Human Gene ATG12 (ENST00000509910.2_7) from GENCODE V47lift37
  Description: autophagy related 12, transcript variant 3 (from RefSeq NR_033363.2)
Gencode Transcript: ENST00000509910.2_7
Gencode Gene: ENSG00000145782.13_11
Transcript (Including UTRs)
   Position: hg19 chr5:115,163,897-115,177,262 Size: 13,366 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr5:115,167,501-115,177,249 Size: 9,749 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:115,163,897-115,177,262)mRNA (may differ from genome)Protein (140 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ATG12_HUMAN
DESCRIPTION: RecName: Full=Ubiquitin-like protein ATG12; AltName: Full=Autophagy-related protein 12; Short=APG12-like;
FUNCTION: Ubiquitin-like protein required for autophagy. Conjugated to ATG3 and ATG5.
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
TISSUE SPECIFICITY: Ubiquitous.
DOMAIN: Shares weak sequence similarity with ubiquitin family, but contains an 'ubiquitin superfold' and the C-terminal Gly is required for isopeptide linkage.
SIMILARITY: Belongs to the ATG12 family.
SEQUENCE CAUTION: Sequence=AAH12266.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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


-  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: 10.64 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 359.02 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
3' UTR -943.923604-0.262 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
IPR007242 - Autophagy-rel_prot_12

Pfam Domains:
PF02991 - Autophagy protein Atg8 ubiquitin like
PF04110 - Ubiquitin-like autophagy protein Apg12

SCOP Domains:
54236 - Ubiquitin-like

ModBase Predicted Comparative 3D Structure on O94817
FrontTopSide
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 orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019776 Atg8 ligase activity

Biological Process:
GO:0000045 autophagosome assembly
GO:0000422 mitophagy
GO:0006501 C-terminal protein lipidation
GO:0006914 autophagy
GO:0016236 macroautophagy
GO:0044804 nucleophagy

Cellular Component:
GO:0005737 cytoplasm
GO:0005776 autophagosome
GO:0005829 cytosol
GO:0016020 membrane
GO:0030670 phagocytic vesicle membrane
GO:0032991 macromolecular complex
GO:0034045 pre-autophagosomal structure membrane
GO:0034274 Atg12-Atg5-Atg16 complex


