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ATG4A Gene

protein-coding   GIFtS: 58
GCID: GC0XP107334

Autophagy Related 4A, Cysteine Peptidase

(Previous names: AUT-like 2, cysteine endopeptidase (S. cerevisiae), APG4...)
(Previous symbols: AUTL2, APG4A)
  See related diseases
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 4A, Cysteine Peptidase1 2     APG4 Autophagy 4 Homolog A2
APG4A1 2 3 5     ATG4 Autophagy Related 4 Homolog A2
AUTL21 2 3 5     AUT-Like 2, Cysteine Endopeptidase2
Autophagy-Related Cysteine Endopeptidase 22 3     Autophagin 22
Autophagy-Related Protein 4 Homolog A2 3     autophagin-22
AUT-Like 2 Cysteine Endopeptidase2 3     Cysteine Protease ATG4A2
hAPG4A2 3     Autophagin-23
APG4 Autophagy 4 Homolog A (S. Cerevisiae)1     EC 3.4.22.-3
ATG4 Autophagy Related 4 Homolog A (S. Cerevisiae)1     EC 3.4.228
AUT-Like 2, Cysteine Endopeptidase (S. Cerevisiae)1     

External Ids:    HGNC: 164891   Entrez Gene: 1152012   Ensembl: ENSG000001018447   OMIM: 3006635   UniProtKB: Q8WYN03   

Export aliases for ATG4A gene to outside databases

Previous GC identifers: GC0XP107142 GC0XP107221 GC0XP096957


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for ATG4A Gene:
Autophagy is the process by which endogenous proteins and damaged organelles are destroyed intracellularly.
Autophagy is postulated to be essential for cell homeostasis and cell remodeling during differentiation,
metamorphosis, non-apoptotic cell death, and aging. Reduced levels of autophagy have been described in some
malignant tumors, and a role for autophagy in controlling the unregulated cell growth linked to cancer has been
proposed. This gene encodes a member of the autophagin protein family. The encoded protein is also designated as
a member of the C-54 family of cysteine proteases. Transcript variants that encode distinct isoforms have been
identified. (provided by RefSeq, Jul 2008)

GeneCards Summary for ATG4A Gene:
ATG4A (autophagy related 4A, cysteine peptidase) is a protein-coding gene. Diseases associated with ATG4A include crohn's disease, and malaria. GO annotations related to this gene include cysteine-type peptidase activity. An important paralog of this gene is ATG4C.

UniProtKB/Swiss-Prot: ATG4A_HUMAN, Q8WYN0
Function: Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Cleaves the
C-terminal amino acid of ATG8 family proteins to reveal a C-terminal glycine. Exposure of the glycine at the
C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to
membranes, which is necessary for autophagy. Preferred substrate is GABARAPL2 followed by MAP1LC3A and GABARAP.
Has also an activity of delipidating enzyme for the PE-conjugated forms

Gene Wiki entry for ATG4A Gene


(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:
NC_000023.11  NT_011651.18  NC_018934.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the ATG4A gene promoter:
         Nkx3-1   C/EBPbeta   Nkx2-2   C/EBPalpha   RORalpha1   Nkx6-1   POU2F1   COMP1   POU2F1a   c-Myb   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidATG4A promoter sequence
   Search Chromatin IP Primers for ATG4A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ATG4A


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

Entrez Gene cytogenetic band: Xq22.1-q22.3   Ensembl cytogenetic band:  Xq22.3   HGNC cytogenetic band: Xq22.1-q22.3

ATG4A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ATG4A gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP107334:  view genomic region     (about GC identifiers)

