LOCUS       NM_052936               2205 bp    mRNA    linear   PRI 11-FEB-2025
DEFINITION  Homo sapiens autophagy related 4A cysteine peptidase (ATG4A),
            transcript variant 1, mRNA.
ACCESSION   NM_052936
VERSION     NM_052936.5
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 2205)
  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   2  (bases 1 to 2205)
  AUTHORS   Li,Y., Li,W., Huang,L., Li,H., He,P. and Xue,C.
  TITLE     Association of ATG4A single nucleotide polymorphism rs807185 on
            risk of microscopic polyangiitis in Chinese population
  JOURNAL   Int Immunopharmacol 123, 110659 (2023)
   PUBMED   37494842
  REMARK    GeneRIF: Association of ATG4A single nucleotide polymorphism
            rs807185 on risk of microscopic polyangiitis in Chinese population.
REFERENCE   3  (bases 1 to 2205)
  AUTHORS   Shirotani,K., Watanabe,K., Hatta,D., Kutoku,Y., Ohsawa,Y.,
            Sunada,Y., Kondo,T., Inoue,H. and Iwata,N.
  TITLE     Alterations of ATG4A and LC3B in neurons derived from Alzheimer's
            disease patients
  JOURNAL   Genes Cells 28 (4), 319-325 (2023)
   PUBMED   36719634
  REMARK    GeneRIF: Alterations of ATG4A and LC3B in neurons derived from
            Alzheimer's disease patients.
REFERENCE   4  (bases 1 to 2205)
  AUTHORS   Stolla,M.C., Reilly,A., Bergantinos,R., Stewart,S., Thom,N.,
            Clough,C.A., Wellington,R.C., Stolitenko,R., Abkowitz,J.L. and
            Doulatov,S.
  TITLE     ATG4A regulates human erythroid maturation and mitochondrial
            clearance
  JOURNAL   Blood Adv 6 (12), 3579-3589 (2022)
   PUBMED   35443024
  REMARK    GeneRIF: ATG4A regulates human erythroid maturation and
            mitochondrial clearance.
REFERENCE   5  (bases 1 to 2205)
  AUTHORS   Li,Q. and Zan,L.
  TITLE     Knockdown of ATG4A inhibits breast cancer progression and promotes
            tamoxifen chemosensitivity by suppressing autophagy
  JOURNAL   Mol Med Rep 25 (3) (2022)
   PUBMED   35088889
  REMARK    GeneRIF: Knockdown of ATG4A inhibits breast cancer progression and
            promotes tamoxifen chemosensitivity by suppressing autophagy.
REFERENCE   6  (bases 1 to 2205)
  AUTHORS   Zhang,X., Yang,H., Lee,J.J., Kim,E., Lippman,S.M., Khuri,F.R.,
            Spitz,M.R., Lotan,R., Hong,W.K. and Wu,X.
  TITLE     MicroRNA-related genetic variations as predictors for risk of
            second primary tumor and/or recurrence in patients with early-stage
            head and neck cancer
  JOURNAL   Carcinogenesis 31 (12), 2118-2123 (2010)
   PUBMED   20819778
  REMARK    GeneRIF: Observational study of gene-disease association and
            gene-gene interaction. (HuGE Navigator)
REFERENCE   7  (bases 1 to 2205)
  AUTHORS   Scherz-Shouval,R., Shvets,E., Fass,E., Shorer,H., Gil,L. and
            Elazar,Z.
  TITLE     Reactive oxygen species are essential for autophagy and
            specifically regulate the activity of Atg4
  JOURNAL   EMBO J 26 (7), 1749-1760 (2007)
   PUBMED   17347651
  REMARK    GeneRIF: The cysteine protease HsAtg4 is identified as a direct
            target for oxidation by hydrogen peroxide, and a cysteine residue
            located near the HsAtg4 catalytic site as critical for this
            regulation.
