LOCUS       NM_001355419            3684 bp    mRNA    linear   ROD 02-MAY-2024
DEFINITION  Mus musculus autophagy related 13 (Atg13), transcript variant 4,
            mRNA.
ACCESSION   NM_001355419 XM_006499890
VERSION     NM_001355419.1
KEYWORDS    RefSeq; RefSeq Select.
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 3684)
  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 3684)
  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 3684)
  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 3684)
  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 3684)
  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 3684)
  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 3684)
  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 3684)
  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 3684)
  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 3684)
  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 20, 2017 this sequence version replaced XM_006499890.3.
            
            Transcript Variant: This variant (4) lacks an alternate in-frame
            exon compared to variant 1. The resulting isoform (4) 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 :: SRR1660817.141902.1,
                                           SRR1660819.190820.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN01164131 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation
            ##RefSeq-Attributes-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
            1146-1256           AL714023.12        29207-29317         c
            1257-1393           AL714023.12        28740-28876         c
            1394-1508           AL714023.12        27524-27638         c
            1509-1586           AL714023.12        27101-27178         c
            1587-1703           AL714023.12        26494-26610         c
            1704-1832           AL714023.12        25908-26036         c
            1833-3684           AL714023.12        21793-23644         c
FEATURES             Location/Qualifiers
     source          1..3684
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 50.63 cM"
     gene            1..3684
                     /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..1910
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /note="isoform 4 is encoded by transcript variant 4;
                     autophagy-related protein 13; ATG13 autophagy related 13
                     homolog"
                     /codon_start=1
                     /product="autophagy-related protein 13 isoform 4"
                     /protein_id="NP_001342348.1"
                     /db_xref="CCDS:CCDS89517.1"
                     /db_xref="GeneID:51897"
                     /db_xref="MGI:MGI:1196429"
                     /translation="METELSSQDRKDLDKFIKFFALKTVQVIVQARLGEKICTRSSSS
                     PTGSDWFNLAIKDIPEVTHEAKKALSGQLPAVGRSMCVEISLKTSEGDSMELEIWCLE
                     MNEKCDKEIKVSYTVYNRLSLLLKSLLAITRVTPAYRLSRKQGHEYVILYRIYFGEVQ
                     LNGLGEGFQTVRVGTVGTPVGTLTLSCAYRINLAFMSTRQFERTPPIMGIIIDHFVDR
                     PYPSSSPMHPCNYRTAEDAGVAYPSVEDSQEVCTTSFSTSPPSQLSSSRLSYQPAVLG
                     LGSADLAYPVVFTAGLNTTHAHQLMVPGKEGGVTLAPSHPTHGAQADPERLVMHMPSD
                     GTHCAATPSSSEDTETVSNSSEGRASPHDILETIFVRKVGAFVNKPINQVTVTSLDIP
                     FAMFAPKNLELEDADPMVNPPESPETTSPLHGSLHSDGSSGGSGGSTHDDFVMIDFKP
                     AFSKDDILPMDLGTFYREFQNPPQLSSLSIDFGAQSMAEDLDSLPEKLAVHEKNVREF
                     DAFVETLQ"
     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..1256
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1257..1393
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1394..1508
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1509..1586
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1587..1703
