LOCUS       NM_013325               2797 bp    mRNA    linear   PRI 05-DEC-2024
DEFINITION  Homo sapiens autophagy related 4B cysteine peptidase (ATG4B),
            transcript variant 1, mRNA.
ACCESSION   NM_013325
VERSION     NM_013325.5
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2797)
  AUTHORS   Torres,P., Rico-Rios,S., Ceron-Codorniu,M., Santacreu-Vilaseca,M.,
            Seoane-Miraz,D., Jad,Y., Ayala,V., Marino,G., Beltran,M.,
            Miralles,M.P., Andres-Benito,P., Fernandez-Irigoyen,J.,
            Santamaria,E., Lopez-Otin,C., Soler,R.M., Povedano,M., Ferrer,I.,
            Pamplona,R., Wood,M.J.A., Varela,M.A. and Portero-Otin,M.
  TITLE     TDP-43 regulates LC3ylation in neural tissue through ATG4B cryptic
            splicing inhibition
  JOURNAL   Acta Neuropathol 148 (1), 45 (2024)
   PUBMED   39305312
  REMARK    GeneRIF: TDP-43 regulates LC3ylation in neural tissue through ATG4B
            cryptic splicing inhibition.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2797)
  AUTHORS   Zhang,N., Shen,M.Y., Meng,Q.L., Sun,H.P., Fan,F.Y., Yi,H. and
            Yang,Y.J.
  TITLE     FAT1 inhibits AML autophagy and proliferation via downregulating
            ATG4B expression
  JOURNAL   Biochim Biophys Acta Gen Subj 1868 (1), 130519 (2024)
   PUBMED   37952564
  REMARK    GeneRIF: FAT1 inhibits AML autophagy and proliferation via
            downregulating ATG4B expression.
REFERENCE   3  (bases 1 to 2797)
  AUTHORS   Xie,W., Zhang,C., Wang,Z., Chen,H., Gu,T., Zhou,T., Wu,Y., Xia,F.,
            Li,M., Wang,J., Jiao,R., Cui,J. and Jin,S.
  TITLE     ATG4B antagonizes antiviral immunity by GABARAP-directed autophagic
            degradation of TBK1
  JOURNAL   Autophagy 19 (11), 2853-2868 (2023)
   PUBMED   37434364
  REMARK    GeneRIF: ATG4B antagonizes antiviral immunity by GABARAP-directed
            autophagic degradation of TBK1.
REFERENCE   4  (bases 1 to 2797)
  AUTHORS   Sathiyaseelan,P., Chittaranjan,S., Kalloger,S.E., Chan,J., Go,N.E.,
            Jardon,M.A., Ho,C.J., Hui,T., Xu,J., Chow,C., Gao,D., Johnson,F.D.,
            Lockwood,W.W., Morin,G.B., Renouf,D.J., Schaeffer,D.F. and
            Gorski,S.M.
  TITLE     Loss of ATG4B and ATG4A results in two-stage cell cycle defects in
            pancreatic ductal adenocarcinoma cells
  JOURNAL   J Cell Sci 136 (19) (2023)
   PUBMED   37701987
  REMARK    GeneRIF: Loss of ATG4B and ATG4A results in two-stage cell cycle
            defects in pancreatic ductal adenocarcinoma cells.
REFERENCE   5  (bases 1 to 2797)
  AUTHORS   Cho,N.H., Cheveralls,K.C., Brunner,A.D., Kim,K., Michaelis,A.C.,
            Raghavan,P., Kobayashi,H., Savy,L., Li,J.Y., Canaj,H., Kim,J.Y.S.,
            Stewart,E.M., Gnann,C., McCarthy,F., Cabrera,J.P., Brunetti,R.M.,
            Chhun,B.B., Dingle,G., Hein,M.Y., Huang,B., Mehta,S.B.,
            Weissman,J.S., Gomez-Sjoberg,R., Itzhak,D.N., Royer,L.A., Mann,M.
            and Leonetti,M.D.