Start:
107,334,898 bp from pter      End:
107,397,901 bp from pter
Size:
63,004 bases      Orientation:
plus 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: ATG4A_HUMAN, Q8WYN0 (See protein sequence)
Recommended Name: Cysteine protease ATG4A  
Size: 398 amino acids; 45378 Da
2 PDB 3D structures from and Proteopedia for ATG4A:
2FUY (3D)        2P82 (3D)    
Secondary accessions: A6NCH2 B2RAZ7 D3DUY0 O95534 Q5JYY9 Q5JYZ0 Q86VE5 Q96KQ0 Q96KQ1
Alternative splicing: 4 isoforms:  Q8WYN0-1   Q8WYN0-2   Q8WYN0-3   Q8WYN0-5   (Gene prediction based on EST data)

Explore the universe of human proteins at neXtProt for ATG4A: NX_Q8WYN0

Explore proteomics data for ATG4A at MOPED

Selected DME Specific Peptides for ATG4A (Q8WYN0) (see all 14)
 WKPLLLI  RLWFTYR  AYYFIGF  EDFEILS 


See ATG4A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_443168.2  NP_840054.1  

ENSEMBL proteins: 
 ENSP00000361306   ENSP00000298131   ENSP00000416218   ENSP00000361320   ENSP00000341833  
 ENSP00000378354   ENSP00000361328   ENSP00000438936  

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Cloud-Clone Corp. CLIAs for ATG4A


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR005078 Peptidase_C54

Graphical View of Domain Structure for InterPro Entry Q8WYN0

ProtoNet protein and cluster: Q8WYN0

UniProtKB/Swiss-Prot: ATG4A_HUMAN, Q8WYN0
Similarity: Belongs to the peptidase C54 family


ATG4A for domains           About GeneDecksing


(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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: ATG4A_HUMAN, Q8WYN0
Function: Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Cleaves the
C-terminal amino acid of ATG8 family proteins to reveal a C-terminal glycine. Exposure of the glycine at the
C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to
membranes, which is necessary for autophagy. Preferred substrate is GABARAPL2 followed by MAP1LC3A and GABARAP.
Has also an activity of delipidating enzyme for the PE-conjugated forms
Enzyme regulation: Inhibited by N-ethylmaleimide. Redox-regulated during autophagy since reducing conditions
activate ATG4A whereas an oxidizing environment such as the presence of H(2)O(2) inhibits its activity
Biophysicochemical properties: Kinetic parameters: KM=33.9 uM for MAP1LC3B; KM=20.8 uM for GABARAP; KM=36.7 uM for
GABARAPL1; KM=15.7 uM for GABARAPL2;

     Enzyme Numbers (IUBMB): EC 3.4.222 EC 3.4.22.-1

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

GO IDQualified GO termEvidencePubMed IDs
GO:0008234cysteine-type peptidase activity IDA12473658
     
ATG4A for ontologies           About GeneDecksing


Phenotypes:
     1 GenomeRNAi human phenotype for ATG4A:
 Synthetic lethal with Ras 

Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for ATG4A
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   genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for ATG4A

miRNA
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miRTarBase miRNAs that target ATG4A:
hsa-mir-877-3p (MIRT036957), hsa-mir-192-5p (MIRT026607), hsa-mir-124-3p (MIRT022814), hsa-mir-215-5p (MIRT024785)

Block miRNA regulation of human, mouse, rat ATG4A using miScript Target Protectors
Selected qRT-PCR Assays for microRNAs that regulate ATG4A (see all 10):
hsa-miR-4264 hsa-miR-3149 hsa-miR-561 hsa-miR-3074-3p hsa-miR-7 hsa-miR-670 hsa-miR-518a-5p hsa-miR-32*
SwitchGear 3'UTR luciferase reporter plasmidATG4A 3' UTR sequence
Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat ATG4A

Gene Editing
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GenScript: all cDNA clones in your preferred vector (see all 2): ATG4A (NM_052936)
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DNA2.0 Custom Codon Optimized Gene Synthesis Service for ATG4A
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat ATG4A

Cell Line
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In Situ Assay
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ATG4A


