Human Gene ATG5 (ENST00000369076.8_8) from GENCODE V47lift37
  Description: autophagy related 5, transcript variant 1 (from RefSeq NM_004849.4)
Gencode Transcript: ENST00000369076.8_8
Gencode Gene: ENSG00000057663.16_11
Transcript (Including UTRs)
   Position: hg19 chr6:106,632,351-106,773,635 Size: 141,285 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr6:106,634,415-106,764,083 Size: 129,669 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:106,632,351-106,773,635)mRNA (may differ from genome)Protein (275 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ATG5_HUMAN
DESCRIPTION: RecName: Full=Autophagy protein 5; AltName: Full=APG5-like; AltName: Full=Apoptosis-specific protein;
FUNCTION: Required for autophagy. Conjugates to ATG12 and associates with isolation membrane to form cup-shaped isolation membrane and autophagosome. The conjugate detaches from the membrane immediately before or after autophagosome formation is completed (By similarity).
FUNCTION: May play an important role in the apoptotic process, possibly within the modified cytoskeleton. Its expression is a relatively late event in the apoptotic process, occurring downstream of caspase activity.
SUBUNIT: The ATG5-ATG12 conjugate forms a complex with several units of ATG16. Interacts with TECPR1; the interaction is direct and does not take place when ATG16 is associated with the ATG5- ATG12 conjugate.
INTERACTION: O95166:GABARAP; NbExp=2; IntAct=EBI-1047414, EBI-712001; Q9GZQ8:MAP1LC3B; NbExp=2; IntAct=EBI-1047414, EBI-373144; Q7Z6L1:TECPR1; NbExp=6; IntAct=EBI-1047414, EBI-2946676; Q8IZQ1:WDFY3; NbExp=6; IntAct=EBI-1047414, EBI-1569256;
SUBCELLULAR LOCATION: Cytoplasm. Note=Colocalizes with nonmuscle actin.
TISSUE SPECIFICITY: Ubiquitous. The mRNA is present at similar levels in viable and apoptotic cells, whereas the protein is dramatically highly expressed in apoptotic cells.
INDUCTION: By apoptotic stimuli.
PTM: Conjugated to ATG12; which is essential for autophagy, but is not required for association with isolation membrane.
SIMILARITY: Belongs to the ATG5 family.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: ATG5
Diseases sorted by gene-association score: spinocerebellar ataxia, autosomal recessive 25* (950), spinocerebellar ataxia 14 (5), bardet-biedl syndrome 4 (5), hepatitis c virus (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 13.40 RPKM in Adrenal Gland
Total median expression: 371.81 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 -121.90293-0.416 Picture PostScript Text
3' UTR -466.502064-0.226 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
IPR007239 - Autophagy-rel_prot_5

Pfam Domains:
PF04106 - Autophagy protein Apg5

ModBase Predicted Comparative 3D Structure on Q9H1Y0
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 orthologNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  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:0001974 blood vessel remodeling
GO:0002376 immune system process
GO:0002739 regulation of cytokine secretion involved in immune response
GO:0006501 C-terminal protein lipidation
GO:0006914 autophagy
GO:0006915 apoptotic process
GO:0006995 cellular response to nitrogen starvation
GO:0009267 cellular response to starvation
GO:0009620 response to fungus
GO:0016236 macroautophagy
GO:0019725 cellular homeostasis
GO:0019883 antigen processing and presentation of endogenous antigen
GO:0031397 negative regulation of protein ubiquitination
GO:0035973 aggrephagy
GO:0039689 negative stranded viral RNA replication
GO:0042311 vasodilation
GO:0042493 response to drug
GO:0043066 negative regulation of apoptotic process
GO:0043687 post-translational protein modification
GO:0044804 nucleophagy
GO:0045060 negative thymic T cell selection
GO:0048840 otolith development
GO:0050765 negative regulation of phagocytosis
GO:0051279 regulation of release of sequestered calcium ion into cytosol
GO:0055015 ventricular cardiac muscle cell development
GO:0060047 heart contraction
GO:0060548 negative regulation of cell death
GO:0061739 protein lipidation involved in autophagosome assembly
GO:0070257 positive regulation of mucus secretion
GO:0071500 cellular response to nitrosative stress
GO:0075044 autophagy of host cells involved in interaction with symbiont
GO:1902017 regulation of cilium assembly
GO:2000377 regulation of reactive oxygen species metabolic process
GO:2000378 negative regulation of reactive oxygen species metabolic process
GO:2000619 negative regulation of histone H4-K16 acetylation

Cellular Component:
GO:0005737 cytoplasm
GO:0005776 autophagosome
GO:0005829 cytosol
GO:0005930 axoneme
GO:0016020 membrane
GO:0030670 phagocytic vesicle membrane
GO:0034045 pre-autophagosomal structure membrane
GO:0034274 Atg12-Atg5-Atg16 complex
GO:0044233 ER-mitochondrion membrane contact site


