LOCUS       NM_001346342            4172 bp    mRNA    linear   PRI 22-SEP-2024
DEFINITION  Homo sapiens autophagy related 13 (ATG13), transcript variant 36,
            mRNA.
ACCESSION   NM_001346342 XM_017018615
VERSION     NM_001346342.2
KEYWORDS    RefSeq.
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 4172)
  AUTHORS   Patel,A. and Faesen,A.C.
  TITLE     Metamorphosis by ATG13 and ATG101 in human autophagy initiation
  JOURNAL   Autophagy 20 (4), 968-969 (2024)
   PUBMED   37394799
  REMARK    GeneRIF: Metamorphosis by ATG13 and ATG101 in human autophagy
            initiation.
REFERENCE   2  (bases 1 to 4172)
  AUTHORS   Nguyen,A. and Faesen,A.C.
  TITLE     The role of the HORMA domain proteins ATG13 and ATG101 in
            initiating autophagosome biogenesis
  JOURNAL   FEBS Lett 598 (1), 114-126 (2024)
   PUBMED   37567770
  REMARK    GeneRIF: The role of the HORMA domain proteins ATG13 and ATG101 in
            initiating autophagosome biogenesis.
            Review article
REFERENCE   3  (bases 1 to 4172)
  AUTHORS   Karabi,Z., Moradian,F. and Kheirabadi,M.
  TITLE     The effect of lactoferrin on ULK1 and ATG13 genes expression in
            breast cancer cell line MCF7 and bioinformatics studies of protein
            interaction between lactoferrin and the autophagy initiation
            complex
  JOURNAL   Cell Biochem Biophys 80 (4), 795-806 (2022)
   PUBMED   36169801
  REMARK    GeneRIF: The effect of lactoferrin on ULK1 and ATG13 genes
            expression in breast cancer cell line MCF7 and bioinformatics
            studies of protein interaction between lactoferrin and the
            autophagy initiation complex.
REFERENCE   4  (bases 1 to 4172)
  AUTHORS   Gottschalk,G., Peterson,D., Knox,K., Maynard,M., Whelan,R.J. and
            Roy,A.
  TITLE     Elevated ATG13 in serum of patients with ME/CFS stimulates
            oxidative stress response in microglial cells via activation of
            receptor for advanced glycation end products (RAGE)
  JOURNAL   Mol Cell Neurosci 120, 103731 (2022)
   PUBMED   35487443
  REMARK    GeneRIF: Elevated ATG13 in serum of patients with ME/CFS stimulates
            oxidative stress response in microglial cells via activation of
            receptor for advanced glycation end products (RAGE).
REFERENCE   5  (bases 1 to 4172)
  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 4172)
  AUTHORS   Jung,C.H., Jun,C.B., Ro,S.H., Kim,Y.M., Otto,N.M., Cao,J., Kundu,M.
            and Kim,D.H.
  TITLE     ULK-Atg13-FIP200 complexes mediate mTOR signaling to the autophagy
            machinery
  JOURNAL   Mol Biol Cell 20 (7), 1992-2003 (2009)
   PUBMED   19225151
  REMARK    GeneRIF: The ULK-Atg13-FIP200 complexes are direct targets of mTOR
            and important regulators of autophagy in response to mTOR
            signaling.
REFERENCE   7  (bases 1 to 4172)
  AUTHORS   Hosokawa,N., Hara,T., Kaizuka,T., Kishi,C., Takamura,A., Miura,Y.,
            Iemura,S., Natsume,T., Takehana,K., Yamada,N., Guan,J.L., Oshiro,N.
            and Mizushima,N.
  TITLE     Nutrient-dependent mTORC1 association with the ULK1-Atg13-FIP200
            complex required for autophagy
  JOURNAL   Mol Biol Cell 20 (7), 1981-1991 (2009)
   PUBMED   19211835
  REMARK    GeneRIF: mTORC1 suppresses autophagy through direct regulation of
            the approximately 3-MDa ULK1-Atg13-FIP200 complex.
REFERENCE   8  (bases 1 to 4172)
  AUTHORS   Chan,E.Y., Longatti,A., McKnight,N.C. and Tooze,S.A.