(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
ATG4A_HUMAN, Q8WYN0: Cytoplasm (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol2
nucleus2
vacuole2
cytoskeleton1
mitochondrion1
peroxisome1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005737cytoplasm ISS12446702

ATG4A for ontologies           About GeneDecksing


(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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SuperPaths for ATG4A About                                                                                                See pathways by source

SuperPathContained pathways About
1Regulation of autophagy
Regulation of autophagy

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways



1 Kegg Pathway  (Kegg details for ATG4A):
    Regulation of autophagy


ATG4A for pathways           About GeneDecksing

    Pathway & Disease-focused RT2 Profiler PCR Array including ATG4A: 
          Autophagy in human mouse rat

Interactions:

    Search GeneGlobe Interaction Network for ATG4A

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

Selected Interacting proteins for ATG4A (Q8WYN02, 3 ENSP000003613064) via UniProtKB, MINT, STRING, and/or I2D (see all 37)
InteractantInteraction Details
GeneCardExternal ID(s)
MAP1LC3BQ9GZQ82, 3, ENSP000002686074MINT-7715703 I2D: score=1 STRING: ENSP00000268607
MAP1LC3AQ9H4923, ENSP000003639704I2D: score=6 STRING: ENSP00000363970
GABARAPL2P605203, ENSP000000372434I2D: score=3 STRING: ENSP00000037243
GABARAPO951663, ENSP000003068664I2D: score=5 STRING: ENSP00000306866
RASSF5Q8WWW03I2D: score=1 
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Gene Ontology (GO): 3 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006508proteolysis IDA12473658
GO:0006914autophagy IEA--
GO:0015031protein transport IEA--

ATG4A for ontologies           About GeneDecksing



(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 ATG4A



(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,
Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for ATG4A gene (3 alternative transcripts): 
NM_052936.3  NM_178270.2  NM_178271.1  

Unigene Cluster for ATG4A:

Autophagy related 4A, cysteine peptidase
Hs.8763  [show with all ESTs]
Unigene Representative Sequence: BC041862
10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000372232(uc004enr.3 uc010npi.3) ENST00000345734(uc004ent.3)
ENST00000457035 ENST00000372246(uc004ens.3 uc011msl.2) ENST00000343524
ENST00000394892 ENST00000474825 ENST00000489247 ENST00000372254 ENST00000545696

miRNA
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Block miRNA regulation of human, mouse, rat ATG4A using miScript Target Protectors
Selected qRT-PCR Assays for microRNAs that regulate ATG4A (see all 10):
hsa-miR-4264 hsa-miR-3149 hsa-miR-561 hsa-miR-3074-3p hsa-miR-7 hsa-miR-670 hsa-miR-518a-5p hsa-miR-32*
SwitchGear 3'UTR luciferase reporter plasmidATG4A 3' UTR sequence
Inhib. RNA
Products:
     
OriGene RNAi products in human, mouse, rat for ATG4A
Predesigned siRNA for gene silencing in human, mouse, rat ATG4A
Clone
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OriGene clones in human, mouse for ATG4A (see all 12)
OriGene ORF clones in mouse, rat for ATG4A
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
GenScript: all cDNA clones in your preferred vector (see all 2): ATG4A (NM_052936)
DNA2.0 Custom Codon Optimized Gene Synthesis Service for ATG4A
Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat ATG4A
Primer
Products:
    
OriGene qPCR primer pairs and template standards for ATG4A
OriGene qSTAR qPCR primer pairs in human, mouse for ATG4A
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat ATG4A
  QuantiTect SYBR Green Assays in human, mouse, rat ATG4A
  QuantiFast Probe-based Assays in human, mouse, rat ATG4A

Additional mRNA sequence: 

AB066214.1 AJ320508.1 AJ320509.1 AJ504651.1 AK054927.1 AK293533.1 AK314429.1 BC041862.1 
BC061696.1 

11 DOTS entries:

DT.92424932  DT.100794490  DT.100794484  DT.415942  DT.100794481  DT.100023367  DT.121291546  DT.91693496 
DT.92424929  DT.92424930  DT.121291534 