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1704..1832
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     exon            1833..3684
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /inference="alignment:Splign:2.1.0"
     polyA_site      2663
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /note="major polyA site"
     regulatory      3654..3659
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Atg13"
                     /gene_synonym="1110053A20Rik; D2Ertd391e; Harbi1"
                     /note="hexamer: AATAAA"
     polyA_site      3671
                     /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 cccagctctc aagctctcgc ctttcctatc agcctgctgt cctgggcctt ggatcggctg
     1201 acctggctta tccagtagtg tttactgctg gcttaaacac tacacacgct caccagctga
     1261 tggttcctgg gaaggaaggc ggggtaactc ttgctcccag ccaccccact catggtgccc
     1321 aggctgatcc cgagagactg gtgatgcaca tgccttctga tgggacccat tgtgccgcca
     1381 cgccctcaag cagtgaggac actgagactg tgtctaacag cagtgaagga cgggcctcac
     1441 cccatgacat cttggagact atctttgtcc gaaaagtggg agcatttgtc aacaaaccca
     1501 tcaatcaggt gactgtgacg agtttggaca tacctttcgc catgtttgct cccaagaatt
     1561 tggagctgga ggatgctgat cctatggtga atcccccgga gtccccagag accacatctc
     1621 ccctccatgg cagcctgcac tcagatggct ccagcggggg cagcgggggc agcacacatg
     1681 acgactttgt tatgattgac tttaaaccag ctttttctaa agacgacatt cttccaatgg
     1741 acttggggac cttctaccgt gaatttcaga acccccctca gctgagcagc ctctccatag
     1801 attttggagc tcagtctatg gcggaagatt tggactcctt accagagaag ctggctgtgc
     1861 atgagaagaa tgtccgagaa ttcgatgcct ttgtggaaac cctgcagtaa aagtgtcccg
     1921 agtgtctgca gcaccccctt tctgtggacc cagcagagaa cctcctcttc ctcagctgct
     1981 tcctagcctt catgctggtt ctggccaggt gaaagacagg gtggttcccc tatgggacct
     2041 acaagtccct gctcttgaac ttcctggaga ctcatggcag cagtcaggcc cagtgccgga
     2101 cttggcgagg actcgggccg tcgagctgga agctggctgt aacagagcct cagcaaggac
     2161 tgtcctcagc tgcttcacaa agggtgtcat ctgttcttcc tgctaccagc ctcctgcctg
     2221 ggtctaccct gaggccggcc cctacctgct tgtccttacc atcaaccacc tgacattcca
     2281 gctggtggct agaacgctgg gcaaggcaga aagaggaaga aaaccaagga gaccaacccg
     2341 ggcgaaggag ggccctgcat cacttcctgg accaccccac tctcccaccc ttctttctcc
     2401 ccttcccttc cttccgtttt cattcactcc ctttctccca ccttccatcc cttgccttcc
     2461 tgggcctgtg cttttgacaa tatgacaggc caatctgcct aaaatgacaa gtattccaaa
     2521 gctagccacc atttcccaaa ggctgcaaca gcctgtttgt agaattcgtt attgagagtc
     2581 acagaaaggt tctttcctcg ttttccctca atcgctgctg cgtggatata gaccatggta
     2641 aatatttatt actttcagag aaatcagata ttttatagaa gtatgtttgg ggttagcagt
     2701 tccactgggg aaggaggagg gtttcttctg ggatgtcggc ctcccgtgaa gattgctcag
     2761 tacctgtgag gatactcctg tcacatctaa ggagagatca ggaatggcct ggcaaaggcc
     2821 aagcggcccc ctcaggctgc gtgtatggac atgtgcaggc gttaggcttc cccagcatgc
     2881 tgcgtacccc aggaaatctc gggtatgttc agtgtggtga ctcctcagag ttgtgttgca
     2941 cacggtgccc caggagcact gtgtgtcctg ctgctcaagt tcctgagcct ggagcaggac
     3001 tagggagctc ttcctccttc ctctagtccc agagtctgta cgaggccctg gctttacaag
     3061 ctggattggt tccccttcaa gaaaccaaag ctgagcttat ggttgacgta aaccttcagg
     3121 tttgcttgag tgagtcaagt gcctctgcca gcctgctctg ttcctctgtc cctggatcct
     3181 cactggcagc agctgttacg cattggagca ggtggctcgc aactgcttgt tagaaatctg
     3241 catgtaacac tggagccttt cccctgtgca tgctttgctg ccacagagaa atgtgcccag
     3301 cggtggtggc caaatgccat tgcagccttt gggtcagggg cacactcatg gcctacttaa
     3361 accagatata ccccccagag ccagaactgt aggggggtga gggcacgggt tctttgcagg
     3421 gctcagccag tggcctttgc agacagcagc ctttatgtcc tagattatta ggaaggaggc
     3481 cagggaagct gagcagagca tccttcacgg tagcctctgc ccttcagccc tacacaatgg
     3541 aaggatgctc tctagaccaa tgcagccaag ctcaggctag gaccaggtaa ggcccctcca
     3601 gtgctttgtt gggaaatgag agctacacct ggaaatataa tcaagagatt tccaataaaa
     3661 agttttctgt acttcatagc ttcc
//