  TITLE     OpenCell: Endogenous tagging for the cartography of human cellular
            organization
  JOURNAL   Science 375 (6585), eabi6983 (2022)
   PUBMED   35271311
REFERENCE   6  (bases 1 to 2797)
  AUTHORS   Sugawara,K., Suzuki,N.N., Fujioka,Y., Mizushima,N., Ohsumi,Y. and
            Inagaki,F.
  TITLE     Structural basis for the specificity and catalysis of human Atg4B
            responsible for mammalian autophagy
  JOURNAL   J Biol Chem 280 (48), 40058-40065 (2005)
   PUBMED   16183633
  REMARK    GeneRIF: analysis of specificity and catalysis of HsAtg4B
REFERENCE   7  (bases 1 to 2797)
  AUTHORS   Stelzl,U., Worm,U., Lalowski,M., Haenig,C., Brembeck,F.H.,
            Goehler,H., Stroedicke,M., Zenkner,M., Schoenherr,A., Koeppen,S.,
            Timm,J., Mintzlaff,S., Abraham,C., Bock,N., Kietzmann,S.,
            Goedde,A., Toksoz,E., Droege,A., Krobitsch,S., Korn,B.,
            Birchmeier,W., Lehrach,H. and Wanker,E.E.
  TITLE     A human protein-protein interaction network: a resource for
            annotating the proteome
  JOURNAL   Cell 122 (6), 957-968 (2005)
   PUBMED   16169070
REFERENCE   8  (bases 1 to 2797)
  AUTHORS   Tanida,I., Ueno,T. and Kominami,E.
  TITLE     Human light chain 3/MAP1LC3B is cleaved at its carboxyl-terminal
            Met121 to expose Gly120 for lipidation and targeting to
            autophagosomal membranes
  JOURNAL   J Biol Chem 279 (46), 47704-47710 (2004)
   PUBMED   15355958
REFERENCE   9  (bases 1 to 2797)
  AUTHORS   Tanida,I., Sou,Y.S., Ezaki,J., Minematsu-Ikeguchi,N., Ueno,T. and
            Kominami,E.
  TITLE     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
  JOURNAL   J Biol Chem 279 (35), 36268-36276 (2004)
   PUBMED   15187094
  REMARK    GeneRIF: HsAtg4B negatively regulates the localization of LC3 to a
            membrane compartment by delipidation
REFERENCE   10 (bases 1 to 2797)
  AUTHORS   Kabeya,Y., Mizushima,N., Yamamoto,A., Oshitani-Okamoto,S.,
            Ohsumi,Y. and Yoshimori,T.
  TITLE     LC3, GABARAP and GATE16 localize to autophagosomal membrane
            depending on form-II formation
  JOURNAL   J Cell Sci 117 (Pt 13), 2805-2812 (2004)
   PUBMED   15169837
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL080168.1, AK123425.1,
            AK125277.1 and BC000719.2.
            
            On Nov 22, 2018 this sequence version replaced NM_013325.4.
            
            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. Alternate transcriptional splice variants,
            encoding different isoforms, have been characterized. [provided by
            RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) is the predominant transcript
            and it encodes the longer isoform (a).