Selected AceView cDNA sequences (see all 167):

AI420352 AW070309 AL523527 BU683507 CR599663 AI358986 NM_052936 CK819294 
AJ504651 NM_178271 AA312414 BM541631 BE550136 BU620926 CB126756 AJ320509 
BM985380 AB066214 AJ320508 BM677777 BE348710 BX343291 BX378154 AI925031 

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for ATG4A (see all 9)    About this scheme

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


ECgene alternative splicing isoforms for ATG4A

(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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ATG4A expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CAAAAGCAGC
ATG4A Expression
About this image

ATG4A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

ATG4A Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.8763

UniProtKB/Swiss-Prot: ATG4A_HUMAN, Q8WYN0
Tissue specificity: Widely expressed, at a low level, and the highest expression is observed in skeletal muscle
and brain. Also detected in fetal liver

    Pathway & Disease-focused RT2 Profiler PCR Array including ATG4A: 
          Autophagy in human mouse rat

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OriGene qSTAR qPCR primer pairs in human, mouse for ATG4A
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat ATG4A
QuantiTect SYBR Green Assays in human, mouse, rat ATG4A
QuantiFast Probe-based Assays in human, mouse, rat ATG4A
In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ATG4A

(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 eukaryotes.

Orthologs for ATG4A gene from Selected species (see all 20)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Atg4a1 , 5 autophagy-related 4A (yeast)5
autophagy related 4A, cysteine peptidase1
90.44(n)1
93.15(a)1
  X (61.67 cM)5
6664681  NM_174875.31  NP_777364.31 
 1409569075 
chicken
(Gallus gallus)
Aves ATG4A1 ATG4 autophagy related 4 homolog A (S. cerevisiae) 76.68(n)
81.98(a)
  772074  NM_001271986.1  NP_001258915.1 
lizard
(Anolis carolinensis)
Reptilia ATG4A6
autophagy related 4A, cysteine peptidase
78(a)
1 ↔ 1
GL343202.1(3976535-3986869)
tropical clawed frog
(Xenopus tropicalis)
Amphibia Str.40652 Transcribed sequence with moderate similarity to protein more 80.69(n)    AL846871.2 
zebrafish
(Danio rerio)
Actinopterygii atg4a1 ATG4 autophagy related 4 homolog A (S. cerevisiae) 69.25(n)
75.62(a)
  554140  NM_001024434.1  NP_001019605.1 
fruit fly
(Drosophila melanogaster)
Insecta Atg41 Autophagy-specific gene 4 52.89(n)
46.81(a)
  33283  NM_134719.4  NP_608563.1 
worm
(Caenorhabditis elegans)
Secernentea atg-4.11 atg-4.1 50.38(n)
45.11(a)
  190777  NM_060974.4  NP_493375.2 
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ATG41 ATG4 45.48(n)
33.46(a)
  855498   NP_014176.2 
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G599501 AT3G59950 47.35(n)
40.28(a)
  825165  NM_115858.6  NP_191554.1 
rice
(Oryza sativa)
Liliopsida Os04g06820001 Os04g0682000 46.1(n)
40.19(a)
  4337435  NM_001060828.1  NP_001054293.1 


ENSEMBL Gene Tree for ATG4A (if available)
TreeFam Gene Tree for ATG4A (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for ATG4A gene
ATG4C2  ATG4D2  ATG4B2  
2 SIMAP similar genes for ATG4A using alignment to 5 protein entries:     ATG4A_HUMAN (see all proteins):
ATG4B    ATG4D

ATG4A for paralogs           About GeneDecksing


1 Pseudogenes.org Pseudogene for ATG4A
PGOHUM00000241877


(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 ATG4A (see all 644)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr X posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs356224171,2
C--107323099(+) TTTTT-/T/TT  
        
