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ATG4B Gene

protein-coding   GIFtS: 60
GCID: GC02P242578

Autophagy Related 4B, Cysteine Peptidase

(Previous names: APG4 autophagy 4 homolog B (S. cerevisiae), ATG4 autophagy...)
(Previous symbol: APG4B)
  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 4B, Cysteine Peptidase1 2     APG4 Autophagy 4 Homolog B2
APG4B1 2 3     ATG4 Autophagy Related 4 Homolog B2
Autophagy-Related Cysteine Endopeptidase 12 3     autophagin-12
Autophagy-Related Protein 4 Homolog B2 3     Cysteine Protease ATG4B2
AUTL12 3     Autophagin-13
AUT-Like 1 Cysteine Endopeptidase2 3     EC 3.4.22.-3
hAPG4B2 3     KIAA09433
APG4 Autophagy 4 Homolog B (S. Cerevisiae)1     EC 3.4.228
ATG4 Autophagy Related 4 Homolog B (S. Cerevisiae)1     

External Ids:    HGNC: 207901   Entrez Gene: 231922   Ensembl: ENSG000001683977   OMIM: 6113385   UniProtKB: Q9Y4P13   

Export aliases for ATG4B gene to outside databases

Previous GC identifers: GC02P242297 GC02P242225 GC02P234345


(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 ATG4B 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. Alternate transcriptional splice variants, encoding different
isoforms, have been characterized. (provided by RefSeq, Jul 2008)

GeneCards Summary for ATG4B Gene:
ATG4B (autophagy related 4B, cysteine peptidase) is a protein-coding gene. Diseases associated with ATG4B include prostate cancer, and prostatitis. GO annotations related to this gene include endopeptidase activity and cysteine-type peptidase activity. An important paralog of this gene is ATG4C.

UniProtKB/Swiss-Prot: ATG4B_HUMAN, Q9Y4P1
Function: Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Cleaves the
C-terminal amino acid of ATG8 family proteins MAP1LC3, GABARAPL1, GABARAPL2 and GABARAP, 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. Has also an activity
of delipidating enzyme for the PE-conjugated forms

Gene Wiki entry for ATG4B 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_000002.12  NT_005403.18  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the ATG4B gene promoter:
         Pax-6   YY1   GATA-1   RORalpha1   MEF-2A   SRY   E2F-1   E2F   HOXA5   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidATG4B promoter sequence
   Search Chromatin IP Primers for ATG4B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ATG4B


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

Entrez Gene cytogenetic band: 2q37.3   Ensembl cytogenetic band:  2q37.3   HGNC cytogenetic band: 2q37.3

ATG4B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ATG4B gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P242578:  view genomic region     (about GC identifiers)

Start:
242,576,628 bp from pter      End:
242,613,272 bp from pter
Size:
36,645 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: ATG4B_HUMAN, Q9Y4P1 (See protein sequence)
Recommended Name: Cysteine protease ATG4B  
Size: 393 amino acids; 44294 Da
Sequence caution: Sequence=BAA76787.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Sequence=BAC86110.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
5 PDB 3D structures from and Proteopedia for ATG4B:
2CY7 (3D)        2D1I (3D)        2Z0D (3D)        2Z0E (3D)        2ZZP (3D)    
Secondary accessions: B7WNK2 Q53NU4 Q6ZUV8 Q8WYM9 Q96K07 Q96K96 Q96SZ1 Q9Y2F2
Alternative splicing: 5 isoforms:  Q9Y4P1-1   Q9Y4P1-2   Q9Y4P1-3   Q9Y4P1-4   Q9Y4P1-6   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ATG4B: NX_Q9Y4P1

Explore proteomics data for ATG4B at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for ATG4B (Q9Y4P1) (see all 9)
     EDFEILS  RLWFTYR  LDPHTTQ  RFFDSEDE 


    See ATG4B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_037457.3  NP_847896.1  