-  Descriptions from all associated GenBank mRNAs
  BX537904 - Homo sapiens mRNA; cDNA DKFZp686F0183 (from clone DKFZp686F0183); complete cds.
CR749386 - Homo sapiens mRNA; cDNA DKFZp781D1825 (from clone DKFZp781D1825).
Y11588 - H.sapiens mRNA for apoptosis specific protein.
BC093011 - Homo sapiens ATG5 autophagy related 5 homolog (S. cerevisiae), mRNA (cDNA clone MGC:110866 IMAGE:30345897), complete cds.
AK001899 - Homo sapiens cDNA FLJ11037 fis, clone PLACE1004316, highly similar to Autophagy protein 5.
BC002699 - Homo sapiens ATG5 autophagy related 5 homolog (S. cerevisiae), mRNA (cDNA clone MGC:3622 IMAGE:3609927), complete cds.
AK299577 - Homo sapiens cDNA FLJ50845 complete cds, highly similar to Autophagy protein 5.
EU283338 - Homo sapiens mutant ATG5 autophagy-related 5-like (ATG5) mRNA, complete sequence.
AF293841 - Homo sapiens apoptosis-related protein (APG5L) mRNA, complete cds, alternatively spliced.
EU283339 - Homo sapiens ATG5 autophagy related 5-like (ATG5) mRNA, complete cds, alternatively spliced.
JQ918353 - Homo sapiens ATG5 variant 2 (ATG5) mRNA, complete cds.
JQ918354 - Homo sapiens ATG5 variant 3 (ATG5) mRNA, complete cds.
JQ924061 - Homo sapiens ATG5 (ATG5) mRNA, complete cds.
AK315800 - Homo sapiens cDNA, FLJ96922.
HQ447996 - Synthetic construct Homo sapiens clone IMAGE:100071365; CCSB004090_02 ATG5 autophagy related 5 homolog (S. cerevisiae) (ATG5) gene, encodes complete protein.
KJ892779 - Synthetic construct Homo sapiens clone ccsbBroadEn_02173 ATG5 gene, encodes complete protein.
CU678128 - Synthetic construct Homo sapiens gateway clone IMAGE:100020687 5' read ATG5 mRNA.
JD359302 - Sequence 340326 from Patent EP1572962.
JD317178 - Sequence 298202 from Patent EP1572962.
JD384937 - Sequence 365961 from Patent EP1572962.
JD299388 - Sequence 280412 from Patent EP1572962.
JD565343 - Sequence 546367 from Patent EP1572962.
JD491563 - Sequence 472587 from Patent EP1572962.
JD563059 - Sequence 544083 from Patent EP1572962.
JD102205 - Sequence 83229 from Patent EP1572962.
JD433092 - Sequence 414116 from Patent EP1572962.
JD564751 - Sequence 545775 from Patent EP1572962.
JD450521 - Sequence 431545 from Patent EP1572962.
JD170832 - Sequence 151856 from Patent EP1572962.
JD530371 - Sequence 511395 from Patent EP1572962.
JD202093 - Sequence 183117 from Patent EP1572962.
JD273808 - Sequence 254832 from Patent EP1572962.
JD268894 - Sequence 249918 from Patent EP1572962.
JD090038 - Sequence 71062 from Patent EP1572962.
JD155532 - Sequence 136556 from Patent EP1572962.
JD026888 - Sequence 7912 from Patent EP1572962.
JD030970 - Sequence 11994 from Patent EP1572962.
JD071258 - Sequence 52282 from Patent EP1572962.
JD408677 - Sequence 389701 from Patent EP1572962.

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

Protein Q9H1Y0 (Reactome details) participates in the following event(s):

R-HSA-5682010 ATG10:ATG12 binds ATG5
R-HSA-5683588 ATG10 transfers ATG12 from ATG10 to 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-5682012 ATG5:ATG12 binds ATG16L1
R-HSA-5682690 ATG10 dissociates from ATG12:ATG5
R-HSA-936378 Inhibition of DDX58/IFIH1 signaling by ATG5:ATG12:MAVS
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: APG5L, ASP, ATG5_HUMAN, ENST00000369076.1, ENST00000369076.2, ENST00000369076.3, ENST00000369076.4, ENST00000369076.5, ENST00000369076.6, ENST00000369076.7, NM_004849, O60875, Q5JVR2, Q68DI4, Q9H1Y0, Q9H2B8, Q9HCZ7, uc318hhw.1, uc318hhw.2
UCSC ID: ENST00000369076.8_8
RefSeq Accession: NM_004849.4
Protein: Q9H1Y0 (aka ATG5_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.