GCACC
2 -- int10--------
rs1819173631,2
C--107336953(+) TGCCAA/GCATTT 2 -- int10--------
rs1862617521,2
--107337048(+) TTATAA/GTACGG 2 -- int10--------
rs8071831,2
C,F,A,H--107337493(+) tgagaG/Atctaa 2 -- int115Minor allele frequency- A:0.44NS EA NA WA CSA 1775
rs626013791,2
C,F--107337798(+) GAGTAT/CTGGTC 2 -- int11Minor allele frequency- C:0.00NA 2
rs1907295621,2
C--107338186(+) AACTTC/TTATTT 2 -- int10--------
rs1815228531,2
--107338219(+) TCACTC/GTGTCA 2 -- int10--------
rs1857922471,2
--107338294(+) ATTCTC/TCTGCC 2 -- int10--------
rs1113956431,2
F--107338314(+) TGAGGT/CGCATG 2 -- int11Minor allele frequency- C:0.00CSA 1
rs8071841,2
C,F,A--107338552(+) ctagcT/Acaagc 2 -- int13Minor allele frequency- A:0.50NA WA 6

HapMap Linkage Disequilibrium report for ATG4A (107334898 - 107397901 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for ATG4A: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing ATG4A
DNA2.0 Custom Variant and Variant Library Synthesis for ATG4A

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 300663    OMIM disorders: --

2 diseases for ATG4A:    About MalaCards
crohn's disease    malaria


ATG4A for disorders           About GeneDecksing

Genetic Association Database (GAD): ATG4A
Human Genome Epidemiology (HuGE) Navigator: ATG4A (2 documents)

Export disorders for ATG4A 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 ATG4A gene, integrated from 10 sources (see all 18):
(articles sorted by number of sources associating them with ATG4A)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Human autophagins, a family of cysteine proteinases potentially implicated in cell degradation by autophagy. (PubMed id 12446702)1, 2, 3 Marino G....Lopez-Otin C. (J. Biol. Chem. 2003)
  2. The COOH terminus of GATE-16, an intra-Golgi transport modulator, is cleaved by the human cysteine protease HsApg4A. (PubMed id 12473658)1, 2, 3 Scherz-Shouval R.... Elazar Z. (J. Biol. Chem. 2003)
  3. Kinetics comparisons of mammalian Atg4 homologues indicate selective preferences toward diverse Atg8 substrates. (PubMed id 21177865)1, 2 Li M....Yin X.M. (J. Biol. Chem. 2011)
  4. MicroRNA-related genetic variations as predictors for risk of second primary tumor and/or recurrence in patients with early-stage head and neck cancer. (PubMed id 20819778)1, 4 Zhang X....Wu X. (Carcinogenesis 2010)
  5. Reactive oxygen species are essential for autophagy and specifically regulate the activity of Atg4. (PubMed id 17347651)1, 2 Scherz-Shouval R....Elazar Z. (EMBO J. 2007)
  6. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
  7. LC3, GABARAP and GATE16 localize to autophagosomal membrane depending on form-II formation. (PubMed id 15169837)1, 2 Kabeya Y....Yoshimori T. (J. Cell Sci. 2004)
  8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  9. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  10. Autophagy facilitates organelle clearance during differentiation of human erythroblasts: evidence for a role for ATG4 paralogs during autophagosome maturation. (PubMed id 23508006)1 Betin V.M....Lane J.D. (Autophagy 2013)

(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: 115201 HGNC: 16489 AceView: APG4A Ensembl:ENSG00000101844 euGenes: HUgn115201
ECgene: ATG4A Kegg: 115201 H-InvDB: ATG4A

(According to HUGE)
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  --

(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 ATG4A Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for ATG4A Genetics and Cytogenetics in Oncology and Haematology

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for ATG4A gene:
Search GeneIP for patents involving ATG4A

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



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Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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