            Erratum:[EMBO J. 2019 May 15;38(10):e101812. doi:
            10.15252/embj.2019101812.. PMID: 31092559]
REFERENCE   8  (bases 1 to 2205)
  AUTHORS   Ross,M.T., Grafham,D.V., Coffey,A.J., Scherer,S., McLay,K.,
            Muzny,D., Platzer,M., Howell,G.R., Burrows,C., Bird,C.P.,
            Frankish,A., Lovell,F.L., Howe,K.L., Ashurst,J.L., Fulton,R.S.,
            Sudbrak,R., Wen,G., Jones,M.C., Hurles,M.E., Andrews,T.D.,
            Scott,C.E., Searle,S., Ramser,J., Whittaker,A., Deadman,R.,
            Carter,N.P., Hunt,S.E., Chen,R., Cree,A., Gunaratne,P., Havlak,P.,
            Hodgson,A., Metzker,M.L., Richards,S., Scott,G., Steffen,D.,
            Sodergren,E., Wheeler,D.A., Worley,K.C., Ainscough,R.,
            Ambrose,K.D., Ansari-Lari,M.A., Aradhya,S., Ashwell,R.I.,
            Babbage,A.K., Bagguley,C.L., Ballabio,A., Banerjee,R., Barker,G.E.,
            Barlow,K.F., Barrett,I.P., Bates,K.N., Beare,D.M., Beasley,H.,
            Beasley,O., Beck,A., Bethel,G., Blechschmidt,K., Brady,N.,
            Bray-Allen,S., Bridgeman,A.M., Brown,A.J., Brown,M.J., Bonnin,D.,
            Bruford,E.A., Buhay,C., Burch,P., Burford,D., Burgess,J.,
            Burrill,W., Burton,J., Bye,J.M., Carder,C., Carrel,L., Chako,J.,
            Chapman,J.C., Chavez,D., Chen,E., Chen,G., Chen,Y., Chen,Z.,
            Chinault,C., Ciccodicola,A., Clark,S.Y., Clarke,G., Clee,C.M.,
            Clegg,S., Clerc-Blankenburg,K., Clifford,K., Cobley,V., Cole,C.G.,
            Conquer,J.S., Corby,N., Connor,R.E., David,R., Davies,J., Davis,C.,
            Davis,J., Delgado,O., Deshazo,D., Dhami,P., Ding,Y., Dinh,H.,
            Dodsworth,S., Draper,H., Dugan-Rocha,S., Dunham,A., Dunn,M.,
            Durbin,K.J., Dutta,I., Eades,T., Ellwood,M., Emery-Cohen,A.,
            Errington,H., Evans,K.L., Faulkner,L., Francis,F., Frankland,J.,
            Fraser,A.E., Galgoczy,P., Gilbert,J., Gill,R., Glockner,G.,
            Gregory,S.G., Gribble,S., Griffiths,C., Grocock,R., Gu,Y.,
            Gwilliam,R., Hamilton,C., Hart,E.A., Hawes,A., Heath,P.D.,
            Heitmann,K., Hennig,S., Hernandez,J., Hinzmann,B., Ho,S., Hoffs,M.,
            Howden,P.J., Huckle,E.J., Hume,J., Hunt,P.J., Hunt,A.R.,
            Isherwood,J., Jacob,L., Johnson,D., Jones,S., de Jong,P.J.,
            Joseph,S.S., Keenan,S., Kelly,S., Kershaw,J.K., Khan,Z.,
            Kioschis,P., Klages,S., Knights,A.J., Kosiura,A., Kovar-Smith,C.,
            Laird,G.K., Langford,C., Lawlor,S., Leversha,M., Lewis,L., Liu,W.,
            Lloyd,C., Lloyd,D.M., Loulseged,H., Loveland,J.E., Lovell,J.D.,
            Lozado,R., Lu,J., Lyne,R., Ma,J., Maheshwari,M., Matthews,L.H.,
            McDowall,J., McLaren,S., McMurray,A., Meidl,P., Meitinger,T.,
            Milne,S., Miner,G., Mistry,S.L., Morgan,M., Morris,S., Muller,I.,
            Mullikin,J.C., Nguyen,N., Nordsiek,G., Nyakatura,G., O'Dell,C.N.,
            Okwuonu,G., Palmer,S., Pandian,R., Parker,D., Parrish,J.,
            Pasternak,S., Patel,D., Pearce,A.V., Pearson,D.M., Pelan,S.E.,
            Perez,L., Porter,K.M., Ramsey,Y., Reichwald,K., Rhodes,S.,
            Ridler,K.A., Schlessinger,D., Schueler,M.G., Sehra,H.K.,
            Shaw-Smith,C., Shen,H., Sheridan,E.M., Shownkeen,R., Skuce,C.D.,
            Smith,M.L., Sotheran,E.C., Steingruber,H.E., Steward,C.A.,
            Storey,R., Swann,R.M., Swarbreck,D., Tabor,P.E., Taudien,S.,
            Taylor,T., Teague,B., Thomas,K., Thorpe,A., Timms,K., Tracey,A.,
            Trevanion,S., Tromans,A.C., d'Urso,M., Verduzco,D., Villasana,D.,
            Waldron,L., Wall,M., Wang,Q., Warren,J., Warry,G.L., Wei,X.,
            West,A., Whitehead,S.L., Whiteley,M.N., Wilkinson,J.E.,
            Willey,D.L., Williams,G., Williams,L., Williamson,A.,
            Williamson,H., Wilming,L., Woodmansey,R.L., Wray,P.W., Yen,J.,
            Zhang,J., Zhou,J., Zoghbi,H., Zorilla,S., Buck,D., Reinhardt,R.,
            Poustka,A., Rosenthal,A., Lehrach,H., Meindl,A., Minx,P.J.,
            Hillier,L.W., Willard,H.F., Wilson,R.K., Waterston,R.H., Rice,C.M.,
            Vaudin,M., Coulson,A., Nelson,D.L., Weinstock,G., Sulston,J.E.,
            Durbin,R., Hubbard,T., Gibbs,R.A., Beck,S., Rogers,J. and
            Bentley,D.R.