    ENSEMBL proteins: 
     ENSP00000383964   ENSP00000384661   ENSP00000384259   ENSP00000383583   ENSP00000400050  
     ENSP00000409895   ENSP00000390597   ENSP00000383582   ENSP00000407389   ENSP00000344960  
     ENSP00000410526   ENSP00000404783   ENSP00000442378   ENSP00000379692  

    ATG4B Human Recombinant Protein Products:

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    Cloud-Clone Corp. CLIAs for ATG4B


    (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 Q9Y4P1

    ProtoNet protein and cluster: Q9Y4P1

    UniProtKB/Swiss-Prot: ATG4B_HUMAN, Q9Y4P1
    Similarity: Belongs to the peptidase C54 family


    ATG4B 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: ATG4B_HUMAN, Q9Y4P1
    Function: Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Cleaves the
    C-terminal amino acid of ATG8 family proteins MAP1LC3, GABARAPL1, GABARAPL2 and GABARAP, 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. 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=5.1 uM for MAP1LC3B; KM=5.8 uM for GABARAP; KM=4.4 uM for
    GABARAPL1; KM=6.1 uM for GABARAPL2;

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

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004175endopeptidase activity IDA18387192
    GO:0005515protein binding IPI15187094
    GO:0008233peptidase activity ----
    GO:0008234cysteine-type peptidase activity IDA15169837
         
    ATG4B for ontologies           About GeneDecksing


    Phenotypes:
         6 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Atg4b):
     behavior/neurological  cellular  hearing/vestibular/ear  homeostasis/metabolism  mortality/aging 
     nervous system 

    ATG4B for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for ATG4B
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for ATG4B
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for ATG4B

    miRNA
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    miRTarBase miRNAs that target ATG4B:
    hsa-let-7b-5p (MIRT032363)

    Block miRNA regulation of human, mouse, rat ATG4B using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate ATG4B (see all 26):
    hsa-miR-185* hsa-let-7d hsa-miR-3653 hsa-let-7c hsa-miR-1285 hsa-miR-449a hsa-let-7g hsa-miR-3658
    SwitchGear 3'UTR luciferase reporter plasmidATG4B 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat ATG4B

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    GenScript: all cDNA clones in your preferred vector (see all 2): ATG4B (NM_178326)
    Sino Biological Human cDNA Clone for ATG4B
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    (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
    ATG4B_HUMAN, Q9Y4P1: Cytoplasm (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    vacuole2
    cytoskeleton1
    extracellular1
    lysosome1
    nucleus1
    peroxisome1
    plasma membrane1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm ISS12446702

    ATG4B 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 ATG4B 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 ATG4B):
        Regulation of autophagy


    ATG4B for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including ATG4B: 
              Autophagy in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for ATG4B

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

    Selected Interacting proteins for ATG4B (Q9Y4P11, 2, 3 ENSP000003842594) via UniProtKB, MINT, STRING, and/or I2D (see all 221)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000212866P081073I2D: score=1 
    ENSG00000215328P081073I2D: score=1 
    ENSG00000224501P081073I2D: score=1 
    ENSG00000231555P081073I2D: score=1 
    ENSG00000232804P081073I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000045autophagic vacuole assembly IGI12446702
    GO:0006508proteolysis IDA15169837
    GO:0006914autophagy IGI12446702
    GO:0010508positive regulation of autophagy IDA18387192
    GO:0015031protein transport IEA--

    ATG4B 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 ATG4B



    (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 ATG4B gene (2 alternative transcripts): 
    NM_013325.4  NM_178326.2  

    Unigene Cluster for ATG4B:

    Autophagy related 4B, cysteine peptidase
    Hs.283610  [show with all ESTs]
    Unigene Representative Sequence: AK125277
    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 27):
    ENST00000405546(uc002wbw.3 uc010fzp.3) ENST00000402096 ENST00000404914(uc002wbv.3 uc010zox.2 uc010zoy.2 uc010zoz.2)
    ENST00000491867 ENST00000400772 ENST00000494465 ENST00000483778 ENST00000479554
    ENST00000475195 ENST00000419606 ENST00000465399 ENST00000468018 ENST00000482507(uc002wbu.3)
    ENST00000493618 ENST00000425239 ENST00000415107 ENST00000400771 ENST00000430617

