Human Gene ATG3 (uc003dzd.3)
  Description: Homo sapiens autophagy related 3 (ATG3), mRNA.
RefSeq Summary (NM_022488): This gene encodes a ubiquitin-like-conjugating enzyme and is a component of ubiquitination-like systems involved in autophagy, the process of degradation, turnover and recycling of cytoplasmic constituents in eukaryotic cells. This protein is known to play a role in regulation of autophagy during cell death. A pseudogene of this gene is located on chromosome 20. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013].
Transcript (Including UTRs)
   Position: hg19 chr3:112,251,359-112,280,485 Size: 29,127 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr3:112,251,546-112,280,375 Size: 28,830 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:112,251,359-112,280,485)mRNA (may differ from genome)Protein (314 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ATG3_HUMAN
DESCRIPTION: RecName: Full=Ubiquitin-like-conjugating enzyme ATG3; EC=6.3.2.-; AltName: Full=Autophagy-related protein 3; Short=APG3-like; Short=hApg3; AltName: Full=Protein PC3-96;
FUNCTION: E2-like enzyme involved in autophagy and mitochondrial homeostasis. Catalyzes the conjugation of ATG8-like proteins (GABARAP, GABARAPL1, GABARAPL2 or MAP1LC3A) to phosphatidylethanolamine (PE). PE-conjugation to ATG8-like proteins is essential for autophagy. Preferred substrate is MAP1LC3A. Also acts as an autocatalytic E2-like enzyme, catalyzing the conjugation of ATG12 to itself, ATG12 conjugation to ATG3 playing a role in mitochondrial homeostasis but not in autophagy. ATG7 (E1-like enzyme) facilitates this reaction by forming an E1- E2 complex with ATG3.
SUBUNIT: Interacts with ATG7 and ATG12. The complex, composed of ATG3 and ATG7, plays a role in the conjugation of ATG12 to ATG5. Interacts with FNBP1L.
INTERACTION: O95166:GABARAP; NbExp=5; IntAct=EBI-988094, EBI-712001; Q9H0R8:GABARAPL1; NbExp=3; IntAct=EBI-988094, EBI-746969; P60520:GABARAPL2; NbExp=4; IntAct=EBI-988094, EBI-720116; Q9GZQ8:MAP1LC3B; NbExp=7; IntAct=EBI-988094, EBI-373144; Q7Z6L1:TECPR1; NbExp=3; IntAct=EBI-988094, EBI-2946676;
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Widely expressed, with a highest expression in heart, skeletal muscle, kidney, liver and placenta.
PTM: Conjugated to ATG12 at Lys-243. ATG12-conjugation plays a role in regulation of mitochondrial homeostasis and cell death, while it is not involved in PE-conjugation to ATG8-like proteins and autophagy (By similarity).
SIMILARITY: Belongs to the ATG3 family.
SEQUENCE CAUTION: Sequence=BAB15237.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ATG3
CDC HuGE Published Literature: ATG3

-  MalaCards Disease Associations
  MalaCards Gene Search: ATG3
Diseases sorted by gene-association score: bardet-biedl syndrome 4 (2)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 39.74 RPKM in Testis
Total median expression: 635.28 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -46.00110-0.418 Picture PostScript Text
3' UTR -27.80187-0.149 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
IPR007135 - Autophagy-rel_prot_3
IPR019461 - Autophagy-rel_prot_3_C
IPR007134 - Autophagy-rel_prot_3_N

Pfam Domains:
PF03986 - Autophagocytosis associated protein (Atg3), N-terminal domain
PF03987 - Autophagocytosis associated protein, active-site domain
PF10381 - Autophagocytosis associated protein C-terminal

ModBase Predicted Comparative 3D Structure on Q9NT62
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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 BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0019776 Atg8 ligase activity
GO:0019777 Atg12 transferase activity
GO:0019787 ubiquitin-like protein transferase activity
GO:0019899 enzyme binding

