LOCUS       NM_001346311            4246 bp    mRNA    linear   PRI 21-SEP-2024
DEFINITION  Homo sapiens autophagy related 13 (ATG13), transcript variant 7,
            mRNA.
ACCESSION   NM_001346311 XM_005253262
VERSION     NM_001346311.2
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 4246)
  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 4246)
  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 4246)
  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 4246)
  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 4246)
  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 4246)
  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 4246)
  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 4246)
  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 4246)
  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 4246)
  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.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Apr 14, 2020 this sequence version replaced NM_001346311.1.
            
            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 (7), as well as variants 3 and
            8-12, 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 :: SRR1803617.81040.1,
                                           SRR1803614.273324.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968968, SAMEA2145743
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000683050.1/ ENSP00000507809.1
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
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
            866-906             AC115088.6         16755-16795
            907-1003            AC115088.6         17617-17713
            1004-1102           AC115088.6         18046-18144
            1103-1196           AC115088.6         19914-20007
            1197-1295           AC115088.6         24519-24617
            1296-1406           AC115088.6         25371-25481
            1407-1543           AC115088.6         25905-26041
            1544-1658           AC115088.6         28295-28409
            1659-1736           AC115088.6         29021-29098
            1737-1853           AC115088.6         29316-29432
            1854-1982           AC115088.6         29926-30054
            1983-4246           AC115088.6         32777-35040
FEATURES             Location/Qualifiers
     source          1..4246
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11p11.2"
     gene            1..4246
                     /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"
     CDS             408..2060
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="isoform a is encoded by transcript variant 7;
                     autophagy-related protein 13; ATG13 autophagy related 13
                     homolog"
                     /codon_start=1
                     /product="autophagy-related protein 13 isoform a"
                     /protein_id="NP_001333240.1"
                     /db_xref="CCDS:CCDS55760.1"
                     /db_xref="GeneID:9776"
                     /db_xref="HGNC:HGNC:29091"
                     /db_xref="MIM:615088"
                     /translation="METDLNSQDRKDLDKFIKFFALKTVQVIVQARLGEKICTRSSSS
                     PTGSDWFNLAIKDIPEVTHEAKKALAGQLPAVGRSMCVEISLKTSEGDSMELEIWCLE
                     MNEKCDKEIKVSYTVYNRLSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQ
                     LSGLGEGFQTVRVGTVGTPVGTITLSCAYRINLAFMSTRQFERTPPIMGIIIDHFVDR
                     PYPSSSPMHPCNYRTAGEDTGVIYPSVEDSQEVCTTSFSTSPPSQCVFTVTKAHFQTP
                     TPVVTDTLRVPMAGLAFSHQLSSSRLSYQPAALGVGSADLAYPVVFAAGLNATHPHQL
                     MVPGKEGGVPLAPNQPVHGTQADQERLATCTPSDRTHCAATPSSSEDTETVSNSSEGR
                     ASPHDVLETIFVRKVGAFVNKPINQVTLTSLDIPFAMFAPKNLELEDTDPMVNPPDSP
                     ETESPLQGSLHSDGSSGGSSGNTHDDFVMIDFKPAFSKDDILPMDLGTFYREFQNPPQ
                     LSSLSIDIGAQSMAEDLDSLPEKLAVHEKNVREFDAFVETLQ"
     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..906
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            907..1003
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1004..1102
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1103..1196
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1197..1295
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1296..1406
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1407..1543
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1544..1658
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1659..1736
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1737..1853
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1854..1982
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     exon            1983..4246
