LOCUS       NM_001355420            3657 bp    mRNA    linear   ROD 30-APR-2024
DEFINITION  Mus musculus autophagy related 13 (Atg13), transcript variant 5,
            mRNA.
ACCESSION   NM_001355420 XM_006499891
VERSION     NM_001355420.1
KEYWORDS    RefSeq.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 3657)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 3657)
  AUTHORS   Li,H., Li,C., Zhai,W., Zhang,X., Li,L., Wu,B., Yu,B., Zhang,P.,
            Li,J., Cui,C.P. and Zhang,L.
  TITLE     Destabilization of TP53 by USP10 is essential for neonatal
            autophagy and survival
  JOURNAL   Cell Rep 41 (1), 111435 (2022)
   PUBMED   36198274
REFERENCE   3  (bases 1 to 3657)
  AUTHORS   Li,X., Zhu,Y., Lin,X., Chen,C., Liu,H. and Shi,Y.
  TITLE     Beclin1- and Atg13-dependent autophagy activation and morroniside
            have synergistic effect on osteoblastogenesis
  JOURNAL   Exp Biol Med (Maywood) 247 (19), 1764-1775 (2022)
   PUBMED   35957534
  REMARK    GeneRIF: Beclin1- and Atg13-dependent autophagy activation and
            morroniside have synergistic effect on osteoblastogenesis.
REFERENCE   4  (bases 1 to 3657)
  AUTHORS   Ding,S., Abudupataer,M., Zhou,Z., Chen,J., Li,H., Xu,L., Zhang,W.,
            Zhang,S., Zou,Y., Hong,T., Wang,T.C., Yang,X. and Ge,J.
  TITLE     Histamine deficiency aggravates cardiac injury through
            miR-206/216b-Atg13 axis-mediated autophagic-dependant apoptosis
  JOURNAL   Cell Death Dis 9 (6), 694 (2018)
   PUBMED   29880830
  REMARK    GeneRIF: acting through histamine 1 receptor, histamine increased
            miR-206 and miR-216b, which worked in concert to target to Atg13,
            resulting in the reduction of autophagy activation under hypoxia
            and acute myocardial infarction condition.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3657)
  AUTHORS   Wallot-Hieke,N., Verma,N., Schlutermann,D., Berleth,N.,
            Deitersen,J., Bohler,P., Stuhldreier,F., Wu,W., Seggewiss,S.,
            Peter,C., Gohlke,H., Mizushima,N. and Stork,B.
  TITLE     Systematic analysis of ATG13 domain requirements for autophagy
            induction
  JOURNAL   Autophagy 14 (5), 743-763 (2018)
   PUBMED   29173006
  REMARK    GeneRIF: these data establish the interaction between ATG13 and
            ATG101 as a promising target in disease-settings where the
            inhibition of autophagy is desired.
REFERENCE   6  (bases 1 to 3657)
  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
REFERENCE   7  (bases 1 to 3657)
  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
REFERENCE   8  (bases 1 to 3657)
  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
REFERENCE   9  (bases 1 to 3657)
  AUTHORS   Kerns,R.T., Ravindranathan,A., Hassan,S., Cage,M.P., York,T.,
            Sikela,J.M., Williams,R.W. and Miles,M.F.
  TITLE     Ethanol-responsive brain region expression networks: implications
            for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J
            mice
  JOURNAL   J Neurosci 25 (9), 2255-2266 (2005)
   PUBMED   15745951
REFERENCE   10 (bases 1 to 3657)
  AUTHORS   Okazaki,N., Kikuno,R., Ohara,R., Inamoto,S., Aizawa,H., Yuasa,S.,
            Nakajima,D., Nagase,T., Ohara,O. and Koga,H.
  TITLE     Prediction of the coding sequences of mouse homologues of KIAA
            gene: II. The complete nucleotide sequences of 400 mouse
            KIAA-homologous cDNAs identified by screening of terminal sequences
            of cDNA clones randomly sampled from size-fractionated libraries
  JOURNAL   DNA Res 10 (1), 35-48 (2003)
   PUBMED   12693553
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL714023.12.
            
            On Sep 15, 2017 this sequence version replaced XM_006499891.3.
            
            Transcript Variant: This variant (5) lacks an alternate in-frame
            exon and uses an alternate in-frame splice junction compared to
            variant 1. The resulting isoform (5) has the same N- and C-termini
            but is shorter compared to isoform 1.