  TITLE     Kinase-inactivated ULK proteins inhibit autophagy via their
            conserved C-terminal domains using an Atg13-independent mechanism
  JOURNAL   Mol Cell Biol 29 (1), 157-171 (2009)
   PUBMED   18936157
  REMARK    GeneRIF: The functions of ULK1 and ULK2 are controlled by
            autophosphorylation and conformational changes involving exposure
            of the C-terminal domain and interaction with the putative human
            homologue of Atg13.
            GeneRIF: The gene product is the functional homologue of yeast
            Atg13, and required for autophagy in mammalian cells.
REFERENCE   9  (bases 1 to 4172)
  AUTHORS   Meijer,W.H., van der Klei,I.J., Veenhuis,M. and Kiel,J.A.
  TITLE     ATG genes involved in non-selective autophagy are conserved from
            yeast to man, but the selective Cvt and pexophagy pathways also
            require organism-specific genes
  JOURNAL   Autophagy 3 (2), 106-116 (2007)
   PUBMED   17204848
REFERENCE   10 (bases 1 to 4172)
  AUTHORS   Wistow,G., Bernstein,S.L., Wyatt,M.K., Behal,A., Touchman,J.W.,
            Bouffard,G., Smith,D. and Peterson,K.
  TITLE     Expressed sequence tag analysis of adult human lens for the NEIBank
            Project: over 2000 non-redundant transcripts, novel genes and
            splice variants
  JOURNAL   Mol Vis 8, 171-184 (2002)
   PUBMED   12107413
  REMARK    Publication Status: Online-Only
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC127035.6 and AC115088.6.
            
            On Aug 30, 2020 this sequence version replaced NM_001346342.1.
            
            Summary: The protein encoded by this gene is an autophagy factor
            and a target of the TOR kinase signaling pathway. The encoded
            protein is essential for autophagosome formation and mitophagy.
            [provided by RefSeq, Oct 2016].
            
            Transcript Variant: This variant (36), as well as variants 2, 5,
            and 37-45, encodes isoform f.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            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 :: SRR14038191.2177523.1,
                                           SRR1803616.71204.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968968, SAMEA2144333
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-338               AC127035.6         97803-98140
            339-532             AC127035.6         110157-110350
            533-614             AC115088.6         4801-4882
            615-695             AC115088.6         5861-5941
            696-815             AC115088.6         6392-6511
            816-862             AC115088.6         9659-9705
            863-1003            AC115088.6         10699-10839
            1004-1044           AC115088.6         16755-16795
            1045-1141           AC115088.6         17617-17713
            1142-1240           AC115088.6         18046-18144
            1241-1334           AC115088.6         19914-20007
            1335-1471           AC115088.6         25905-26041
            1472-1586           AC115088.6         28295-28409
            1587-1664           AC115088.6         29021-29098
            1665-1781           AC115088.6         29316-29432
            1782-1910           AC115088.6         29926-30054
            1911-2419           AC115088.6         32777-33285
            2420-4172           AC115088.6         33288-35040
FEATURES             Location/Qualifiers
     source          1..4172
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11p11.2"
     gene            1..4172
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="autophagy related 13"
                     /db_xref="GeneID:9776"
                     /db_xref="HGNC:HGNC:29091"
                     /db_xref="MIM:615088"
     exon            1..338
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            339..532
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            533..614