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate ATG4B (see all 26):
    hsa-miR-185* hsa-let-7d hsa-miR-3653 hsa-let-7c hsa-miR-1285 hsa-miR-449a hsa-let-7g hsa-miR-3658
    SwitchGear 3'UTR luciferase reporter plasmidATG4B 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector (see all 2): ATG4B (NM_178326)
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      QuantiTect SYBR Green Assays in human, mouse, rat ATG4B
      QuantiFast Probe-based Assays in human, mouse, rat ATG4B

    Additional mRNA sequence: 

    AB066215.1 AJ504652.1 AK027332.1 AK027462.1 AK027763.1 AK125277.1 AK296818.1 AK298109.1 
    AK302963.1 AK316167.1 AL050288.1 AL080168.1 AL133638.1 BC000719.2 BX648007.1 

    Selected DOTS entries (see all 33):

    DT.100806180  DT.100852458  DT.100770594  DT.452866  DT.100852464  DT.100852460  DT.99989778  DT.100852471 
    DT.87002224  DT.102830339  DT.120930192  DT.40133226  DT.91832275  DT.100852454  DT.120930132  DT.120930182 
    DT.97778464  DT.120930201  DT.91665530  DT.95328398  DT.100641019  DT.100852455  DT.120930167  DT.95188813 

    Selected AceView cDNA sequences (see all 472):

    BF061979 BU182476 CR617577 BF034300 CR605500 BX401153 BX398978 AI364141 
    AL540213 AI919218 CR605379 AI284039 AI694405 BQ072451 BE396343 BE220298 
    CR610655 BQ716661 BM451574 AW090753 CR616109 Z40448 BX344005 AL524899 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for ATG4B (see all 16)    About this scheme

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

    ExUns: 13a · 13b · 13c · 13d · 13e ^ 14a · 14b · 14c
    SP1:                    -     -                     
    SP2:              -     -     -                     
    SP3:                          -                     
    SP4:                                                
    SP5:                                                


    ECgene alternative splicing isoforms for ATG4B

    (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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    ATG4B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTGCGCCGCT
    ATG4B Expression
    About this image

    ATG4B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ATG4B Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.283610

    UniProtKB/Swiss-Prot: ATG4B_HUMAN, Q9Y4P1
    Tissue specificity: Mainly expressed in the skeletal muscle, followed by brain, heart, liver and pancreas

        Pathway & Disease-focused RT2 Profiler PCR Array including ATG4B: 
              Autophagy in human mouse rat

    Primer
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    In Situ
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    (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 animals and fungi.

    Orthologs for ATG4B gene from Selected species (see all 20)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Atg4b1 , 5 autophagy-related 4B (yeast)5
    autophagy related 4B, cysteine peptidase1
    87.62(n)1
    94.66(a)1
      1 (47.32 cM)5
    666151  NM_174874.31  NP_777363.11 
     937515005 
    chicken
    (Gallus gallus)
    Aves ATG4B1 ATG4 autophagy related 4 homolog B (S. cerevisiae) 78.49(n)
    85.71(a)
      404750  NM_213573.1  NP_998738.1 
    lizard
    (Anolis carolinensis)
    Reptilia ATG4B6
    autophagy related 4B, cysteine peptidase
    86(a)
    1 ↔ 1
    3(30535140-30557980)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.143622 Xenopus laevis transcribed sequence with moderate similarity more 75.4(n)    BU908586.1 
    zebrafish
    (Danio rerio)
    Actinopterygii atg4b1 ATG4 autophagy related 4 homolog B (S. cerevisiae) 69.64(n)
    73.98(a)
      448859  NM_001089352.1  NP_001082821.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Atg46
    Autophagy-specific gene 4
    39(a)
    1 → many
    2L(1080911-1083378)
    worm
    (Caenorhabditis elegans)
    Secernentea atg-4.16
    Protein ATG-4.1, isoform b (atg-4.1) mRNA, complet...
    32(a)
    1 → many
    I(13536966-13542413) WBGene00013595
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes ATG46
    Conserved cysteine protease required for autophagy...
    20(a)
    1 → many
    XIV(227370-228854) YNL223W


