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ATG4D autophagy related 4D cysteine peptidase [ Homo sapiens (human) ]

Gene ID: 84971, updated on 13-Mar-2020

Summary

Official Symbol
ATG4Dprovided by HGNC
Official Full Name
autophagy related 4D cysteine peptidaseprovided by HGNC
Primary source
HGNC:HGNC:20789
See related
Ensembl:ENSG00000130734 MIM:611340
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
APG4D; AUTL4; APG4-D
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 belongs to the autophagy-related protein 4 (Atg4) family of C54 endopeptidases. Members of this family encode proteins that play a role in the biogenesis of autophagosomes, which sequester the cytosol and organelles for degradation by lysosomes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
Expression
Broad expression in testis (RPKM 21.1), duodenum (RPKM 13.4) and 25 other tissues See more
Orthologs

Genomic context

See ATG4D in Genome Data Viewer
Location:
19p13.2
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (10543897..10553418)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (10654570..10664099)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene kelch like ECH associated protein 1 Neighboring gene sphingosine-1-phosphate receptor 5 Neighboring gene RNA, U7 small nuclear 140 pseudogene Neighboring gene microRNA 1238 Neighboring gene KRI1 homolog Neighboring gene cyclin dependent kinase inhibitor 2D Neighboring gene adaptor related protein complex 1 subunit mu 2

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 Functions

What'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

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 peptidase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
autophagy IEA
Inferred from Electronic Annotation
more info
 
protein transport IEA
Inferred from Electronic Annotation
more info
 
proteolysis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
mitochondrial matrix IEA
Inferred from Electronic Annotation
more info
 
mitochondrion IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
cysteine protease ATG4D
Names
APG4 autophagy 4 homolog D
ATG4 autophagy related 4 homolog D
AUT-like 4 cysteine endopeptidase
autophagin-4
autophagy-related cysteine endopeptidase 4
autophagy-related protein 4 homolog D
cysteine protease involved in autophagy

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_001281504.2NP_001268433.1  cysteine protease ATG4D isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 2, which has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK294676, BC068992
    UniProtKB/Swiss-Prot
    Q86TL0
    UniProtKB/TrEMBL
    B4DGM8
    Conserved Domains (1) summary
    pfam03416
    Location:47348
    Peptidase_C54; Peptidase family C54
  2. NM_032885.6NP_116274.3  cysteine protease ATG4D isoform 1 precursor

    See identical proteins and their annotated locations for NP_116274.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    BC068992, HY063028
    Consensus CDS
    CCDS12241.1
    UniProtKB/Swiss-Prot
    Q86TL0
    Related
    ENSP00000311318.3, ENST00000309469.9
    Conserved Domains (1) summary
    pfam03416
    Location:110411
    Peptidase_C54; Peptidase family C54

RNA

  1. NR_104024.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK056210, AK314712, BC007639, HY063028
    Related
    ENST00000588857.5
  2. NR_104025.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC007639, HY063028
    Related
    ENST00000588667.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    10543897..10553418
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006722927.1XP_006722990.1  cysteine protease ATG4D isoform X1

    See identical proteins and their annotated locations for XP_006722990.1

    Conserved Domains (1) summary
    pfam03416
    Location:110297
    Peptidase_C54; Peptidase family C54
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