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ATG2A Gene

protein-coding   GIFtS: 49
GCID: GC11M064662

Autophagy Related 2A

(Previous name: ATG2 autophagy related 2 homolog A (S. cerevisiae))
  Search for ATG2A
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Autophagy Related 2A1 2
ATG2 Autophagy Related 2 Homolog A (S. Cerevisiae)1
ATG2 Autophagy Related 2 Homolog A2
Autophagy-Related Protein 2 Homolog A2
KIAA04043

External Ids:    HGNC: 290281   Entrez Gene: 231302   Ensembl: ENSG000001100467   UniProtKB: Q2TAZ03   

Export aliases for ATG2A gene to outside databases

Previous GC identifers: GC11M064430 GC11M064431 GC11M064434 GC11M060989


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for ATG2A Gene:
ATG2A (autophagy related 2A) is a protein-coding gene. An important paralog of this gene is ATG2B.

UniProtKB/Swiss-Prot: ATG2A_HUMAN, Q2TAZ0
Function: Required for both autophagosome formation and regulation of lipid droplet morphology and dispersion




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000011.9  NT_167190.2  NC_018922.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the ATG2A gene promoter:
         Egr-3   TBP   p53   Sp1   Nkx2-5   Ik-3   C/EBPalpha   YY1   FOXC1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidATG2A promoter sequence
   Search Chromatin IP Primers for ATG2A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ATG2A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11q13.1   Ensembl cytogenetic band:  11q13.1   HGNC cytogenetic band: 11q13.1

ATG2A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ATG2A gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M064662:  view genomic region     (about GC identifiers)

Start:
64,662,004 bp from pter      End:
64,684,722 bp from pter
Size:
22,719 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: ATG2A_HUMAN, Q2TAZ0 (See protein sequence)
Recommended Name: Autophagy-related protein 2 homolog A  
Size: 1938 amino acids; 212860 Da
Sequence caution: Sequence=BAA23700.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: O43154 Q14DM2 Q6ZTV2 Q7Z6K8 Q8IVY5 Q8TAI8 Q96HH7
Alternative splicing: 4 isoforms:  Q2TAZ0-1   Q2TAZ0-3   Q2TAZ0-4   Q2TAZ0-5   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ATG2A: NX_Q2TAZ0

Explore proteomics data for ATG2A at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ATG2A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_055919.2  
    ENSEMBL proteins: 
     ENSP00000413716   ENSP00000366475   ENSP00000410522  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR015412 Autophagy-rel_C
     IPR026849 ATG2
     IPR026854 VPS13A_N

    Graphical View of Domain Structure for InterPro Entry Q2TAZ0

    ProtoNet protein and cluster: Q2TAZ0

    1 Blocks protein domain: IPB006093 Oxygen oxidoreductase covalent FAD-binding site

    UniProtKB/Swiss-Prot: ATG2A_HUMAN, Q2TAZ0
    Similarity: Belongs to the ATG2 family


    Find genes that share domains with ATG2A           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ATG2A_HUMAN, Q2TAZ0
    Function: Required for both autophagosome formation and regulation of lipid droplet morphology and dispersion

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--
         
    Find genes that share ontologies with ATG2A           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for ATG2A
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    Selected qRT-PCR Assays for microRNAs that regulate ATG2A (see all 21):
    hsa-miR-4265 hsa-miR-106a hsa-miR-519a hsa-miR-27b* hsa-miR-629* hsa-miR-654-5p hsa-miR-93 hsa-miR-526b*
    SwitchGear 3'UTR luciferase reporter plasmidATG2A 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    ATG2A_HUMAN, Q2TAZ0: Preautophagosomal structure membrane; Peripheral membrane protein. Lipid droplet
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol3
    nucleus3
    lysosome1
    vacuole1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005811lipid particle IEA--
    GO:0034045pre-autophagosomal structure membrane IEA--