Biological Process:
GO:0000045 autophagosome assembly
GO:0000422 mitophagy
GO:0006464 cellular protein modification process
GO:0006612 protein targeting to membrane
GO:0006914 autophagy
GO:0015031 protein transport
GO:0016236 macroautophagy
GO:0016567 protein ubiquitination
GO:0043653 mitochondrial fragmentation involved in apoptotic process
GO:0044804 nucleophagy
GO:0050765 negative regulation of phagocytosis
GO:1902017 regulation of cilium assembly

Cellular Component:
GO:0000153 cytoplasmic ubiquitin ligase complex
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  LF210620 - JP 2014500723-A/18123: Polycomb-Associated Non-Coding RNAs.
BC043267 - Homo sapiens ATG3 autophagy related 3 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:5296971).
AK025778 - Homo sapiens cDNA: FLJ22125 fis, clone HEP19410.
AL137515 - Homo sapiens mRNA; cDNA DKFZp564M1178 (from clone DKFZp564M1178).
BC002830 - Homo sapiens ATG3 autophagy related 3 homolog (S. cerevisiae), mRNA (cDNA clone MGC:3478 IMAGE:3633903), complete cds.
BC024221 - Homo sapiens ATG3 autophagy related 3 homolog (S. cerevisiae), mRNA (cDNA clone MGC:15201 IMAGE:3938447), complete cds.
AK123511 - Homo sapiens cDNA FLJ41517 fis, clone BRTHA2012129.
AF202092 - Homo sapiens PC3-96 mRNA, complete cds.
JD333456 - Sequence 314480 from Patent EP1572962.
AK307432 - Homo sapiens cDNA, FLJ97380.
JD049516 - Sequence 30540 from Patent EP1572962.
AB079384 - Homo sapiens mRNA for Apg3p, complete cds.
DQ893424 - Synthetic construct clone IMAGE:100006054; FLH199510.01X; RZPDo839F0682D ATG3 autophagy related 3 homolog (S. cerevisiae) (ATG3) gene, encodes complete protein.
KJ894556 - Synthetic construct Homo sapiens clone ccsbBroadEn_03950 ATG3 gene, encodes complete protein.
DQ896774 - Synthetic construct Homo sapiens clone IMAGE:100011234; FLH199416.01L; RZPDo839F0681D ATG3 autophagy related 3 homolog (S. cerevisiae) (ATG3) gene, encodes complete protein.
CU692886 - Synthetic construct Homo sapiens gateway clone IMAGE:100021910 5' read ATG3 mRNA.
AK308919 - Homo sapiens cDNA, FLJ98960.
LF339377 - JP 2014500723-A/146880: Polycomb-Associated Non-Coding RNAs.
LF339373 - JP 2014500723-A/146876: Polycomb-Associated Non-Coding RNAs.
LF339372 - JP 2014500723-A/146875: Polycomb-Associated Non-Coding RNAs.
MA446197 - JP 2018138019-A/18123: Polycomb-Associated Non-Coding RNAs.
MA574954 - JP 2018138019-A/146880: Polycomb-Associated Non-Coding RNAs.
MA574950 - JP 2018138019-A/146876: Polycomb-Associated Non-Coding RNAs.
MA574949 - JP 2018138019-A/146875: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04140 - Regulation of autophagy

Reactome (by CSHL, EBI, and GO)

Protein Q9NT62 (Reactome details) participates in the following event(s):

R-HSA-5682896 LC3:ATG7 dimer binds ATG3
R-HSA-5678490 ATG16L1 complex transfers LC3 from ATG3 to PE
R-HSA-5681981 ATG3 transfers LC3 from ATG7 to ATG3
R-HSA-5683593 ATG7:ATG3:LC3 dissociates
R-HSA-1632852 Macroautophagy
R-HSA-8953897 Cellular responses to external stimuli

-  Other Names for This Gene
  Alternate Gene Symbols: APG3, APG3L, ATG3_HUMAN, NM_022488, NP_071933, Q6PKC5, Q9H6L9, Q9NT62
UCSC ID: uc003dzd.3
RefSeq Accession: NM_022488
Protein: Q9NT62 (aka ATG3_HUMAN)
CCDS: CCDS2966.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_022488.3
exon count: 12CDS single in 3' UTR: no RNA size: 1372
ORF size: 945CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2073.50frame shift in genome: no % Coverage: 90.52
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
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.