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2745..2750
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="hexamer: AATAAA"
     polyA_site      2764
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="major polyA site"
     regulatory      4224..4229
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG13"
                     /gene_synonym="KIAA0652; PARATARG8"
                     /note="hexamer: AATAAA"
     polyA_site      4246
                     /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 gagaaggctt ccagacagtt cgtgttggga cagtgggcac ccctgtgggc accatcactc
      961 tttcttgtgc ttacagaatt aacttggcat tcatgtctac caggcaattt gagaggaccc
     1021 cacctatcat ggggattatt attgatcact ttgtggaccg tccctatccc agctcctctc
     1081 ccatgcaccc ctgcaattac agaactgctg gtgaggacac tggagtaata tacccgtctg
     1141 tagaagactc tcaagaagtg tgtaccacct ctttttccac ctccccacca tcccagtgtg
     1201 tgtttactgt cacaaaggca cattttcaga cccctactcc tgtggtgacg gacaccctga
     1261 gggtccccat ggcaggactg gccttttccc atcaactctc aagctctcgc ctttcctatc
     1321 agcctgctgc cctgggcgtt ggatcagctg acctggctta tccagtagtg tttgctgctg
     1381 gcttaaatgc tacacaccct caccagctga tggttcctgg gaaggaaggt ggggtacccc
     1441 ttgctcccaa ccagcctgtc catggtaccc aggctgacca ggagagactg gcaacctgca
     1501 ccccttctga cagaacccac tgtgctgcca caccctccag tagtgaggat actgaaaccg
     1561 tatcaaacag cagtgaggga cgggcctccc ctcacgatgt cttggagacc atctttgtcc
     1621 gaaaagtggg ggcttttgtc aacaaaccca ttaaccaggt gaccctgacg agtttggata
     1681 taccctttgc catgtttgct cccaagaatt tggagctgga ggataccgat ccaatggtga
     1741 atcctccaga ttccccagag actgaatctc ctctccaggg cagcctgcac tcagatggct
     1801 ccagcggggg cagcagtggc aatacccatg atgactttgt tatgatagac tttaaaccag
     1861 ctttttctaa agatgacatt cttccgatgg acctggggac cttctatcgg gagtttcaga
     1921 acccacctca gctgagcagc ctctccatag atattggagc acagtccatg gctgaagact
     1981 tggactcatt accagagaag ctggctgtgc atgagaagaa tgtccgcgag tttgatgcct
     2041 ttgtggaaac cctgcagtaa aagtatcctt gagtcccagc agcaccccct ttttgtggcc
     2101 ccagggcata agcagcctcc catgcatcag ctgctcccac ccctcatcct gctctgagcc
     2161 aggtggaagg gaggctggct tctcccatgg ggacccagaa gtccctactc ttggacctcc
     2221 tggagactcc gtggcggcag tcaagcccag tgcccagttg gagaagactc acgtgctggc
     2281 cttggagatg ggaagaacct tcgtacgaaa aagccctcag cagggccatc tgtgtgccct
     2341 gcccatcacc aactgcttcc caagggtgtc atcctgttcc tcctgctgcc ggcctcctgc
     2401 ctgggcctgc cttgcagctg gccccttccc tgcctgctgt caccatccac tgtttgacat
     2461 tccagctggt ggccaagaga ttggtgtgga gtcgcagaaa gaggaaggag acagtgccag
     2521 gaggaagaag gaaggagtcc cttagctctc ttcattgtcc cctttacttc ctgctatctt
     2581 cttctcctct tcttctctct cttgcctcta tgcctgtatt tctggcaata tgacaggcct
     2641 gcctacccaa gatcagaact ccaaaaccac tcccacccct gaaggtcggg agggtctgag
     2701 cagccctggt ggctgcctgt gctcaggtcc tcagctccat gggaaataaa aatggcaccc
     2761 tgaatctcta ggattttgtc acttggagtc acagcaaagt tctcttcctc ttgtcccccc
     2821 gttgctgctc cttggttata gaacatggta aatatttatt actttcagag aaaccagata
     2881 ttttatagag gaaatatgtt tgaggtgagt tgtttttcac ttggagaagg cggagggctc
     2941 ttcctgggac ggagacctcc tcctccggag gttattgaga atccgggctg ctgctttgag
     3001 gatcttccca ccatacagac agcgagatcc aagaagaggg ctggccgggg gcaaagtcac
     3061 ctcccagtgt ggctgcactg gaactgacta aaggctttac cttggatagt tgcgtattcc
     3121 tggtgagagc cttacatctc ccacagtttc tgcagagtga ctgactccat tctggcagcc
     3181 caggaagtcc tgggtgctaa atgtgatggc cacatgtagt ggttagggga tgttgtgtgt
     3241 gtcccccaac tgcctgggta cttgttcctg atccctgggg ctgtcctgtg gagcttttcc
     3301 tcctgcttgg gcctagctac catctccctc taatcccagg ttctctacac tgccctgggg
     3361 tttaccagct ggattggctt ctggttgaga aatcaaagct gggcgtatga ttgacttaac
     3421 ccttcaggta ttgttacttg aataagtcaa gtgcctagcc tcacccacct atgatctgtc
     3481 ctttcccagc ctcgctggta gtcctggtca aggagatcta ggtctactcc attcctcctg
     3541 gcccacctgg ggcattcact ggcagcagct gtgcttcagt ggagcaggtg gttctcagct
     3601 gcttgttagt atactgcatg tgacactgtt cccacataca aggctgactt ctgaggattg
     3661 gagcaggctc tggcggggac cagagctctg cgtgctgctg ctgccaccaa gaagtgttag
     3721 cagaagcagt agcagccaac tggccctcct gactttggcc cagagcacat gcgtggcttg
     3781 ctgaacccag gctcaggttt atccccaagg ccccagcttt gagaaggggg aaggcccctg
     3841 gtaagttatt gatgccccca tatttcagct actgctctct ttccaaggcc ttgcatggaa
     3901 aggcctagcc attgtctgag gcagcaatct ttggcatcta caggtggcag cagcctttca
     3961 ccagggctcc atctgtgaag agtctcagcc atgactttga gctgagcttg ggagaagtaa
     4021 agcaactgtt aaggccagcc cttgcccctc agacctgcca tgaaaggaat gagccctaga
     4081 ctgactcctg cagcaccccc gggacaggct gggaccagct gtttgtctcc aggtgtcaga
     4141 gtccctcctc ctcctccaac ctctccaacc tactttgttt ggaaataccg agctacactt
     4201 caaaatgtat tcaagggatt tccaataaat ttttttctgt acttta
//