    Find genes that share ontologies with ATG2A           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for ATG2A
    Interactions:

        Search GeneGlobe Interaction Network for ATG2A

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for ATG2A (Q2TAZ01, 3 ENSP000003664754) via UniProtKB, MINT, STRING, and/or I2D (see all 381)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006914autophagy IEA--

    Find genes that share ontologies with ATG2A           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for ATG2A



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for ATG2A gene: 
    NM_015104.2  

    Unigene Cluster for ATG2A:

    Autophagy related 2A
    Hs.370671  [show with all ESTs]
    Unigene Representative Sequence: BC110650
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000418259 ENST00000377264 ENST00000472525 ENST00000461701(uc010rnt.1)
    ENST00000461955 ENST00000421419(uc001obw.3 uc001obx.3)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate ATG2A (see all 21):
    hsa-miR-4265 hsa-miR-106a hsa-miR-519a hsa-miR-27b* hsa-miR-629* hsa-miR-654-5p hsa-miR-93 hsa-miR-526b*
    SwitchGear 3'UTR luciferase reporter plasmidATG2A 3' UTR sequence
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      QuantiTect SYBR Green Assays in human, mouse, rat ATG2A
      QuantiFast Probe-based Assays in human, mouse, rat ATG2A

    Additional mRNA sequence: 

    AB007864.1 AF001545.1 AK300925.1 AK307684.1 BC008593.1 BC027481.1 BC033850.1 BC053596.1 
    BC110650.1 BC113090.1 BC113091.1 

    5 DOTS entries:

    DT.408726  DT.120701664  DT.70104463  DT.101975828  DT.91742874 

    Selected AceView cDNA sequences (see all 99):

    BM915672 AV700614 CB216526 AB007864 BC008593 BU951730 CD671341 BQ064111 
    BM560754 BC027481 BE254933 BM980863 BM454673 BQ066013 AW339554 CA432115 
    BC053596 BQ057657 BU182094 BM855676 BQ071019 BF984155 BX283921 AW827063 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for ATG2A (see all 10)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^ 14a · 14b ^ 15a · 15b · 15c ^ 16 ^ 17 ^ 18 ^
    SP1:                                                                                                                                                            
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:              -                                                                                                                                             

    ExUns: 19 ^ 20 ^ 21a · 21b ^ 22a · 22b ^ 23a · 23b ^ 24a · 24b · 24c ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35
    SP1:                                                                                                                                    
    SP2:                                                                                                                                    
    SP3:                                                                                                                                    
    SP4:                                                                                                                                    
    SP5:                                                                                                                                    


    ECgene alternative splicing isoforms for ATG2A

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    ATG2A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAGTGGAATA
    ATG2A Expression
    About this image

    ATG2A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ATG2A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.370671
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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for ATG2A gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Atg2a1 , 5 ATG2 autophagy related 2 homolog A (S. cerevisiae)5
    autophagy related 2A1
    84.1(n)1
    85.98(a)1
      19 (4.37 cM)5
    3290151  NM_194348.31  NP_919329.21 
     62416685 
    lizard
    (Anolis carolinensis)
    Reptilia ATG2A6
    autophagy related 2A
    55(a)
    1 ↔ 1
    GL344659.1(148-22704)
    African clawed frog
    (Xenopus laevis)
    Amphibia BG815119.12   -- 78.41(n)    BG815119.1 
    zebrafish
    (Danio rerio)
    Actinopterygii 570915022   -- 79.52(n)    57091502 
    fruit fly
    (Drosophila melanogaster)
    Insecta Atg26
    Autophagy-specific gene 2
    25(a)
    1 → many
    3L(2774338-2780677)
    worm
    (Caenorhabditis elegans)
    Secernentea atg-21 atg-2 40.76(n)
    29.83(a)
      180949  NM_076744.6  NP_509145.3 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes ATG26
    Peripheral membrane protein required for vesicle f...
    16(a)
    1 → many
    XIV(191324-196102) YNL242W