            
            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 :: SRR7974084.1560.1,
                                           SRR1660817.213103.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164131 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-346               AL714023.12        57428-57773         c
            347-428             AL714023.12        43099-43180         c
            429-509             AL714023.12        41106-41186         c
            510-629             AL714023.12        39609-39728         c
            630-676             AL714023.12        36972-37018         c
            677-817             AL714023.12        35822-35962         c
            818-858             AL714023.12        33682-33722         c
            859-955             AL714023.12        32963-33059         c
            956-1054            AL714023.12        32332-32430         c
            1055-1145           AL714023.12        31850-31940         c
            1146-1229           AL714023.12        29207-29290         c
            1230-1366           AL714023.12        28740-28876         c
            1367-1481           AL714023.12        27524-27638         c
            1482-1559           AL714023.12        27101-27178         c
            1560-1676           AL714023.12        26494-26610         c
            1677-1805           AL714023.12        25908-26036         c
            1806-3657           AL714023.12        21793-23644         c
FEATURES             Location/Qualifiers
     source          1..3657
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 50.63 cM"
     gene            1..3657
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /note="autophagy related 13"
                     /db_xref="GeneID:51897"
                     /db_xref="MGI:MGI:1196429"
     exon            1..346
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            347..428
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     CDS             360..1883
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /note="isoform 5 is encoded by transcript variant 5;
                     autophagy-related protein 13; ATG13 autophagy related 13
                     homolog"
                     /codon_start=1
                     /product="autophagy-related protein 13 isoform 5"
                     /protein_id="NP_001342349.1"
                     /db_xref="GeneID:51897"
                     /db_xref="MGI:MGI:1196429"
                     /translation="METELSSQDRKDLDKFIKFFALKTVQVIVQARLGEKICTRSSSS
                     PTGSDWFNLAIKDIPEVTHEAKKALSGQLPAVGRSMCVEISLKTSEGDSMELEIWCLE
                     MNEKCDKEIKVSYTVYNRLSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQ
                     LNGLGEGFQTVRVGTVGTPVGTLTLSCAYRINLAFMSTRQFERTPPIMGIIIDHFVDR
                     PYPSSSPMHPCNYRTAEDAGVAYPSVEDSQEVCTTSFSTSPPSQPAVLGLGSADLAYP
                     VVFTAGLNTTHAHQLMVPGKEGGVTLAPSHPTHGAQADPERLVMHMPSDGTHCAATPS
                     SSEDTETVSNSSEGRASPHDILETIFVRKVGAFVNKPINQVTVTSLDIPFAMFAPKNL
                     ELEDADPMVNPPESPETTSPLHGSLHSDGSSGGSGGSTHDDFVMIDFKPAFSKDDILP
                     MDLGTFYREFQNPPQLSSLSIDFGAQSMAEDLDSLPEKLAVHEKNVREFDAFVETLQ"
     exon            429..509
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            510..629
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            630..676
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            677..817
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            818..858
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            859..955
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            956..1054
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1055..1145
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1146..1229
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1230..1366
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1367..1481
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1482..1559
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1560..1676
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1677..1805
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1806..3657
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     polyA_site      2636
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /note="major polyA site"
     regulatory      3627..3632
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /note="hexamer: AATAAA"
     polyA_site      3644
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /note="major polyA site"
ORIGIN      
