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atg4b autophagy related 4B, cysteine peptidase [ Danio rerio (zebrafish) ]

Gene ID: 448859, updated on 27-Mar-2024

Summary

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Official Symbol
atg4bprovided by ZNC
Official Full Name
autophagy related 4B, cysteine peptidaseprovided by ZNC
Primary source
ZFIN:ZDB-GENE-040917-3
See related
Ensembl:ENSDARG00000052104 AllianceGenome:ZFIN:ZDB-GENE-040917-3
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
apg4b
Summary
Predicted to enable cysteine-type endopeptidase activity. Predicted to act upstream of or within autophagy; protein transport; and proteolysis. Predicted to be located in cytoplasm. Is expressed in brain; liver; and muscle. Orthologous to human ATG4B (autophagy related 4B cysteine peptidase). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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See atg4b in Genome Data Viewer
Location:
chromosome: 6
Exon count:
14
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 6 NC_007117.7 (27090859..27105007)
105 previous assembly GRCz10 (GCF_000002035.5) 6 NC_007117.6 (27100298..27114446)

Chromosome 6 - NC_007117.7Genomic Context describing neighboring genes Neighboring gene serine/threonine kinase 25a Neighboring gene BCL2 family apoptosis regulator BOK a Neighboring gene deoxythymidylate kinase (thymidylate kinase) Neighboring gene alanine--glyoxylate and serine--pyruvate aminotransferase a Neighboring gene zgc:103559

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Glycogen storage in a zebrafish Pompe disease model is reduced by 3-BrPA treatment. Bragato C, et al. Biochim Biophys Acta Mol Basis Dis, 2020 May 1. PMID 31917327
  2. Distribution of H3K27me3, H3K9me3, and H3K4me3 along autophagy-related genes highly expressed in starved zebrafish myotubes. Biga PR, et al. Biol Open, 2017 Nov 15. PMID 29025701, Free PMC Article
  3. Fructose leads to hepatic steatosis in zebrafish that is reversed by mechanistic target of rapamycin (mTOR) inhibition. Sapp V, et al. Hepatology, 2014 Nov. PMID 25043405
  4. Intracellular Insulin and Impaired Autophagy in a Zebrafish model and a Cell Model of Type 2 diabetes. Meng XH, et al. Int J Biol Sci, 2017. PMID 28924380, Free PMC Article
  5. Postprandial regulation of growth- and metabolism-related factors in zebrafish. Seiliez I, et al. Zebrafish, 2013 Jun. PMID 23659367, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cysteine-type endopeptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables cysteine-type peptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables peptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein-phosphatidylethanolamide deconjugating activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein-phosphatidylethanolamide deconjugating activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in C-terminal protein lipidation IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  
acts_upstream_of_or_within autophagy IEA
Inferred from Electronic Annotation
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein processing IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within protein transport IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within proteolysis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in autophagosome IEA
Inferred from Electronic Annotation
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
cysteine protease ATG4B
Names
APG4 autophagy 4 homolog B
ATG4 autophagy related 4 homolog B
autophagy-related protein 4 homolog B
NP_001082821.1
XP_005165980.1
XP_017211960.1

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_001089352.1 → NP_001082821.1  cysteine protease ATG4B

    See identical proteins and their annotated locations for NP_001082821.1

    Status: PROVISIONAL

    Source sequence(s)
    BC134886
    UniProtKB/Swiss-Prot
    Q6DG88
    UniProtKB/TrEMBL
    A4QN52
    Related
    ENSDARP00000106508.1, ENSDART00000121558.4
    Conserved Domains (1) summary
    pfam03416
    Location:40 → 337
    Peptidase_C54; Peptidase family C54

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007117.7 Reference GRCz11 Primary Assembly

    Range
    27090859..27105007
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017356471.2 → XP_017211960.1  cysteine protease ATG4B isoform X2

    UniProtKB/Swiss-Prot
    Q6DG88
    UniProtKB/TrEMBL
    A0A8M6YZJ8

  2. XM_005165923.3 → XP_005165980.1  cysteine protease ATG4B isoform X1

    UniProtKB/Swiss-Prot
    Q6DG88
    UniProtKB/TrEMBL
    A0A8M2BD94
    Conserved Domains (1) summary
    pfam03416
    Location:70 → 367
    Peptidase_C54; Peptidase family C54

RNA

  1. XR_002458998.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6DG88.2 GenPept UniProtKB/Swiss-Prot:Q6DG88

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