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Atg4c autophagy related 4C, cysteine peptidase [ Rattus norvegicus (Norway rat) ]

Gene ID: 313391, updated on 18-Sep-2024

Summary

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Official Symbol
Atg4cprovided by RGD
Official Full Name
autophagy related 4C, cysteine peptidaseprovided by RGD
Primary source
RGD:1598323
See related
EnsemblRapid:ENSRNOG00000008767 AllianceGenome:RGD:1598323
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable cysteine-type peptidase activity. Predicted to be involved in proteolysis. Predicted to be located in cytoplasm. Orthologous to human ATG4C (autophagy related 4C cysteine peptidase). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Liver (RPKM 107.0), Brain (RPKM 106.4) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Atg4c in Genome Data Viewer
Location:
5q33
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (118977594..119050894)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (113867218..113935534)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (117861517..117932116)

Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene dedicator of cytokinesis 7 Neighboring gene noelin-like Neighboring gene ribosomal protein L15, pseudogene 14 Neighboring gene cytochrome c oxidase assembly factor 3 homolog, mitochondrial-like Neighboring gene uncharacterized LOC102556219

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Kinetics comparisons of mammalian Atg4 homologues indicate selective preferences toward diverse Atg8 substrates. Li M, et al. J Biol Chem, 2011 Mar 4. PMID 21177865, Free PMC Article
  2. LC3 conjugation system in mammalian autophagy. Tanida I, et al. Int J Biochem Cell Biol, 2004 Dec. PMID 15325588, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cysteine-type endopeptidase activity ISO
Inferred from Sequence Orthology
more info
  
enables cysteine-type peptidase activity ISO
Inferred from Sequence Orthology
more info
  
enables protein-phosphatidylethanolamide deconjugating activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in aggrephagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in autophagosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in autophagosome assembly ISO
Inferred from Sequence Orthology
more info
  
involved_in autophagy ISO
Inferred from Sequence Orthology
more info
  
involved_in biological_process ND
No biological Data available
more info
  
involved_in mitophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in piecemeal microautophagy of the nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein delipidation IEA
Inferred from Electronic Annotation
more info
  
involved_in protein delipidation ISO
Inferred from Sequence Orthology
more info
  
involved_in protein processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in proteolysis ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
cysteine protease ATG4C
Names
ATG4 autophagy related 4 homolog C
autophagy-related 4C
NP_001101418.1
XP_038965839.1
XP_038965840.1
XP_038965841.1
XP_038965842.1
XP_038965843.1
XP_038965844.1
XP_063143722.1

NCBI Reference Sequences (RefSeq)

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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_001107948.1 → NP_001101418.1  cysteine protease ATG4C

    See identical proteins and their annotated locations for NP_001101418.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473998
    UniProtKB/TrEMBL
    A0A8I5ZXZ8, A6JRL6, F1M3M0
    Related
    ENSRNOP00000106807.1, ENSRNOT00000146775.1
    Conserved Domains (1) summary
    pfam03416
    Location:76 → 395
    Peptidase_C54; Peptidase family C54

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086023.1 Reference GRCr8

    Range
    118977594..119050894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039109912.2 → XP_038965840.1  cysteine protease ATG4C isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZXZ8, A6JRL6, F1M3M0
    Conserved Domains (1) summary
    pfam03416
    Location:76 → 395
    Peptidase_C54; Peptidase family C54

  2. XM_039109911.2 → XP_038965839.1  cysteine protease ATG4C isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZXZ8, A6JRL6, F1M3M0
    Related
    ENSRNOP00000011631.8, ENSRNOT00000011631.8
    Conserved Domains (1) summary
    pfam03416
    Location:76 → 395
    Peptidase_C54; Peptidase family C54

  3. XM_039109915.2 → XP_038965843.1  cysteine protease ATG4C isoform X4

    UniProtKB/TrEMBL
    F1M3M0
    Conserved Domains (1) summary
    pfam03416
    Location:76 → 343
    Peptidase_C54; Peptidase family C54

  4. XM_039109913.2 → XP_038965841.1  cysteine protease ATG4C isoform X2

    UniProtKB/TrEMBL
    A0A8I5Y0E2, A0A8I6AKI4
    Related
    ENSRNOP00000076527.1, ENSRNOT00000104305.2
    Conserved Domains (1) summary
    pfam03416
    Location:48 → 367
    Peptidase_C54; Peptidase family C54

  5. XM_039109914.2 → XP_038965842.1  cysteine protease ATG4C isoform X3

    UniProtKB/TrEMBL
    F1M3M0
    Related
    ENSRNOP00000084390.2, ENSRNOT00000116538.2
    Conserved Domains (1) summary
    pfam03416
    Location:76 → 395
    Peptidase_C54; Peptidase family C54

  6. XM_063287652.1 → XP_063143722.1  cysteine protease ATG4C isoform X5

  7. XM_039109916.2 → XP_038965844.1  cysteine protease ATG4C isoform X5

    Conserved Domains (1) summary
    pfam03416
    Location:76 → 315
    Peptidase_C54; Peptidase family C54
Nucleotide Protein Strain
Heading Accession and Version

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