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     CDS             546..1988
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="isoform f is encoded by transcript variant 36;
                     autophagy-related protein 13; ATG13 autophagy related 13
                     homolog"
                     /codon_start=1
                     /product="autophagy-related protein 13 isoform f"
                     /protein_id="NP_001333271.1"
                     /db_xref="CCDS:CCDS7921.1"
                     /db_xref="GeneID:9776"
                     /db_xref="HGNC:HGNC:29091"
                     /db_xref="MIM:615088"
                     /translation="METDLNSQDRKDLDKFIKFFALKTVQVIVQARLGEKICTRSSSS
                     PTGSDWFNLAIKDIPEVTHEAKKALAGQLPAVGRSMCVEISLKTSEGDSMELEIWCLE
                     MNEKCDKEIKVSYTVYNRLSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQ
                     LSGLGEGFQTVRVGTVGTPVGTITLSCAYRINLAFMSTRQFERTPPIMGIIIDHFVDR
                     PYPSSSPMHPCNYRTAGEDTGVIYPSVEDSQEVCTTSFSTSPPSQLMVPGKEGGVPLA
                     PNQPVHGTQADQERLATCTPSDRTHCAATPSSSEDTETVSNSSEGRASPHDVLETIFV
                     RKVGAFVNKPINQVTLTSLDIPFAMFAPKNLELEDTDPMVNPPDSPETESPLQGSLHS
                     DGSSGGSSGNTHDDFVMIDFKPAFSKDDILPMDLGTFYREFQNPPQLSSLSIDIGAQS
                     MAEDLDSLPEKLAVHEKNVREFDAFVETLQ"
     exon            615..695
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            696..815
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            816..862
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            863..1003
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1004..1044
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1045..1141
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1142..1240
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1241..1334
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1335..1471
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1472..1586
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1587..1664
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1665..1781
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1782..1910
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1911..4172
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2671..2676
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="hexamer: AATAAA"
     polyA_site      2690
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="major polyA site"
     regulatory      4150..4155
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="hexamer: AATAAA"
     polyA_site      4172
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="major polyA site"
ORIGIN      
        1 ggccattacc gaagcggatg aaaacaaaca ctaacgatgg cggcgccggg aagcgaccgg
       61 ctgctgggct taaggcggga gtgaccgctt aaccagtgag ggaagcactg aagagcgcca
      121 gtcgacgtgg gtgcgacaac tcgcggagtc ttaggagcaa aacgtctggg gcctgcgagc
      181 caggaccctt ctgaagcctt aggtgtctat cggcgacgtg tacggtcact gcagctccgg
      241 agcgcggaac cctcagccag gaggcgcggc tggtcggtcc caggtcccgg cctccgtaat
      301 gagagcccgg aaccactctt tgtgccgcag cttcgcaggc tgtgtcgtcc caaagatact
      361 aagtaacagg cagaattgga tatggcacaa atttctgttt aaagagatgc ggtctcgctc
      421 tgttgcccag gctgttgtgc agtggtattc acagtcatga tcatatttct ctacagcatc
      481 ttggactcaa gtgattctcc tgcctcagcc tcctgagtag ctgggactac agattcctat
      541 aggcaatgga aactgatctc aattcccagg acagaaagga cctggacaag tttattaaat
      601 tttttgccct caagactgtc caagtgattg tccaggctcg gcttggtgaa aagatttgca
      661 ctcgttcatc atcttctcca acgggttcag attggttcaa cttagcaatc aaagacatcc
      721 cagaggttac acatgaagca aagaaggcac tggcaggaca gctgcctgca gtcgggaggt
      781 ccatgtgtgt ggagatttca cttaagactt ctgagggaga ttccatggag ctggaaatat
      841 ggtgtcttga aatgaatgaa aagtgtgata aagaaatcaa agtttcctac acggtgtaca
      901 acagactgtc attgctgctg aagtcccttc ttgctataac tagggtgaca ccagcctata
      961 ggctctccag gaaacaaggg catgaatatg tcatattata caggatatat tttggagaag