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR3476690.449131.1,
                                           SRR1803614.152383.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000404914.8/ ENSP00000384259.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1082              AL080168.1         83-1164
            1083-1940           AK123425.1         531-1388
            1941-2794           AK125277.1         2466-3319
            2795-2797           BC000719.2         2782-2784
FEATURES             Location/Qualifiers
     source          1..2797
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q37.3"
     gene            1..2797
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /note="autophagy related 4B cysteine peptidase"
                     /db_xref="GeneID:23192"
                     /db_xref="HGNC:HGNC:20790"
                     /db_xref="MIM:611338"
     exon            1..32
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /inference="alignment:Splign:2.1.0"
     CDS             23..1204
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /note="isoform a is encoded by transcript variant 1;
                     autophagin-1; cysteine protease ATG4B; hAPG4B; AUT-like 1
                     cysteine endopeptidase; autophagy-related protein 4
                     homolog B; autophagy-related cysteine endopeptidase 1;
                     APG4 autophagy 4 homolog B; ATG4 autophagy related 4
                     homolog B"
                     /codon_start=1
                     /product="cysteine protease ATG4B isoform a"
                     /protein_id="NP_037457.3"
                     /db_xref="CCDS:CCDS46564.1"
                     /db_xref="GeneID:23192"
                     /db_xref="HGNC:HGNC:20790"
                     /db_xref="MIM:611338"
                     /translation="MDAATLTYDTLRFAEFEDFPETSEPVWILGRKYSIFTEKDEILS
                     DVASRLWFTYRKNFPAIGGTGPTSDTGWGCMLRCGQMIFAQALVCRHLGRDWRWTQRK
                     RQPDSYFSVLNAFIDRKDSYYSIHQIAQMGVGEGKSIGQWYGPNTVAQVLKKLAVFDT
                     WSSLAVHIAMDNTVVMEEIRRLCRTSVPCAGATAFPADSDRHCNGFPAGAEVTNRPSP
                     WRPLVLLIPLRLGLTDINEAYVETLKHCFMMPQSLGVIGGKPNSAHYFIGYVGEELIY
                     LDPHTTQPAVEPTDGCFIPDESFHCQHPPCRMSIAELDPSIAVGFFCKTEDDFNDWCQ
                     QVKKLSLLGGALPMFELVELQPSHLACPDVLNLSLDSSDVERLERFFDSEDEDFEILS
                     L"
     exon            33..134
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /inference="alignment:Splign:2.1.0"
     exon            135..206
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /inference="alignment:Splign:2.1.0"
     exon            207..305
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /inference="alignment:Splign:2.1.0"
     exon            306..407
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /inference="alignment:Splign:2.1.0"
     exon            408..480
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /inference="alignment:Splign:2.1.0"
     exon            481..560
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /inference="alignment:Splign:2.1.0"
     exon            561..754
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /inference="alignment:Splign:2.1.0"
     exon            755..833
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /inference="alignment:Splign:2.1.0"
     exon            834..979
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /inference="alignment:Splign:2.1.0"
     exon            980..1036
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /inference="alignment:Splign:2.1.0"
     exon            1037..1130
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /inference="alignment:Splign:2.1.0"
     exon            1131..2797
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1545..1550
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /note="hexamer: ATTAAA"
     polyA_site      1569
