LOCUS       NM_001346353            4094 bp    mRNA    linear   PRI 22-SEP-2024
DEFINITION  Homo sapiens autophagy related 13 (ATG13), transcript variant 44,
            mRNA.
ACCESSION   NM_001346353 XM_017018613
VERSION     NM_001346353.2
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 4094)
  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 4094)
  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 4094)
  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 4094)
  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 4094)
  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 4094)
  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 4094)
  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 4094)
  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 4094)
  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 4094)
  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_001346353.1.
            
            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 (44), as well as variants 2, 5,
            36-43, and 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 :: SRR11853565.4865.1,
                                           SRR18074969.319494.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [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
            339-454             AC127035.6         98510-98625
            455-536             AC115088.6         4801-4882
            537-617             AC115088.6         5861-5941
            618-737             AC115088.6         6392-6511
            738-784             AC115088.6         9659-9705
            785-925             AC115088.6         10699-10839
            926-966             AC115088.6         16755-16795
            967-1063            AC115088.6         17617-17713
            1064-1162           AC115088.6         18046-18144
            1163-1256           AC115088.6         19914-20007
            1257-1393           AC115088.6         25905-26041
            1394-1508           AC115088.6         28295-28409
            1509-1586           AC115088.6         29021-29098
            1587-1703           AC115088.6         29316-29432
            1704-1832           AC115088.6         29926-30054
            1833-2341           AC115088.6         32777-33285
            2342-4094           AC115088.6         33288-35040
FEATURES             Location/Qualifiers
     source          1..4094
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11p11.2"
     gene            1..4094
                     /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..536
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     CDS             468..1910
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="isoform f is encoded by transcript variant 44;
                     autophagy-related protein 13; ATG13 autophagy related 13
                     homolog"
                     /codon_start=1
                     /product="autophagy-related protein 13 isoform f"
                     /protein_id="NP_001333282.1"
                     /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            537..617
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            618..737
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            738..784
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            785..925
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            926..966
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            967..1063
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1064..1162
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1163..1256
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1257..1393
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1394..1508
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1509..1586
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1587..1703
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1704..1832
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1833..4094
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2593..2598
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="hexamer: AATAAA"
     polyA_site      2612
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="major polyA site"
     regulatory      4072..4077
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="hexamer: AATAAA"
     polyA_site      4094
                     /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 ctggattcct ataggcaatg gaaactgatc
