LOCUS       NM_001346322            4378 bp    mRNA    linear   PRI 22-SEP-2024
DEFINITION  Homo sapiens autophagy related 13 (ATG13), transcript variant 18,
            mRNA.
ACCESSION   NM_001346322
VERSION     NM_001346322.2
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 4378)
  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 4378)
  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 4378)
  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 4378)
  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 4378)
  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 4378)
  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 4378)
  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 4378)
  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 4378)
  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 4378)
  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_001346322.1.
            
            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 (18), as well as variants 1, 4,
            15-17, and 19-28, encodes isoform c.
            
            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 :: SRR1660807.70068.1,
                                           SRR1660809.215933.1 [ECO:0000332]
            RNAseq introns              :: partial sample support SAMEA1968968,
                                           SAMEA2144120 [ECO:0000350]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-338               AC127035.6         97803-98140
            339-454             AC127035.6         98510-98625
            455-571             AC127035.6         105551-105667
            572-627             AC127035.6         110295-110350
            628-709             AC115088.6         4801-4882
            710-790             AC115088.6         5861-5941
            791-910             AC115088.6         6392-6511
            911-957             AC115088.6         9659-9705
            958-1098            AC115088.6         10699-10839
            1099-1139           AC115088.6         16755-16795
            1140-1236           AC115088.6         17617-17713
            1237-1335           AC115088.6         18046-18144
            1336-1429           AC115088.6         19914-20007
            1430-1540           AC115088.6         25371-25481
            1541-1677           AC115088.6         25905-26041
            1678-1792           AC115088.6         28295-28409
            1793-1870           AC115088.6         29021-29098
            1871-1987           AC115088.6         29316-29432
            1988-2116           AC115088.6         29926-30054
            2117-2625           AC115088.6         32777-33285
            2626-4378           AC115088.6         33288-35040
FEATURES             Location/Qualifiers
     source          1..4378
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11p11.2"
     gene            1..4378
                     /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..454
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            455..571
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            572..627
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            628..709
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     CDS             641..2194
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="isoform c is encoded by transcript variant 18;
                     autophagy-related protein 13; ATG13 autophagy related 13
                     homolog"
                     /codon_start=1
                     /product="autophagy-related protein 13 isoform c"
                     /protein_id="NP_001333251.1"
                     /db_xref="CCDS:CCDS44582.1"