  TITLE     The DNA sequence of the human X chromosome
  JOURNAL   Nature 434 (7031), 325-337 (2005)
   PUBMED   15772651
REFERENCE   9  (bases 1 to 2205)
  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
REFERENCE   10 (bases 1 to 2205)
  AUTHORS   Scherz-Shouval,R., Sagiv,Y., Shorer,H. and Elazar,Z.
  TITLE     The COOH terminus of GATE-16, an intra-Golgi transport modulator,
            is cleaved by the human cysteine protease HsApg4A
  JOURNAL   J Biol Chem 278 (16), 14053-14058 (2003)
   PUBMED   12473658
  REMARK    GeneRIF: HsApg4A cleaves the COOH terminus of GATE-16
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BC061696.1, BC041862.1 and
            AA648264.1.
            
            On Nov 22, 2018 this sequence version replaced NM_052936.4.
            
            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. [provided by RefSeq, Mar 2016].
            
            Transcript Variant: This variant (1) encodes 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 :: SRR1660805.88819.1,
                                           SRR1803617.170474.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000372232.8/ ENSP00000361306.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1709              BC061696.1         114-1822
            1710-2134           BC041862.1         2006-2430
            2135-2205           AA648264.1         13-83               c
FEATURES             Location/Qualifiers
     source          1..2205
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xq22.3"
     gene            1..2205
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /note="autophagy related 4A cysteine peptidase"
                     /db_xref="GeneID:115201"
                     /db_xref="HGNC:HGNC:16489"
                     /db_xref="MIM:300663"
     exon            1..59
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /inference="alignment:Splign:2.1.0"
     CDS             50..1246
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /note="isoform a is encoded by transcript variant 1;
                     autophagy-related cysteine endopeptidase 2; autophagin 2;
                     cysteine protease ATG4A; hAPG4A; autophagy-related protein
                     4 homolog A; AUT-like 2, cysteine endopeptidase; APG4
                     autophagy 4 homolog A; ATG4 autophagy related 4 homolog A"
                     /codon_start=1
                     /product="cysteine protease ATG4A isoform a"
                     /protein_id="NP_443168.2"
                     /db_xref="CCDS:CCDS14538.1"
                     /db_xref="GeneID:115201"
                     /db_xref="HGNC:HGNC:16489"
                     /db_xref="MIM:300663"
                     /translation="MESVLSKYEDQITIFTDYLEEYPDTDELVWILGKQHLLKTEKSK
                     LLSDISARLWFTYRRKFSPIGGTGPSSDAGWGCMLRCGQMMLAQALICRHLGRDWSWE
                     KQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGKSIGEWFGPNTVAQVLKKLAL
                     FDEWNSLAVYVSMDNTVVIEDIKKMCRVLPLSADTAGDRPPDSLTASNQSKGTSAYCS
                     AWKPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELI
                     FLDPHTTQTFVDTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWC
                     SLVQKEILKENLRMFELVQKHPSHWPPFVPPAKPEVTTTGAEFIDSTEQLEEFDLEED
                     FEILSV"
     exon            60..170
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /inference="alignment:Splign:2.1.0"
     exon            171..242
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /inference="alignment:Splign:2.1.0"
     exon            243..341
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /inference="alignment:Splign:2.1.0"
     exon            342..443
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /inference="alignment:Splign:2.1.0"
     exon            444..516
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /inference="alignment:Splign:2.1.0"
     exon            517..596
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /inference="alignment:Splign:2.1.0"
