LOCUS       NM_001346360            4173 bp    mRNA    linear   PRI 22-SEP-2024
DEFINITION  Homo sapiens autophagy related 13 (ATG13), transcript variant 51,
            mRNA.
ACCESSION   NM_001346360 XM_017018622
VERSION     NM_001346360.2
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 4173)
  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 4173)
  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 4173)
  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 4173)
  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 4173)
  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 4173)
  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 4173)
  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 4173)
  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 4173)
  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 4173)
  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_001346360.1.
            
            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 (51) encodes isoform j.
            
            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 :: SRR14038194.3098558.1,
                                           SRR14038191.277818.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1968968
                                           [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
            339-394             AC127035.6         110295-110350
            395-476             AC115088.6         4801-4882
            477-557             AC115088.6         5861-5941
            558-677             AC115088.6         6392-6511
            678-724             AC115088.6         9659-9705
            725-865             AC115088.6         10699-10839
            866-1045            AC115088.6         16755-16934
            1046-1142           AC115088.6         17617-17713
            1143-1241           AC115088.6         18046-18144
            1242-1335           AC115088.6         19914-20007
            1336-1472           AC115088.6         25905-26041
            1473-1587           AC115088.6         28295-28409
            1588-1665           AC115088.6         29021-29098
            1666-1782           AC115088.6         29316-29432
            1783-1911           AC115088.6         29926-30054
            1912-2420           AC115088.6         32777-33285
            2421-4173           AC115088.6         33288-35040
FEATURES             Location/Qualifiers
     source          1..4173
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11p11.2"
     gene            1..4173
                     /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..394
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            395..476
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            477..557
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            558..677
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            678..724
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            725..865
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            866..1045
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1046..1142
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     CDS             1132..1989
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="isoform j is encoded by transcript variant 51;
                     autophagy-related protein 13; ATG13 autophagy related 13
                     homolog"
                     /codon_start=1
                     /product="autophagy-related protein 13 isoform j"
                     /protein_id="NP_001333289.1"
                     /db_xref="GeneID:9776"
                     /db_xref="HGNC:HGNC:29091"
                     /db_xref="MIM:615088"
                     /translation="MSTRQFERTPPIMGIIIDHFVDRPYPSSSPMHPCNYRTAGEDTG
                     VIYPSVEDSQEVCTTSFSTSPPSQLMVPGKEGGVPLAPNQPVHGTQADQERLATCTPS
                     DRTHCAATPSSSEDTETVSNSSEGRASPHDVLETIFVRKVGAFVNKPINQVTLTSLDI
                     PFAMFAPKNLELEDTDPMVNPPDSPETESPLQGSLHSDGSSGGSSGNTHDDFVMIDFK
                     PAFSKDDILPMDLGTFYREFQNPPQLSSLSIDIGAQSMAEDLDSLPEKLAVHEKNVRE
                     FDAFVETLQ"
     exon            1143..1241
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1242..1335
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1336..1472
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1473..1587
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1588..1665
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1666..1782
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1783..1911
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1912..4173
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2672..2677
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="hexamer: AATAAA"
     polyA_site      2691
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="major polyA site"
     regulatory      4151..4156
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="hexamer: AATAAA"