    ENSEMBL Gene Tree for ATG2A (if available)
    TreeFam Gene Tree for ATG2A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ATG2A gene
    ATG2B2  
    1 SIMAP similar gene for ATG2A using alignment to 3 protein entries:     ATG2A_HUMAN (see all proteins):
    ATG2B

    Find genes that share paralogs with ATG2A           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for ATG2A (see all 903)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1845733431,2
    --64661524(+) ATTCCA/GGCTGC 1 -- int10--------
    rs112319001,2
    C,F,H--64661532(+) TGCAGC/TGCTGC 1 -- int14Minor allele frequency- T:0.01NS NA 506
    rs1133447431,2
    F--64661542(+) CTCCAG/CCACCC 1 -- int12Minor allele frequency- C:0.10CSA WA 120
    rs1122144471,2
    F--64661880(+) CTGATC/TTGCTG 1 -- int11Minor allele frequency- T:0.50CSA 2
    rs1823191971,2
    C--64661958(+) TGGGGC/TGGGGC 1 -- int10--------
    rs776926801,2
    F--64661970(+) AAGGTC/TAAGGC 1 -- int11Minor allele frequency- T:0.09WA 118
    rs1857142841,2
    --64662179(+) CCTCCA/GTCCTG 1 -- ut310--------
    rs782132051,2
    C,F--64662206(+) TGGGCC/ACAGGT 1 -- ut311Minor allele frequency- A:0.07WA 118
    rs1129237081,2
    C--64662415(+) TGGGCC/AGCACC 1 -- ut311Minor allele frequency- A:0.50CSA 2
    rs764228221,2
    C,F--64662423(+) ACCCTC/TTGGGT 1 -- ut311Minor allele frequency- T:0.07WA 118

    HapMap Linkage Disequilibrium report for ATG2A (64662004 - 64684722 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for ATG2A:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv1173n71CNV Loss21882294
    nsv528506CNV Loss19592680
    dgv1171n71CNV Loss21882294
    nsv526181CNV Gain19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ATG2A
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    Find genes that share disorders with ATG2A           About GenesLikeMe

    Genetic Association Database (GAD): ATG2A
    Human Genome Epidemiology (HuGE) Navigator: ATG2A (1 document)

    Export disorders for ATG2A gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for ATG2A gene, integrated from 10 sources (see all 13):
    (articles sorted by number of sources associating them with ATG2A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Human hAtg2A protein expressed in yeast is recruited to preautophagosomal structure but does not complement autophagy defects of atg2Delta strain. (PubMed id 21887408)1, 2, 3 Romanyuk D....Zoladek T. (Acta Biochim. Pol. 2011)
    2. Mammalian Atg2 proteins are essential for autophagosome formation and important for regulation of size and distribution of lipid droplets. (PubMed id 22219374)1, 2 Velikkakath A.K.... Mizushima N. (Mol. Biol. Cell 2012)
    3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    4. Prediction of the coding sequences of unidentified human genes. VIII. 78 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 9455477)1, 2 Ishikawa K.... Ohara O. (DNA Res. 1997)
    5. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    6. Network organization of the human autophagy system. (PubMed id 20562859)1 Behrends C....Harper J.W. (Nature 2010)
    7. Defining the human deubiquitinating enzyme interaction landscape. (PubMed id 19615732)1 Sowa M.E....Harper J.W. (Cell 2009)
    8. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (Proc. Natl. Acad. Sci. U.S.A. 2008)
    9. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)2 Taylor T.D....Sakaki Y. (Nature 2006)
    10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 23130 HGNC: 29028 AceView: KIAA0404 Ensembl:ENSG00000110046 euGenes: HUgn23130
    ECgene: ATG2A H-InvDB: ATG2A

    (According to HUGE)
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    HUGE: KIAA0404

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for ATG2A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for ATG2A gene:
    Search GeneIP for patents involving ATG2A

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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