     exon            597..784
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /inference="alignment:Splign:2.1.0"
     exon            785..863
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /inference="alignment:Splign:2.1.0"
     exon            864..1009
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /inference="alignment:Splign:2.1.0"
     exon            1010..1066
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /inference="alignment:Splign:2.1.0"
     exon            1067..1175
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /inference="alignment:Splign:2.1.0"
     exon            1176..2205
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1691..1696
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /note="hexamer: AATAAA"
     polyA_site      1718
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /note="major polyA site"
     regulatory      2179..2184
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /note="hexamer: AATAAA"
     polyA_site      2205
                     /gene="ATG4A"
                     /gene_synonym="APG4A; AUTL2; HsAPG4A"
                     /note="major polyA site"
ORIGIN      
        1 gtccgtagtc aagttgccgg tggaattggc ccaggatgac agctggagaa tggagtcagt
       61 tttatccaag tatgaagatc agattactat tttcactgac tacctagaag aatatccaga
      121 tacagatgag ctggtatgga tcttagggaa gcagcatctc cttaaaacag aaaaatctaa
      181 gctgttgtct gatataagtg ctcgtctatg gtttacatac agaaggaaat tttcaccaat
      241 tggtggaacg ggcccttcat cagatgctgg ttggggatgt atgctacgct gtggacagat
      301 gatgctggct caagccctta tctgtagaca cttgggaagg gactggagct gggagaaaca
      361 aaaagaacaa cccaaagaat accaacgcat cctacagtgc ttcttagata gaaaagattg
      421 ttgctactct atccatcaaa tggcacaaat gggtgtagga gaagggaaat caattggaga
      481 atggtttgga ccaaatacag ttgcacaggt gttaaaaaaa cttgctttat ttgacgaatg
      541 gaattccttg gctgtttatg tttcaatgga taacacagtg gtcattgaag atatcaaaaa
      601 aatgtgccgt gtccttccct tgagtgctga cacagctggt gacaggcctc ccgattcttt
      661 aactgcttca aaccagagta agggcacctc tgcctactgc tcagcctgga aacccctgct
      721 gctcattgtg ccccttcgcc tgggcataaa ccaaatcaat cctgtctatg ttgatgcatt
      781 caaagagtgt tttaagatgc cacagtcttt aggggcatta ggaggaaaac caaataacgc
      841 gtattatttc ataggattct taggtgacga gctcatcttc ttggaccctc atacaaccca
      901 gacctttgtt gacactgaag agaatggaac ggttaatgac cagactttcc attgcctgca
      961 gtccccacag cgaatgaaca tcctaaacct ggatccttca gttgcattgg gatttttctg
     1021 caaagaagaa aaagactttg ataactggtg tagccttgtt cagaaggaaa ttctaaagga
     1081 gaatttaagg atgtttgaat tagttcagaa acatccatca cactggcctc cctttgtacc
     1141 tccagccaag ccagaagtga caaccactgg ggcagaattc attgactcta ctgagcaact
     1201 ggaggagttt gatctggagg aagattttga gattctgagt gtgtagaatc ctgggaactc
     1261 aacttgaagg tctgtcttcc atctggcacc ataaaaacat gaacttattg cataaaactt
     1321 ttctagtcag caagtgcctg atatgccaat agcatacaaa ctcaatagca atcatgactg
     1381 agccaatcac tgtttctcag aaaaacaaaa caaaacaaaa caaatgacag taacccttcc
     1441 ccggaaagaa atagaacaat catggagcct aggagcagag agatgaggag gagttcattg
     1501 cttcccagct tgtgttatat ggctacagca agtcttcagc tgctgcaatg aggaaatggg
     1561 catctggaag acaaacagca actctcagct tgcttcaaga accagcagat aagagatggt
     1621 taagctgttc ttcacccttt cagatgtgac ctcttttgga ctaagcagca atctgttctc
     1681 ttgctcaaat aataaagtga ctgaatcagg gaggaaaagg ttcttgttaa attatttgat
     1741 tgtgtagttg aagtaattat aatttatatc aaaacgtttg tcaaagaaac gatgtcaaat
     1801 atacacttct tgatctccct tctgtttgcg gggatcttac tatttgatgg gtcactgtcc
     1861 ccattcttac tgatactttt gtcagatatc accctgtcct taaatcatga tcacttaaat
     1921 caggggtcag caaacttttt ctgtaaaggg ccagacggga aatattttgg gctttgcagg
     1981 ccatgcggcc tctgtcacat ctactcaact ctgctgttga catgcaaaag cagcaataga
     2041 caatatgcgt gtaaatgagt gtggctgtaa tccaagaaaa ctttatttac aaaagcaggt
     2101 ggagggctgg gtttggcctg caggctgtag cttgccaatc agtgacttaa attgttgatt
     2161 tttgtttgat aaattaaaaa taaattgtgt ttgaagtata cccta
//