     polyA_site      4173
                     /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 cttcgcagca tcttggactc aagtgattct
      361 cctgcctcag cctcctgagt agctgggact acagattcct ataggcaatg gaaactgatc
      421 tcaattccca ggacagaaag gacctggaca agtttattaa attttttgcc ctcaagactg
      481 tccaagtgat tgtccaggct cggcttggtg aaaagatttg cactcgttca tcatcttctc
      541 caacgggttc agattggttc aacttagcaa tcaaagacat cccagaggtt acacatgaag
      601 caaagaaggc actggcagga cagctgcctg cagtcgggag gtccatgtgt gtggagattt
      661 cacttaagac ttctgaggga gattccatgg agctggaaat atggtgtctt gaaatgaatg
      721 aaaagtgtga taaagaaatc aaagtttcct acacggtgta caacagactg tcattgctgc
      781 tgaagtccct tcttgctata actagggtga caccagccta taggctctcc aggaaacaag
      841 ggcatgaata tgtcatatta tacaggatat attttggaga agttcagctg agtggcttag
      901 gagaaggtat gtatcaacgg ttgaaaaaca tcgtagtgtt cagagctctc ctaacttcag
      961 agatgatctt cgtttctact tgttataata tgtagattgt catcttaata tgcataatac
     1021 aagtaaagaa aagatgagaa tgcaggcttc cagacagttc gtgttgggac agtgggcacc
     1081 cctgtgggca ccatcactct ttcttgtgct tacagaatta acttggcatt catgtctacc
     1141 aggcaatttg agaggacccc acctatcatg gggattatta ttgatcactt tgtggaccgt
     1201 ccctatccca gctcctctcc catgcacccc tgcaattaca gaactgctgg tgaggacact
     1261 ggagtaatat acccgtctgt agaagactct caagaagtgt gtaccacctc tttttccacc
     1321 tccccaccat cccagctgat ggttcctggg aaggaaggtg gggtacccct tgctcccaac
     1381 cagcctgtcc atggtaccca ggctgaccag gagagactgg caacctgcac cccttctgac
     1441 agaacccact gtgctgccac accctccagt agtgaggata ctgaaaccgt atcaaacagc
     1501 agtgagggac gggcctcccc tcacgatgtc ttggagacca tctttgtccg aaaagtgggg
     1561 gcttttgtca acaaacccat taaccaggtg accctgacga gtttggatat accctttgcc
     1621 atgtttgctc ccaagaattt ggagctggag gataccgatc caatggtgaa tcctccagat
     1681 tccccagaga ctgaatctcc tctccagggc agcctgcact cagatggctc cagcgggggc
     1741 agcagtggca atacccatga tgactttgtt atgatagact ttaaaccagc tttttctaaa
     1801 gatgacattc ttccgatgga cctggggacc ttctatcggg agtttcagaa cccacctcag
     1861 ctgagcagcc tctccataga tattggagca cagtccatgg ctgaagactt ggactcatta
     1921 ccagagaagc tggctgtgca tgagaagaat gtccgcgagt ttgatgcctt tgtggaaacc
     1981 ctgcagtaaa agtatccttg agtcccagca gcaccccctt tttgtggccc cagggcataa
     2041 gcagcctccc atgcatcagc tgctcccacc cctcatcctg ctctgagcca ggtggaaggg
     2101 aggctggctt ctcccatggg gacccagaag tccctactct tggacctcct ggagactccg
     2161 tggcggcagt caagcccagt gcccagttgg agaagactca cgtgctggcc ttggagatgg
     2221 gaagaacctt cgtacgaaaa agccctcagc agggccatct gtgtgccctg cccatcacca
     2281 actgcttccc aagggtgtca tcctgttcct cctgctgccg gcctcctgcc tgggcctgcc
     2341 ttgcagctgg ccccttccct gcctgctgtc accatccact gtttgacatt ccagctggtg
     2401 gccaagagat tggtgtggag gcagaaagag gaaggagaca gtgccaggag gaagaaggaa
     2461 ggagtccctt agctctcttc attgtcccct ttacttcctg ctatcttctt ctcctcttct
     2521 tctctctctt gcctctatgc ctgtatttct ggcaatatga caggcctgcc tacccaagat
     2581 cagaactcca aaaccactcc cacccctgaa ggtcgggagg gtctgagcag ccctggtggc
     2641 tgcctgtgct caggtcctca gctccatggg aaataaaaat ggcaccctga atctctagga
     2701 ttttgtcact tggagtcaca gcaaagttct cttcctcttg tccccccgtt gctgctcctt
     2761 ggttatagaa catggtaaat atttattact ttcagagaaa ccagatattt tatagaggaa
     2821 atatgtttga ggtgagttgt ttttcacttg gagaaggcgg agggctcttc ctgggacgga
     2881 gacctcctcc tccggaggtt attgagaatc cgggctgctg ctttgaggat cttcccacca
     2941 tacagacagc gagatccaag aagagggctg gccgggggca aagtcacctc ccagtgtggc
     3001 tgcactggaa ctgactaaag gctttacctt ggatagttgc gtattcctgg tgagagcctt
     3061 acatctccca cagtttctgc agagtgactg actccattct ggcagcccag gaagtcctgg
     3121 gtgctaaatg tgatggccac atgtagtggt taggggatgt tgtgtgtgtc ccccaactgc
     3181 ctgggtactt gttcctgatc cctggggctg tcctgtggag cttttcctcc tgcttgggcc
     3241 tagctaccat ctccctctaa tcccaggttc tctacactgc cctggggttt accagctgga
     3301 ttggcttctg gttgagaaat caaagctggg cgtatgattg acttaaccct tcaggtattg
     3361 ttacttgaat aagtcaagtg cctagcctca cccacctatg atctgtcctt tcccagcctc
     3421 gctggtagtc ctggtcaagg agatctaggt ctactccatt cctcctggcc cacctggggc
     3481 attcactggc agcagctgtg cttcagtgga gcaggtggtt ctcagctgct tgttagtata
     3541 ctgcatgtga cactgttccc acatacaagg ctgacttctg aggattggag caggctctgg
     3601 cggggaccag agctctgcgt gctgctgctg ccaccaagaa gtgttagcag aagcagtagc
     3661 agccaactgg ccctcctgac tttggcccag agcacatgcg tggcttgctg aacccaggct
     3721 caggtttatc cccaaggccc cagctttgag aagggggaag gcccctggta agttattgat
     3781 gcccccatat ttcagctact gctctctttc caaggccttg catggaaagg cctagccatt
     3841 gtctgaggca gcaatctttg gcatctacag gtggcagcag cctttcacca gggctccatc
     3901 tgtgaagagt ctcagccatg actttgagct gagcttggga gaagtaaagc aactgttaag
     3961 gccagccctt gcccctcaga cctgccatga aaggaatgag ccctagactg actcctgcag
     4021 cacccccggg acaggctggg accagctgtt tgtctccagg tgtcagagtc cctcctcctc
     4081 ctccaacctc tccaacctac tttgtttgga aataccgagc tacacttcaa aatgtattca
     4141 agggatttcc aataaatttt tttctgtact tta
//