    ENSEMBL Gene Tree for ATG4B (if available)
    TreeFam Gene Tree for ATG4B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ATG4B gene
    ATG4C2  ATG4A2  ATG4D2  
    3 SIMAP similar genes for ATG4B using alignment to 11 protein entries:     ATG4B_HUMAN (see all proteins):
    DKFZp686G0859    ATG4A    ATG4D

    ATG4B for paralogs           About GeneDecksing



    (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 ATG4B (see all 954)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs346185341,2
    C,F--242578750(+) AGGGGT/GTGTTG 2 -- int17Minor allele frequency- G:0.29NA CSA 14
    rs1383633601,2
    --242578801(+) AGGCTA/CTAGCT 2 -- int10--------
    rs1427647201,2
    C--242578887(+) TTTGCC/TGGCAG 2 -- int10--------
    rs1882095031,2
    --242578933(+) ACTTGC/GATTCA 2 -- int10--------
    rs1820873241,2
    --242578987(+) ACACTA/TAACAC 2 -- int10--------
    rs1506165481,2
    --242579135(+) ATAGGC/TTCAGA 2 -- int10--------
    rs1864200111,2
    --242579147(+) TGGGGA/TGTGTG 2 -- int10--------
    rs1902342641,2
    --242579268(+) GTGAAA/GGGTGG 2 -- int10--------
    rs782087361,2
    C--242579275(+) GTGGGG/TATTAA 2 -- int11Minor allele frequency- T:0.50CSA 2
    rs1499615411,2
    --242579324(+) ATCCAA/GTCTGT 2 -- int10--------

    HapMap Linkage Disequilibrium report for ATG4B (242576628 - 242613272 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for ATG4B (see all 13):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2722016CNV Deletion23290073
    esv2722014CNV Deletion23290073
    esv2722015CNV Deletion23290073
    nsv508901CNV Insertion20534489
    dgv4495n71CNV Loss21882294
    dgv4493n71CNV Loss21882294
    dgv4494n71CNV Loss21882294
    dgv4496n71CNV Loss21882294
    nsv876229CNV Loss21882294
    nsv876242CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
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    (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: 611338    OMIM disorders: --

    2 diseases for ATG4B:    
    About MalaCards
    prostate cancer    prostatitis


    ATG4B for disorders           About GeneDecksing


    Export disorders for ATG4B 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 ATG4B gene, integrated from 10 sources (see all 48):
    (articles sorted by number of sources associating them with ATG4B)
        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, 9 Marino G....Lopez-Otin C. (J. Biol. Chem. 2003)
    2. HsAtg4B/HsApg4B/autophagin-1 cleaves the carboxyl termini of three human Atg8 homologues and delipidates microtubule-associated protein light chain 3- and GABAA receptor-associated protein-phospholipid conjugates. (PubMed id 15187094)1, 2, 9 Tanida I....Kominami E. (J. Biol. Chem. 2004)
    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. The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy. (PubMed id 19322194)1, 2 Satoo K....Inagaki F. (EMBO J. 2009)
    5. The crystal structure of human Atg4b, a processing and de-conjugating enzyme for autophagosome-forming modifiers. (PubMed id 16325851)1, 2 Kumanomidou T.... Yamane T. (J. Mol. Biol. 2006)
    6. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    7. Structural basis for the specificity and catalysis of human Atg4B responsible for mammalian autophagy. (PubMed id 16183633)1, 2 Sugawara K....Inagaki F. (J. Biol. Chem. 2005)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    9. 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)
    10. 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)

    (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: 23192 HGNC: 20790 AceView: APG4B.1 Ensembl:ENSG00000168397 euGenes: HUgn23192
    ECgene: ATG4B Kegg: 23192 H-InvDB: ATG4B

    (According to HUGE)
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    HUGE: KIAA0943

    (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 ATG4B Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for ATG4B 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 ATG4B gene:
    Search GeneIP for patents involving ATG4B

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



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