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /note="major polyA site"
     regulatory      2775..2780
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /note="hexamer: AATAAG"
     polyA_site      2797
                     /gene="ATG4B"
                     /gene_synonym="APG4B; AUTL1; HsAPG4B"
                     /note="major polyA site"
ORIGIN      
        1 agtcggcggc cggactggga agatggacgc agctactctg acctacgaca ctctccggtt
       61 tgctgagttt gaagattttc ctgagacctc agagcccgtt tggatactgg gtagaaaata
      121 cagcattttc acagaaaagg acgagatctt gtctgatgtg gcatctagac tttggtttac
      181 atacaggaaa aactttccag ccattggggg gacaggcccc acctcggaca caggctgggg
      241 ctgcatgctg cggtgtggac agatgatctt tgcccaagcc ctggtgtgcc ggcacctagg
      301 ccgagattgg aggtggacac aaaggaagag gcagccagac agctacttca gcgtcctcaa
      361 cgcattcatc gacaggaagg acagttacta ctccattcac cagatagcgc aaatgggagt
      421 tggcgaaggc aagtccatag gccagtggta cgggcccaac actgtcgccc aggtcctgaa
      481 gaagcttgct gtcttcgata cgtggagctc cttggcggtc cacattgcaa tggacaacac
      541 tgttgtgatg gaggaaatca gaaggttgtg caggaccagc gttccctgtg caggcgccac
      601 tgcgtttcct gcagattccg accggcactg caacggattc cctgccggag ctgaggtcac
      661 caacaggccg tcgccatgga gacccctggt acttctcatt cccctgcgcc tggggctcac
      721 ggacatcaac gaggcctacg tggagacgct gaagcactgc ttcatgatgc cccagtccct
      781 gggcgtcatc ggagggaagc ccaacagcgc ccactacttc atcggctacg ttggtgagga
      841 gctcatctac ctggaccccc acaccacgca gccagccgtg gagcccactg atggctgctt
      901 catcccggac gagagcttcc actgccagca cccgccgtgc cgcatgagca tcgcggagct
      961 tgacccgtcc atcgctgtgg ggtttttctg taagactgaa gatgacttca atgattggtg
     1021 ccagcaagtc aaaaagctgt ctctgcttgg aggtgccctg cccatgtttg agctggtgga
     1081 gctgcagcct tcacatctgg cctgccccga cgtcctgaac ctgtccctag attcttctga
     1141 tgtagagcga ctggaaagat tcttcgactc agaagatgaa gactttgaaa tcctgtccct
     1201 ttgaaaatcc tggggtcggg ggtggcacct gtgagagcct ggggctcctg gtgccgctgc
     1261 gtttcatcca tcccgcccgc tcgcctgccg agggctgcgc cccgtgctgc ctccccccag
     1321 agggccaccc gctgtgctcg tggactgagg ctgcgctgcc cgggaggcct tactgcttgg
     1381 tgtcagactg cccagctcag agtgcccgtc agggcctgtg catccgcacg cggagccgtc
     1441 tgttaggagc ttccagagtg ttctctcgac actgccagcc ccgtgttagc acctgggcct
     1501 cagtcccact tgctcccagg cgccggttct gtggttggtt tggaattaaa gtcctgtttg
     1561 aagttgtcag acacagacat gaatttctgg gcgctccctg agtcagagtc tcagaagacc
     1621 tgtgcaggct ggcgtgagag gagcggcagc cacactgcgg ccccacgccc aaggactggg
     1681 ctgctctcga ggggggcgcg cccaccgctg tgtcctctct gcccagcctg gcttaccaag
     1741 ggctacctca gtgggagatg aggttggagg aacgaaggcg aggttcctcc ttgctttggg
     1801 gagaaaagta ttcaggaagt gggtgtgtgg gaaacctgaa gatggcgtgc acaggacaca
     1861 gcgtgggcgg cctgggcaga agggcggctg gctgtcctgg agctgctgct ggagcctgcc
     1921 ctcagagtgt ccctttccag tgctgtggca ttctgtggca gcttccccag gtgtggtgac
     1981 gggggggggg cggggcctcc acctgtgaca gccaggcttg agggtggacg gcgtgcctct
     2041 cccaggagcc ttccccatgt ccttgccttg ctgagaattg ccctcccatg ccgctgaggt
     2101 gttaggtggt ttagggccaa aaggggaaaa ccacttgagt cttgtggtgt gtggtgggca
     2161 gacaccacag ggtggcatca cctggtggca tttccagaac ctcagccccg attccagcac
     2221 ccaccaccgc ctgaccctgt gtaacctgct gtcccgggtc ccagagtgca ctctgccccg
     2281 ctgctctgct gcctgtcctg ggaaagtatc tttgccccac taggaaatgt aaacaggagg
     2341 gcttggggag cgtgggcact tttctcatga gcagctactg cggcgttggc aggactcgct
     2401 gctgctgctg ctgcttgtgt aggtcgggga gccagagatc cccgaggacg cgcgccggac
     2461 agtcggcact gaccggccca cctggtagca gaggacaccc ccagcccccc aagcattgaa
     2521 gacatagtgt atttcctcgt atcctttctc ccttgggtgt agttggggtg gggaagcagg
     2581 gaaggctggt gcgatctcca ttccttgggc tccacgtccg agttcatggt gcgccgctgt
     2641 gctgggagct gcagtggtaa tgtgtgggac accttgacca aaggggagct ttgtctcgtg
     2701 tgttttgaaa aaggcttaat gaagagaatg ttgttcattc ttagtagtat agtttgcaat
     2761 tcttaatggc aaataataag tttcagtaga aaacaaa
//