      481 tcaattccca ggacagaaag gacctggaca agtttattaa attttttgcc ctcaagactg
      541 tccaagtgat tgtccaggct cggcttggtg aaaagatttg cactcgttca tcatcttctc
      601 caacgggttc agattggttc aacttagcaa tcaaagacat cccagaggtt acacatgaag
      661 caaagaaggc actggcagga cagctgcctg cagtcgggag gtccatgtgt gtggagattt
      721 cacttaagac ttctgaggga gattccatgg agctggaaat atggtgtctt gaaatgaatg
      781 aaaagtgtga taaagaaatc aaagtttcct acacggtgta caacagactg tcattgctgc
      841 tgaagtccct tcttgctata actagggtga caccagccta taggctctcc aggaaacaag
      901 ggcatgaata tgtcatatta tacaggatat attttggaga agttcagctg agtggcttag
      961 gagaaggctt ccagacagtt cgtgttggga cagtgggcac ccctgtgggc accatcactc
     1021 tttcttgtgc ttacagaatt aacttggcat tcatgtctac caggcaattt gagaggaccc
     1081 cacctatcat ggggattatt attgatcact ttgtggaccg tccctatccc agctcctctc
     1141 ccatgcaccc ctgcaattac agaactgctg gtgaggacac tggagtaata tacccgtctg
     1201 tagaagactc tcaagaagtg tgtaccacct ctttttccac ctccccacca tcccagctga
     1261 tggttcctgg gaaggaaggt ggggtacccc ttgctcccaa ccagcctgtc catggtaccc
     1321 aggctgacca ggagagactg gcaacctgca ccccttctga cagaacccac tgtgctgcca
     1381 caccctccag tagtgaggat actgaaaccg tatcaaacag cagtgaggga cgggcctccc
     1441 ctcacgatgt cttggagacc atctttgtcc gaaaagtggg ggcttttgtc aacaaaccca
     1501 ttaaccaggt gaccctgacg agtttggata taccctttgc catgtttgct cccaagaatt
     1561 tggagctgga ggataccgat ccaatggtga atcctccaga ttccccagag actgaatctc
     1621 ctctccaggg cagcctgcac tcagatggct ccagcggggg cagcagtggc aatacccatg
     1681 atgactttgt tatgatagac tttaaaccag ctttttctaa agatgacatt cttccgatgg
     1741 acctggggac cttctatcgg gagtttcaga acccacctca gctgagcagc ctctccatag
     1801 atattggagc acagtccatg gctgaagact tggactcatt accagagaag ctggctgtgc
     1861 atgagaagaa tgtccgcgag tttgatgcct ttgtggaaac cctgcagtaa aagtatcctt
     1921 gagtcccagc agcaccccct ttttgtggcc ccagggcata agcagcctcc catgcatcag
     1981 ctgctcccac ccctcatcct gctctgagcc aggtggaagg gaggctggct tctcccatgg
     2041 ggacccagaa gtccctactc ttggacctcc tggagactcc gtggcggcag tcaagcccag
     2101 tgcccagttg gagaagactc acgtgctggc cttggagatg ggaagaacct tcgtacgaaa
     2161 aagccctcag cagggccatc tgtgtgccct gcccatcacc aactgcttcc caagggtgtc
     2221 atcctgttcc tcctgctgcc ggcctcctgc ctgggcctgc cttgcagctg gccccttccc
     2281 tgcctgctgt caccatccac tgtttgacat tccagctggt ggccaagaga ttggtgtgga
     2341 ggcagaaaga ggaaggagac agtgccagga ggaagaagga aggagtccct tagctctctt
     2401 cattgtcccc tttacttcct gctatcttct tctcctcttc ttctctctct tgcctctatg
     2461 cctgtatttc tggcaatatg acaggcctgc ctacccaaga tcagaactcc aaaaccactc
     2521 ccacccctga aggtcgggag ggtctgagca gccctggtgg ctgcctgtgc tcaggtcctc
     2581 agctccatgg gaaataaaaa tggcaccctg aatctctagg attttgtcac ttggagtcac
     2641 agcaaagttc tcttcctctt gtccccccgt tgctgctcct tggttataga acatggtaaa
     2701 tatttattac tttcagagaa accagatatt ttatagagga aatatgtttg aggtgagttg
     2761 tttttcactt ggagaaggcg gagggctctt cctgggacgg agacctcctc ctccggaggt
     2821 tattgagaat ccgggctgct gctttgagga tcttcccacc atacagacag cgagatccaa
     2881 gaagagggct ggccgggggc aaagtcacct cccagtgtgg ctgcactgga actgactaaa
     2941 ggctttacct tggatagttg cgtattcctg gtgagagcct tacatctccc acagtttctg
     3001 cagagtgact gactccattc tggcagccca ggaagtcctg ggtgctaaat gtgatggcca
     3061 catgtagtgg ttaggggatg ttgtgtgtgt cccccaactg cctgggtact tgttcctgat
     3121 ccctggggct gtcctgtgga gcttttcctc ctgcttgggc ctagctacca tctccctcta
     3181 atcccaggtt ctctacactg ccctggggtt taccagctgg attggcttct ggttgagaaa
     3241 tcaaagctgg gcgtatgatt gacttaaccc ttcaggtatt gttacttgaa taagtcaagt
     3301 gcctagcctc acccacctat gatctgtcct ttcccagcct cgctggtagt cctggtcaag
     3361 gagatctagg tctactccat tcctcctggc ccacctgggg cattcactgg cagcagctgt
     3421 gcttcagtgg agcaggtggt tctcagctgc ttgttagtat actgcatgtg acactgttcc
     3481 cacatacaag gctgacttct gaggattgga gcaggctctg gcggggacca gagctctgcg
     3541 tgctgctgct gccaccaaga agtgttagca gaagcagtag cagccaactg gccctcctga
     3601 ctttggccca gagcacatgc gtggcttgct gaacccaggc tcaggtttat ccccaaggcc
     3661 ccagctttga gaagggggaa ggcccctggt aagttattga tgcccccata tttcagctac
     3721 tgctctcttt ccaaggcctt gcatggaaag gcctagccat tgtctgaggc agcaatcttt
     3781 ggcatctaca ggtggcagca gcctttcacc agggctccat ctgtgaagag tctcagccat
     3841 gactttgagc tgagcttggg agaagtaaag caactgttaa ggccagccct tgcccctcag
     3901 acctgccatg aaaggaatga gccctagact gactcctgca gcacccccgg gacaggctgg
     3961 gaccagctgt ttgtctccag gtgtcagagt ccctcctcct cctccaacct ctccaaccta
     4021 ctttgtttgg aaataccgag ctacacttca aaatgtattc aagggatttc caataaattt
     4081 ttttctgtac ttta
//