        1 catttcctcc gtagcgctct acctccccac cgcctgcact gaagcggatg aaaacaaaca
       61 ctaaggatgg cggcgccggg cagcgactgg ttgctggctt agggcgggag agatcgtttg
      121 acgtgtgaag gggaagctct gagaaaaacc agtccacacc agtccgacag ctttttcagt
      181 tctgggatcc cggagcctcg ttagcgtgag atatctctct gcgacctgtg ctgtcactac
      241 cgcccgggag cgcggaaccc tctgctggga ggtgcagttg gccggcccca ggccccggcc
      301 tccggaatga gagcccggag ccactctctg tgccgtagct tcgcaggttc cagcaggcaa
      361 tggaaactga actcagctcc caggacagga aggacttgga caagtttatt aagttttttg
      421 ccctcaagac tgtccaagtg attgtccagg ctcgacttgg agaaaagatt tgcacccgct
      481 catcatcttc cccgacgggt tcagattggt tcaatttagc aatcaaagac atcccagaag
      541 tcacccatga agcaaagaag gccctgtcag ggcagctgcc tgctgtgggg cgatctatgt
      601 gtgtggaaat ctcactcaag acttctgagg gagattctat ggagttggaa atttggtgtc
      661 ttgaaatgaa tgaaaagtgt gacaaagaaa tcaaagtttc ctacactgta tacaaccgat
      721 tgtcactgct gctgaagtct cttctcgcta ttacaagggt gacaccagcc tatcgactct
      781 ccaggaagca agggcatgaa tatgtaattt tgtacaggat ttattttggg gaagttcaac
      841 tgaatggctt aggagaaggc ttccagacag ttcgagttgg aacagtgggc acccctgtgg
      901 gcaccctcac tctttcctgt gcttatagaa ttaacttggc attcatgtcc accaggcaat
      961 ttgagaggac cccacctatc atggggatta tcattgatca ctttgttgac cgtccctatc
     1021 ccagctcttc tcctatgcac ccctgtaatt acagaactgc tgaggacgca ggggtcgcgt
     1081 acccgtcagt ggaagactct caggaagtgt gtaccacatc tttttccaca tcccctccct
     1141 cccagcctgc tgtcctgggc cttggatcgg ctgacctggc ttatccagta gtgtttactg
     1201 ctggcttaaa cactacacac gctcaccagc tgatggttcc tgggaaggaa ggcggggtaa
     1261 ctcttgctcc cagccacccc actcatggtg cccaggctga tcccgagaga ctggtgatgc
     1321 acatgccttc tgatgggacc cattgtgccg ccacgccctc aagcagtgag gacactgaga
     1381 ctgtgtctaa cagcagtgaa ggacgggcct caccccatga catcttggag actatctttg
     1441 tccgaaaagt gggagcattt gtcaacaaac ccatcaatca ggtgactgtg acgagtttgg
     1501 acataccttt cgccatgttt gctcccaaga atttggagct ggaggatgct gatcctatgg
     1561 tgaatccccc ggagtcccca gagaccacat ctcccctcca tggcagcctg cactcagatg
     1621 gctccagcgg gggcagcggg ggcagcacac atgacgactt tgttatgatt gactttaaac
     1681 cagctttttc taaagacgac attcttccaa tggacttggg gaccttctac cgtgaatttc
     1741 agaacccccc tcagctgagc agcctctcca tagattttgg agctcagtct atggcggaag
     1801 atttggactc cttaccagag aagctggctg tgcatgagaa gaatgtccga gaattcgatg
     1861 cctttgtgga aaccctgcag taaaagtgtc ccgagtgtct gcagcacccc ctttctgtgg
     1921 acccagcaga gaacctcctc ttcctcagct gcttcctagc cttcatgctg gttctggcca
     1981 ggtgaaagac agggtggttc ccctatggga cctacaagtc cctgctcttg aacttcctgg
     2041 agactcatgg cagcagtcag gcccagtgcc ggacttggcg aggactcggg ccgtcgagct
     2101 ggaagctggc tgtaacagag cctcagcaag gactgtcctc agctgcttca caaagggtgt
     2161 catctgttct tcctgctacc agcctcctgc ctgggtctac cctgaggccg gcccctacct
     2221 gcttgtcctt accatcaacc acctgacatt ccagctggtg gctagaacgc tgggcaaggc
     2281 agaaagagga agaaaaccaa ggagaccaac ccgggcgaag gagggccctg catcacttcc
     2341 tggaccaccc cactctccca cccttctttc tccccttccc ttccttccgt tttcattcac
     2401 tccctttctc ccaccttcca tcccttgcct tcctgggcct gtgcttttga caatatgaca
     2461 ggccaatctg cctaaaatga caagtattcc aaagctagcc accatttccc aaaggctgca
     2521 acagcctgtt tgtagaattc gttattgaga gtcacagaaa ggttctttcc tcgttttccc
     2581 tcaatcgctg ctgcgtggat atagaccatg gtaaatattt attactttca gagaaatcag
     2641 atattttata gaagtatgtt tggggttagc agttccactg gggaaggagg agggtttctt
     2701 ctgggatgtc ggcctcccgt gaagattgct cagtacctgt gaggatactc ctgtcacatc
     2761 taaggagaga tcaggaatgg cctggcaaag gccaagcggc cccctcaggc tgcgtgtatg
     2821 gacatgtgca ggcgttaggc ttccccagca tgctgcgtac cccaggaaat ctcgggtatg
     2881 ttcagtgtgg tgactcctca gagttgtgtt gcacacggtg ccccaggagc actgtgtgtc
     2941 ctgctgctca agttcctgag cctggagcag gactagggag ctcttcctcc ttcctctagt
     3001 cccagagtct gtacgaggcc ctggctttac aagctggatt ggttcccctt caagaaacca
     3061 aagctgagct tatggttgac gtaaaccttc aggtttgctt gagtgagtca agtgcctctg
     3121 ccagcctgct ctgttcctct gtccctggat cctcactggc agcagctgtt acgcattgga
     3181 gcaggtggct cgcaactgct tgttagaaat ctgcatgtaa cactggagcc tttcccctgt
     3241 gcatgctttg ctgccacaga gaaatgtgcc cagcggtggt ggccaaatgc cattgcagcc
     3301 tttgggtcag gggcacactc atggcctact taaaccagat atacccccca gagccagaac
     3361 tgtagggggg tgagggcacg ggttctttgc agggctcagc cagtggcctt tgcagacagc
     3421 agcctttatg tcctagatta ttaggaagga ggccagggaa gctgagcaga gcatccttca
     3481 cggtagcctc tgcccttcag ccctacacaa tggaaggatg ctctctagac caatgcagcc
     3541 aagctcaggc taggaccagg taaggcccct ccagtgcttt gttgggaaat gagagctaca
     3601 cctggaaata taatcaagag atttccaata aaaagttttc tgtacttcat agcttcc
//