                     /db_xref="GeneID:9776"
                     /db_xref="HGNC:HGNC:29091"
                     /db_xref="MIM:615088"
                     /translation="METDLNSQDRKDLDKFIKFFALKTVQVIVQARLGEKICTRSSSS
                     PTGSDWFNLAIKDIPEVTHEAKKALAGQLPAVGRSMCVEISLKTSEGDSMELEIWCLE
                     MNEKCDKEIKVSYTVYNRLSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQ
                     LSGLGEGFQTVRVGTVGTPVGTITLSCAYRINLAFMSTRQFERTPPIMGIIIDHFVDR
                     PYPSSSPMHPCNYRTAGEDTGVIYPSVEDSQEVCTTSFSTSPPSQLSSSRLSYQPAAL
                     GVGSADLAYPVVFAAGLNATHPHQLMVPGKEGGVPLAPNQPVHGTQADQERLATCTPS
                     DRTHCAATPSSSEDTETVSNSSEGRASPHDVLETIFVRKVGAFVNKPINQVTLTSLDI
                     PFAMFAPKNLELEDTDPMVNPPDSPETESPLQGSLHSDGSSGGSSGNTHDDFVMIDFK
                     PAFSKDDILPMDLGTFYREFQNPPQLSSLSIDIGAQSMAEDLDSLPEKLAVHEKNVRE
                     FDAFVETLQ"
     exon            710..790
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            791..910
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            911..957
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            958..1098
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1099..1139
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1140..1236
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1237..1335
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1336..1429
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1430..1540
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1541..1677
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1678..1792
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1793..1870
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1871..1987
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1988..2116
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            2117..4378
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2877..2882
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="hexamer: AATAAA"
     polyA_site      2896
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="major polyA site"
     regulatory      4356..4361
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="hexamer: AATAAA"
     polyA_site      4378
                     /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 cttcgcaggt gagggtgact gttgactagt
      361 gaaaaaaggg acccatggtt cacgactgtc ttcttactgg cagtggaacg acctgtggaa
      421 acctgtgatc cattctcatt aaataaatct ctggggtttt gctttgtcac ccaggctgga
      481 gtgcaatgac atgatcacag ctcactgcag ccatacctcc tgggttcgag tgatcttccc
      541 acatcagcct cctgagtagc tgggactata gcatcttgga ctcaagtgat tctcctgcct
      601 cagcctcctg agtagctggg actacagatt cctataggca atggaaactg atctcaattc
      661 ccaggacaga aaggacctgg acaagtttat taaatttttt gccctcaaga ctgtccaagt
      721 gattgtccag gctcggcttg gtgaaaagat ttgcactcgt tcatcatctt ctccaacggg
      781 ttcagattgg ttcaacttag caatcaaaga catcccagag gttacacatg aagcaaagaa
      841 ggcactggca ggacagctgc ctgcagtcgg gaggtccatg tgtgtggaga tttcacttaa
      901 gacttctgag ggagattcca tggagctgga aatatggtgt cttgaaatga atgaaaagtg
      961 tgataaagaa atcaaagttt cctacacggt gtacaacaga ctgtcattgc tgctgaagtc
     1021 ccttcttgct ataactaggg tgacaccagc ctataggctc tccaggaaac aagggcatga
     1081 atatgtcata ttatacagga tatattttgg agaagttcag ctgagtggct taggagaagg
     1141 cttccagaca gttcgtgttg ggacagtggg cacccctgtg ggcaccatca ctctttcttg
     1201 tgcttacaga attaacttgg cattcatgtc taccaggcaa tttgagagga ccccacctat
     1261 catggggatt attattgatc actttgtgga ccgtccctat cccagctcct ctcccatgca
     1321 cccctgcaat tacagaactg ctggtgagga cactggagta atatacccgt ctgtagaaga
     1381 ctctcaagaa gtgtgtacca cctctttttc cacctcccca ccatcccagc tctcaagctc
