associated Non-Coding RNAs.
MA445532 - JP 2018138019-A/17458: Polycomb-Associated Non-Coding RNAs.
AK001565 - Homo sapiens cDNA FLJ10703 fis, clone NT2RP3000836.
JD243163 - Sequence 224187 from Patent EP1572962.
JD545812 - Sequence 526836 from Patent EP1572962.
JD363138 - Sequence 344162 from Patent EP1572962.
JD238307 - Sequence 219331 from Patent EP1572962.
JD135717 - Sequence 116741 from Patent EP1572962.
JD378218 - Sequence 359242 from Patent EP1572962.
JD144589 - Sequence 125613 from Patent EP1572962.
JD283318 - Sequence 264342 from Patent EP1572962.
JD112299 - Sequence 93323 from Patent EP1572962.
JD144588 - Sequence 125612 from Patent EP1572962.
JD089486 - Sequence 70510 from Patent EP1572962.
JD112298 - Sequence 93322 from Patent EP1572962.
JD188045 - Sequence 169069 from Patent EP1572962.
LF333243 - JP 2014500723-A/140746: Polycomb-Associated Non-Coding RNAs.
AL133610 - Homo sapiens mRNA; cDNA DKFZp434M2217 (from clone DKFZp434M2217).
JD315585 - Sequence 296609 from Patent EP1572962.
JD282306 - Sequence 263330 from Patent EP1572962.
JD256199 - Sequence 237223 from Patent EP1572962.
JD040652 - Sequence 21676 from Patent EP1572962.
JD379938 - Sequence 360962 from Patent EP1572962.
JD038971 - Sequence 19995 from Patent EP1572962.
JD537045 - Sequence 518069 from Patent EP1572962.
JD109866 - Sequence 90890 from Patent EP1572962.
JD085928 - Sequence 66952 from Patent EP1572962.
JD166869 - Sequence 147893 from Patent EP1572962.
JD251745 - Sequence 232769 from Patent EP1572962.
JD328811 - Sequence 309835 from Patent EP1572962.
JD122391 - Sequence 103415 from Patent EP1572962.
JD378506 - Sequence 359530 from Patent EP1572962.
LF333244 - JP 2014500723-A/140747: Polycomb-Associated Non-Coding RNAs.
JD399711 - Sequence 380735 from Patent EP1572962.
JD566256 - Sequence 547280 from Patent EP1572962.
JD564837 - Sequence 545861 from Patent EP1572962.
LF333245 - JP 2014500723-A/140748: Polycomb-Associated Non-Coding RNAs.
JD108423 - Sequence 89447 from Patent EP1572962.
JD275218 - Sequence 256242 from Patent EP1572962.
JD160450 - Sequence 141474 from Patent EP1572962.
LF333246 - JP 2014500723-A/140749: Polycomb-Associated Non-Coding RNAs.
JD427069 - Sequence 408093 from Patent EP1572962.
LF333247 - JP 2014500723-A/140750: Polycomb-Associated Non-Coding RNAs.
JD279998 - Sequence 261022 from Patent EP1572962.
JD074251 - Sequence 55275 from Patent EP1572962.
JD188449 - Sequence 169473 from Patent EP1572962.
LF333248 - JP 2014500723-A/140751: Polycomb-Associated Non-Coding RNAs.
JD348156 - Sequence 329180 from Patent EP1572962.
JD203020 - Sequence 184044 from Patent EP1572962.
LF333250 - JP 2014500723-A/140753: Polycomb-Associated Non-Coding RNAs.
MA568820 - JP 2018138019-A/140746: Polycomb-Associated Non-Coding RNAs.
MA568821 - JP 2018138019-A/140747: Polycomb-Associated Non-Coding RNAs.
MA568822 - JP 2018138019-A/140748: Polycomb-Associated Non-Coding RNAs.
MA568823 - JP 2018138019-A/140749: Polycomb-Associated Non-Coding RNAs.
MA568824 - JP 2018138019-A/140750: Polycomb-Associated Non-Coding RNAs.
MA568825 - JP 2018138019-A/140751: Polycomb-Associated Non-Coding RNAs.
MA568827 - JP 2018138019-A/140753: Polycomb-Associated Non-Coding RNAs.
LF333251 - JP 2014500723-A/140754: Polycomb-Associated Non-Coding RNAs.
MA568828 - JP 2018138019-A/140754: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04142 - Lysosome

Reactome (by CSHL, EBI, and GO)

Protein Q9Y2T2 (Reactome details) participates in the following event(s):

R-HSA-390470 Association of CCT/TriC with other substrates during biosynthesis (unknown chaperone)
R-HSA-390471 Association of TriC/CCT with target proteins during biosynthesis
R-HSA-390466 Chaperonin-mediated protein folding
R-HSA-391251 Protein folding
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: AP3M1_HUMAN, NM_012095, NP_996895, Q5JQ12, Q9H5L2, Q9Y2T2
UCSC ID: uc001jwh.3
RefSeq Accession: NM_012095
Protein: Q9Y2T2 (aka AP3M1_HUMAN or A3M1_HUMAN)
CCDS: CCDS7342.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_012095.4
exon count: 9CDS single in 3' UTR: no RNA size: 5144
ORF size: 1257CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2663.00frame shift in genome: no % Coverage: 99.67
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.