     1021 ttcagctgag tggcttagga gaaggcttcc agacagttcg tgttgggaca gtgggcaccc
     1081 ctgtgggcac catcactctt tcttgtgctt acagaattaa cttggcattc atgtctacca
     1141 ggcaatttga gaggacccca cctatcatgg ggattattat tgatcacttt gtggaccgtc
     1201 cctatcccag ctcctctccc atgcacccct gcaattacag aactgctggt gaggacactg
     1261 gagtaatata cccgtctgta gaagactctc aagaagtgtg taccacctct ttttccacct
     1321 ccccaccatc ccagctgatg gttcctggga aggaaggtgg ggtacccctt gctcccaacc
     1381 agcctgtcca tggtacccag gctgaccagg agagactggc aacctgcacc ccttctgaca
     1441 gaacccactg tgctgccaca ccctccagta gtgaggatac tgaaaccgta tcaaacagca
     1501 gtgagggacg ggcctcccct cacgatgtct tggagaccat ctttgtccga aaagtggggg
     1561 cttttgtcaa caaacccatt aaccaggtga ccctgacgag tttggatata ccctttgcca
     1621 tgtttgctcc caagaatttg gagctggagg ataccgatcc aatggtgaat cctccagatt
     1681 ccccagagac tgaatctcct ctccagggca gcctgcactc agatggctcc agcgggggca
     1741 gcagtggcaa tacccatgat gactttgtta tgatagactt taaaccagct ttttctaaag
     1801 atgacattct tccgatggac ctggggacct tctatcggga gtttcagaac ccacctcagc
     1861 tgagcagcct ctccatagat attggagcac agtccatggc tgaagacttg gactcattac
     1921 cagagaagct ggctgtgcat gagaagaatg tccgcgagtt tgatgccttt gtggaaaccc
     1981 tgcagtaaaa gtatccttga gtcccagcag cacccccttt ttgtggcccc agggcataag
     2041 cagcctccca tgcatcagct gctcccaccc ctcatcctgc tctgagccag gtggaaggga
     2101 ggctggcttc tcccatgggg acccagaagt ccctactctt ggacctcctg gagactccgt
     2161 ggcggcagtc aagcccagtg cccagttgga gaagactcac gtgctggcct tggagatggg
     2221 aagaaccttc gtacgaaaaa gccctcagca gggccatctg tgtgccctgc ccatcaccaa
     2281 ctgcttccca agggtgtcat cctgttcctc ctgctgccgg cctcctgcct gggcctgcct
     2341 tgcagctggc cccttccctg cctgctgtca ccatccactg tttgacattc cagctggtgg
     2401 ccaagagatt ggtgtggagg cagaaagagg aaggagacag tgccaggagg aagaaggaag
     2461 gagtccctta gctctcttca ttgtcccctt tacttcctgc tatcttcttc tcctcttctt
     2521 ctctctcttg cctctatgcc tgtatttctg gcaatatgac aggcctgcct acccaagatc
     2581 agaactccaa aaccactccc acccctgaag gtcgggaggg tctgagcagc cctggtggct
     2641 gcctgtgctc aggtcctcag ctccatggga aataaaaatg gcaccctgaa tctctaggat
     2701 tttgtcactt ggagtcacag caaagttctc ttcctcttgt ccccccgttg ctgctccttg
     2761 gttatagaac atggtaaata tttattactt tcagagaaac cagatatttt atagaggaaa
     2821 tatgtttgag gtgagttgtt tttcacttgg agaaggcgga gggctcttcc tgggacggag
     2881 acctcctcct ccggaggtta ttgagaatcc gggctgctgc tttgaggatc ttcccaccat
     2941 acagacagcg agatccaaga agagggctgg ccgggggcaa agtcacctcc cagtgtggct
     3001 gcactggaac tgactaaagg ctttaccttg gatagttgcg tattcctggt gagagcctta
     3061 catctcccac agtttctgca gagtgactga ctccattctg gcagcccagg aagtcctggg
     3121 tgctaaatgt gatggccaca tgtagtggtt aggggatgtt gtgtgtgtcc cccaactgcc
     3181 tgggtacttg ttcctgatcc ctggggctgt cctgtggagc ttttcctcct gcttgggcct
     3241 agctaccatc tccctctaat cccaggttct ctacactgcc ctggggttta ccagctggat
     3301 tggcttctgg ttgagaaatc aaagctgggc gtatgattga cttaaccctt caggtattgt
     3361 tacttgaata agtcaagtgc ctagcctcac ccacctatga tctgtccttt cccagcctcg
     3421 ctggtagtcc tggtcaagga gatctaggtc tactccattc ctcctggccc acctggggca
     3481 ttcactggca gcagctgtgc ttcagtggag caggtggttc tcagctgctt gttagtatac
     3541 tgcatgtgac actgttccca catacaaggc tgacttctga ggattggagc aggctctggc
     3601 ggggaccaga gctctgcgtg ctgctgctgc caccaagaag tgttagcaga agcagtagca
     3661 gccaactggc cctcctgact ttggcccaga gcacatgcgt ggcttgctga acccaggctc
     3721 aggtttatcc ccaaggcccc agctttgaga agggggaagg cccctggtaa gttattgatg
     3781 cccccatatt tcagctactg ctctctttcc aaggccttgc atggaaaggc ctagccattg
     3841 tctgaggcag caatctttgg catctacagg tggcagcagc ctttcaccag ggctccatct
     3901 gtgaagagtc tcagccatga ctttgagctg agcttgggag aagtaaagca actgttaagg
     3961 ccagcccttg cccctcagac ctgccatgaa aggaatgagc cctagactga ctcctgcagc
     4021 acccccggga caggctggga ccagctgttt gtctccaggt gtcagagtcc ctcctcctcc
     4081 tccaacctct ccaacctact ttgtttggaa ataccgagct acacttcaaa atgtattcaa
     4141 gggatttcca ataaattttt ttctgtactt ta
//