-  Descriptions from all associated GenBank mRNAs
  KJ904621 - Synthetic construct Homo sapiens clone ccsbBroadEn_14015 ATG12 gene, encodes complete protein.
AB002449 - Homo sapiens mRNA, clone: 843Ex, from chromosome 5q21-q22.
JD082587 - Sequence 63611 from Patent EP1572962.
LF211046 - JP 2014500723-A/18549: Polycomb-Associated Non-Coding RNAs.
JD355508 - Sequence 336532 from Patent EP1572962.
JD331510 - Sequence 312534 from Patent EP1572962.
JD509725 - Sequence 490749 from Patent EP1572962.
JD501676 - Sequence 482700 from Patent EP1572962.
JD279867 - Sequence 260891 from Patent EP1572962.
JD527368 - Sequence 508392 from Patent EP1572962.
JD292818 - Sequence 273842 from Patent EP1572962.
JD326317 - Sequence 307341 from Patent EP1572962.
AX810713 - Sequence 37 from Patent EP1333092.
JD155123 - Sequence 136147 from Patent EP1572962.
JD297272 - Sequence 278296 from Patent EP1572962.
JD281206 - Sequence 262230 from Patent EP1572962.
JD347413 - Sequence 328437 from Patent EP1572962.
JD345996 - Sequence 327020 from Patent EP1572962.
JD450751 - Sequence 431775 from Patent EP1572962.
JD358706 - Sequence 339730 from Patent EP1572962.
JD242425 - Sequence 223449 from Patent EP1572962.
JD509681 - Sequence 490705 from Patent EP1572962.
AL161968 - Homo sapiens mRNA; cDNA DKFZp761A0411 (from clone DKFZp761A0411).
BC011033 - Homo sapiens ATG12 autophagy related 12 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:4103628), complete cds.
JD100943 - Sequence 81967 from Patent EP1572962.
JD538375 - Sequence 519399 from Patent EP1572962.
JD112447 - Sequence 93471 from Patent EP1572962.
JD089546 - Sequence 70570 from Patent EP1572962.
JD112446 - Sequence 93470 from Patent EP1572962.
JD226061 - Sequence 207085 from Patent EP1572962.
LF343417 - JP 2014500723-A/150920: Polycomb-Associated Non-Coding RNAs.
JD088452 - Sequence 69476 from Patent EP1572962.
JD082644 - Sequence 63668 from Patent EP1572962.
JD504177 - Sequence 485201 from Patent EP1572962.
JD067581 - Sequence 48605 from Patent EP1572962.
AB002440 - Homo sapiens mRNA, clone: FBR93-B, from chromosome 5q21-q22.
BC012266 - Homo sapiens ATG12 autophagy related 12 homolog (S. cerevisiae), mRNA (cDNA clone MGC:9094 IMAGE:3864058), complete cds.
AK098251 - Homo sapiens cDNA FLJ40932 fis, clone UTERU2007075, highly similar to Homo sapiens mRNA for Apg12.
JD114598 - Sequence 95622 from Patent EP1572962.
AB017507 - Homo sapiens mRNA for Apg12, complete cds.
JD264201 - Sequence 245225 from Patent EP1572962.
EU554057 - Homo sapiens Atg12 mRNA, complete cds.
AK313320 - Homo sapiens cDNA, FLJ93837, highly similar to Homo sapiens APG12 autophagy 12-like (S. cerevisiae) (APG12L),mRNA.
AB590693 - Synthetic construct DNA, clone: pFN21AE1667, Homo sapiens ATG12 gene for ATG12 autophagy related 12 homolog, without stop codon, in Flexi system.
JD380643 - Sequence 361667 from Patent EP1572962.
MA578994 - JP 2018138019-A/150920: Polycomb-Associated Non-Coding RNAs.
MA446623 - JP 2018138019-A/18549: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O94817 (Reactome details) participates in the following event(s):

R-HSA-5681980 ATG12 binds ATG7 dimer
R-HSA-5682010 ATG10:ATG12 binds ATG5
R-HSA-5683583 ATG10:ATG12:ATG7 dimer dissociates
R-HSA-5682893 ATG12:ATG7:CysO572-ATG7 binds ATG10
R-HSA-9020616 ATG12 forms a thioester bond with ATG7 dimer
R-HSA-5682012 ATG5:ATG12 binds ATG16L1
R-HSA-5682690 ATG10 dissociates from ATG12:ATG5
R-HSA-5205663 LC3 binds the autophagosome membrane Atg5-Atg12 complex
R-HSA-8959571 LC3 binds the autophagosome membrane Atg5-Atg12 complex
R-HSA-936378 Inhibition of DDX58/IFIH1 signaling by ATG5:ATG12:MAVS
R-HSA-5683588 ATG10 transfers ATG12 from ATG10 to ATG5
R-HSA-5681999 ATG10 transfers ATG12 from ATG7 to ATG10
R-HSA-5679255 WIPI2 binds ATG12:ATG5:ATG16L
R-HSA-5678490 ATG16L1 complex transfers LC3 from ATG3 to PE
R-HSA-1632852 Macroautophagy
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-5205685 Pink/Parkin Mediated Mitophagy
R-HSA-8934903 Receptor Mediated Mitophagy
R-HSA-936440 Negative regulators of DDX58/IFIH1 signaling
R-HSA-5205647 Mitophagy
R-HSA-168928 DDX58/IFIH1-mediated induction of interferon-alpha/beta
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: APG12, APG12L, ATG12_HUMAN, ENST00000509910.1, NR_033363, O94817, Q6PJV2, uc323fpn.1, uc323fpn.2
UCSC ID: ENST00000509910.2_7
RefSeq Accession: NM_004707.4
Protein: O94817 (aka ATG12_HUMAN)

-  Gene Model Information
  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.