     1441 tcgcctttcc tatcagcctg ctgccctggg cgttggatca gctgacctgg cttatccagt
     1501 agtgtttgct gctggcttaa atgctacaca ccctcaccag ctgatggttc ctgggaagga
     1561 aggtggggta ccccttgctc ccaaccagcc tgtccatggt acccaggctg accaggagag
     1621 actggcaacc tgcacccctt ctgacagaac ccactgtgct gccacaccct ccagtagtga
     1681 ggatactgaa accgtatcaa acagcagtga gggacgggcc tcccctcacg atgtcttgga
     1741 gaccatcttt gtccgaaaag tgggggcttt tgtcaacaaa cccattaacc aggtgaccct
     1801 gacgagtttg gatataccct ttgccatgtt tgctcccaag aatttggagc tggaggatac
     1861 cgatccaatg gtgaatcctc cagattcccc agagactgaa tctcctctcc agggcagcct
     1921 gcactcagat ggctccagcg ggggcagcag tggcaatacc catgatgact ttgttatgat
     1981 agactttaaa ccagcttttt ctaaagatga cattcttccg atggacctgg ggaccttcta
     2041 tcgggagttt cagaacccac ctcagctgag cagcctctcc atagatattg gagcacagtc
     2101 catggctgaa gacttggact cattaccaga gaagctggct gtgcatgaga agaatgtccg
     2161 cgagtttgat gcctttgtgg aaaccctgca gtaaaagtat ccttgagtcc cagcagcacc
     2221 ccctttttgt ggccccaggg cataagcagc ctcccatgca tcagctgctc ccacccctca
     2281 tcctgctctg agccaggtgg aagggaggct ggcttctccc atggggaccc agaagtccct
     2341 actcttggac ctcctggaga ctccgtggcg gcagtcaagc ccagtgccca gttggagaag
     2401 actcacgtgc tggccttgga gatgggaaga accttcgtac gaaaaagccc tcagcagggc
     2461 catctgtgtg ccctgcccat caccaactgc ttcccaaggg tgtcatcctg ttcctcctgc
     2521 tgccggcctc ctgcctgggc ctgccttgca gctggcccct tccctgcctg ctgtcaccat
     2581 ccactgtttg acattccagc tggtggccaa gagattggtg tggaggcaga aagaggaagg
     2641 agacagtgcc aggaggaaga aggaaggagt cccttagctc tcttcattgt cccctttact
     2701 tcctgctatc ttcttctcct cttcttctct ctcttgcctc tatgcctgta tttctggcaa
     2761 tatgacaggc ctgcctaccc aagatcagaa ctccaaaacc actcccaccc ctgaaggtcg
     2821 ggagggtctg agcagccctg gtggctgcct gtgctcaggt cctcagctcc atgggaaata
     2881 aaaatggcac cctgaatctc taggattttg tcacttggag tcacagcaaa gttctcttcc
     2941 tcttgtcccc ccgttgctgc tccttggtta tagaacatgg taaatattta ttactttcag
     3001 agaaaccaga tattttatag aggaaatatg tttgaggtga gttgtttttc acttggagaa
     3061 ggcggagggc tcttcctggg acggagacct cctcctccgg aggttattga gaatccgggc
     3121 tgctgctttg aggatcttcc caccatacag acagcgagat ccaagaagag ggctggccgg
     3181 gggcaaagtc acctcccagt gtggctgcac tggaactgac taaaggcttt accttggata
     3241 gttgcgtatt cctggtgaga gccttacatc tcccacagtt tctgcagagt gactgactcc
     3301 attctggcag cccaggaagt cctgggtgct aaatgtgatg gccacatgta gtggttaggg
     3361 gatgttgtgt gtgtccccca actgcctggg tacttgttcc tgatccctgg ggctgtcctg
     3421 tggagctttt cctcctgctt gggcctagct accatctccc tctaatccca ggttctctac
     3481 actgccctgg ggtttaccag ctggattggc ttctggttga gaaatcaaag ctgggcgtat
     3541 gattgactta acccttcagg tattgttact tgaataagtc aagtgcctag cctcacccac
     3601 ctatgatctg tcctttccca gcctcgctgg tagtcctggt caaggagatc taggtctact
     3661 ccattcctcc tggcccacct ggggcattca ctggcagcag ctgtgcttca gtggagcagg
     3721 tggttctcag ctgcttgtta gtatactgca tgtgacactg ttcccacata caaggctgac
     3781 ttctgaggat tggagcaggc tctggcgggg accagagctc tgcgtgctgc tgctgccacc
     3841 aagaagtgtt agcagaagca gtagcagcca actggccctc ctgactttgg cccagagcac
     3901 atgcgtggct tgctgaaccc aggctcaggt ttatccccaa ggccccagct ttgagaaggg
     3961 ggaaggcccc tggtaagtta ttgatgcccc catatttcag ctactgctct ctttccaagg
     4021 ccttgcatgg aaaggcctag ccattgtctg aggcagcaat ctttggcatc tacaggtggc
     4081 agcagccttt caccagggct ccatctgtga agagtctcag ccatgacttt gagctgagct
     4141 tgggagaagt aaagcaactg ttaaggccag cccttgcccc tcagacctgc catgaaagga
     4201 atgagcccta gactgactcc tgcagcaccc ccgggacagg ctgggaccag ctgtttgtct
     4261 ccaggtgtca gagtccctcc tcctcctcca acctctccaa cctactttgt ttggaaatac
     4321 cgagctacac ttcaaaatgt attcaaggga tttccaataa atttttttct gtacttta
//
