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ATG4A autophagy related 4A cysteine peptidase [ Homo sapiens (human) ]

Gene ID: 115201, updated on 22-Dec-2018

Summary

Official Symbol
ATG4Aprovided by HGNC
Official Full Name
autophagy related 4A cysteine peptidaseprovided by HGNC
Primary source
HGNC:HGNC:16489
See related
Ensembl:ENSG00000101844 MIM:300663
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
APG4A; AUTL2
Summary
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. [provided by RefSeq, Mar 2016]
Expression
Ubiquitous expression in thyroid (RPKM 5.4), colon (RPKM 5.0) and 25 other tissues See more
Orthologs

Genomic context

See ATG4A in Genome Data Viewer
Location:
Xq22.3
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) X NC_000023.11 (108091667..108154671)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (107334899..107397901)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene V-set and immunoglobulin domain containing 1 Neighboring gene proteasome 26S subunit, non-ATPase 10 Neighboring gene collagen type IV alpha 6 chain Neighboring gene collagen type IV alpha 5 chain

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vif vif HIV-1 Vif binds more strongly to autophagy-related protein 4 (ATG4)-cleaved form I (LC3-I) than to ATG4-cleaved form II (LC3-II) in an A3G-independent manner PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Autophagy - animal, organism-specific biosystem (from KEGG)
    Autophagy - animal, organism-specific biosystemAutophagy (or macroautophagy) is a cellular catabolic pathway involving in protein degradation, organelle turnover, and non-selective breakdown of cytoplasmic components, which is evolutionarily cons...
  • Autophagy - animal, conserved biosystem (from KEGG)
    Autophagy - animal, conserved biosystemAutophagy (or macroautophagy) is a cellular catabolic pathway involving in protein degradation, organelle turnover, and non-selective breakdown of cytoplasmic components, which is evolutionarily cons...
  • Autophagy - other, organism-specific biosystem (from KEGG)
    Autophagy - other, organism-specific biosystemAutophagy is a degradative pathway for the removal of cytoplasmic materials in eukaryotic cells, and is characterized by the formation of a double-membrane structure called the autophagosome, either ...
  • Autophagy - other, conserved biosystem (from KEGG)
    Autophagy - other, conserved biosystemAutophagy is a degradative pathway for the removal of cytoplasmic materials in eukaryotic cells, and is characterized by the formation of a double-membrane structure called the autophagosome, either ...
  • Cellular responses to stress, organism-specific biosystem (from REACTOME)
    Cellular responses to stress, organism-specific biosystemCells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissu...
  • Macroautophagy, organism-specific biosystem (from REACTOME)
    Macroautophagy, organism-specific biosystemMacroautophagy (hereafter referred to as autophagy) acts as a buffer against starvation by liberating building materials and energy sources from cellular components. It has additional roles in embryo...
  • Nanoparticle triggered autophagic cell death, organism-specific biosystem (from WikiPathways)
    Nanoparticle triggered autophagic cell death, organism-specific biosystemProgrammed cell death: autophagic cell death. Autophagy (self-eating) is a survival mechanism deployed by cells to cope with conditions of nutrient deprivation. However, unrestrained autophagy can re...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cysteine-type peptidase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
autophagosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein delipidation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein transport IEA
Inferred from Electronic Annotation
more info
 
proteolysis IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 

General protein information

Preferred Names
cysteine protease ATG4A
Names
APG4 autophagy 4 homolog A
ATG4 autophagy related 4 homolog A
AUT-like 2, cysteine endopeptidase
autophagin 2
autophagy-related cysteine endopeptidase 2
autophagy-related protein 4 homolog A
hAPG4A
NP_001308216.1
NP_001308217.1
NP_001308218.1
NP_001308219.1
NP_443168.2
NP_840054.1
NP_840055.1
XP_011529144.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001321287.1NP_001308216.1  cysteine protease ATG4A isoform c

    Status: REVIEWED

    Source sequence(s)
    AL031177
    UniProtKB/Swiss-Prot
    Q8WYN0
    Conserved Domains (1) summary
    pfam03416
    Location:1258
    Peptidase_C54; Peptidase family C54
  2. NM_001321288.1NP_001308217.1  cysteine protease ATG4A isoform c

    Status: REVIEWED

    Source sequence(s)
    AL031177
    UniProtKB/Swiss-Prot
    Q8WYN0
    Conserved Domains (1) summary
    pfam03416
    Location:1258
    Peptidase_C54; Peptidase family C54
  3. NM_001321289.1NP_001308218.1  cysteine protease ATG4A isoform d

    Status: REVIEWED

    Source sequence(s)
    AA648264, AK293533, AL031177, BC041862, BC061696
    UniProtKB/Swiss-Prot
    Q8WYN0
    UniProtKB/TrEMBL
    B4DEA4
    Conserved Domains (1) summary
    pfam03416
    Location:1196
    Peptidase_C54; Peptidase family C54
  4. NM_001321290.1NP_001308219.1  cysteine protease ATG4A isoform e

    Status: REVIEWED

    Source sequence(s)
    AL031177
    Conserved Domains (1) summary
    pfam03416
    Location:1163
    Peptidase_C54; Peptidase family C54
  5. NM_052936.5NP_443168.2  cysteine protease ATG4A isoform a

    See identical proteins and their annotated locations for NP_443168.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform (a).
    Source sequence(s)
    AA648264, BC041862, BC061696
    Consensus CDS
    CCDS14538.1
    UniProtKB/Swiss-Prot
    Q8WYN0
    Related
    ENSP00000361306.3, ENST00000372232.7
    Conserved Domains (1) summary
    pfam03416
    Location:43335
    Peptidase_C54; Peptidase family C54
  6. NM_178270.3NP_840054.1  cysteine protease ATG4A isoform b

    See identical proteins and their annotated locations for NP_840054.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes isoform b.
    Source sequence(s)
    AA648264, AJ320509, BC041862, BC061696
    Consensus CDS
    CCDS14539.1
    UniProtKB/Swiss-Prot
    Q8WYN0
    Related
    ENSP00000298131.5, ENST00000345734.7
    Conserved Domains (1) summary
    pfam03416
    Location:43273
    Peptidase_C54; Peptidase family C54
  7. NM_178271.2NP_840055.1  cysteine protease ATG4A isoform c

    Status: REVIEWED

    Source sequence(s)
    AA648264, BC041862, BC061696, BM541631
    UniProtKB/Swiss-Prot
    Q8WYN0
    Conserved Domains (1) summary
    pfam03416
    Location:1258
    Peptidase_C54; Peptidase family C54

RNA

  1. NR_135608.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL031177
    Related
    ENST00000343524.9

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p12 Primary Assembly

    Range
    108091667..108154671
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011530842.1XP_011529144.1  cysteine protease ATG4A isoform X1

    See identical proteins and their annotated locations for XP_011529144.1

    UniProtKB/Swiss-Prot
    Q8WYN0
    Conserved Domains (1) summary
    pfam03416
    Location:1258
    Peptidase_C54; Peptidase family C54
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