LOCUS       NM_029846               3149 bp    mRNA    linear   ROD 28-JAN-2025
DEFINITION  Mus musculus autophagy related 16 like 1 (Atg16l1), transcript
            variant 2, mRNA.
ACCESSION   NM_029846
VERSION     NM_029846.4
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 3149)
  AUTHORS   Chvanov,M., Voronina,S., Jefferson,M., Mayer,U., Sutton,R.,
            Criddle,D.N., Wileman,T. and Tepikin,A.V.
  TITLE     Deletion of the WD40 domain of ATG16L1 exacerbates acute
            pancreatitis, abolishes LAP-like non-canonical autophagy and slows
            trypsin degradation
  JOURNAL   Autophagy 21 (1), 210-222 (2025)
   PUBMED   39216469
REFERENCE   2  (bases 1 to 3149)
  AUTHORS   Salesse,L., Duval,A., Sauvanet,P., Da Silva,A., Barnich,N.,
            Godfraind,C., Dalmasso,G. and Nguyen,H.T.T.
  TITLE     ATG16L1 in myeloid cells limits colorectal tumor growth in ApcMin/+
            mice infected with colibactin-producing Escherichia coli via
            decreasing inflammasome activation
  JOURNAL   Autophagy 20 (10), 2186-2204 (2024)
   PUBMED   38818900
REFERENCE   3  (bases 1 to 3149)
  AUTHORS   Wang,Q., Bu,Q., Xu,Z., Liang,Y., Zhou,J., Pan,Y., Zhou,H. and Lu,L.
  TITLE     Macrophage ATG16L1 expression suppresses metabolic
            dysfunction-associated steatohepatitis progression by promoting
            lipophagy
  JOURNAL   Clin Mol Hepatol 30 (3), 515-538 (2024)
   PUBMED   38726504
  REMARK    GeneRIF: Macrophage ATG16L1 expression suppresses metabolic
            dysfunction-associated steatohepatitis progression by promoting
            lipophagy.
REFERENCE   4  (bases 1 to 3149)
  AUTHORS   Martinez-Mayer,J., Brinkmeier,M.L., O'Connell,S.P., Ukagwu,A.,
            Marti,M.A., Miras,M., Forclaz,M.V., Benzrihen,M.G., Cheung,L.Y.M.,
            Camper,S.A., Ellsworth,B.S., Raetzman,L.T., Perez-Millan,M.I. and
            Davis,S.W.
  TITLE     Knockout mice with pituitary malformations help identify human
            cases of hypopituitarism
  JOURNAL   Genome Med 16 (1), 75 (2024)
   PUBMED   38822427
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3149)
  AUTHORS   Feng,S., McNehlan,M.E., Kinsella,R.L., Sur Chowdhury,C.,
            Chavez,S.M., Naik,S.K., McKee,S.R., Van Winkle,J.A., Dubey,N.,
            Samuels,A., Swain,A., Cui,X., Hendrix,S.V., Woodson,R.,
            Kreamalmeyer,D., Smirnov,A., Artyomov,M.N., Virgin,H.W., Wang,Y.T.
            and Stallings,C.L.
  TITLE     Autophagy promotes efficient T cell responses to restrict high-dose
            Mycobacterium tuberculosis infection in mice
  JOURNAL   Nat Microbiol 9 (3), 684-697 (2024)
   PUBMED   38413834
REFERENCE   6  (bases 1 to 3149)
  AUTHORS   Itoh,T., Fujita,N., Kanno,E., Yamamoto,A., Yoshimori,T. and
            Fukuda,M.
  TITLE     Golgi-resident small GTPase Rab33B interacts with Atg16L and
            modulates autophagosome formation
  JOURNAL   Mol Biol Cell 19 (7), 2916-2925 (2008)
   PUBMED   18448665
  REMARK    GeneRIF: Rab33 modulates autophagosome formation through
            interaction with Atg16L
REFERENCE   7  (bases 1 to 3149)
  AUTHORS   Fujita,N., Itoh,T., Omori,H., Fukuda,M., Noda,T. and Yoshimori,T.
  TITLE     The Atg16L complex specifies the site of LC3 lipidation for
            membrane biogenesis in autophagy
  JOURNAL   Mol Biol Cell 19 (5), 2092-2100 (2008)
   PUBMED   18321988
  REMARK    GeneRIF: Atg16L complex is a new type of E3-like enzyme that
            functions as a scaffold for LC3 lipidation by dynamically
            localizing to the putative source membranes for autophagosome
            formation.
REFERENCE   8  (bases 1 to 3149)
  AUTHORS   Okazaki,N., Kikuno,R., Ohara,R., Inamoto,S., Koseki,H., Hiraoka,S.,
            Saga,Y., Kitamura,H., Nakagawa,T., Nagase,T., Ohara,O. and Koga,H.
  TITLE     Prediction of the coding sequences of mouse homologues of FLJ
            genes: the complete nucleotide sequences of 110 mouse
            FLJ-homologous cDnas identified by screening of terminal sequences
            of cDNA clones randomly sampled from size-fractionated libraries
  JOURNAL   DNA Res 11 (2), 127-135 (2004)
   PUBMED   15449545
REFERENCE   9  (bases 1 to 3149)
  AUTHORS   Mizushima,N., Kuma,A., Kobayashi,Y., Yamamoto,A., Matsubae,M.,
            Takao,T., Natsume,T., Ohsumi,Y. and Yoshimori,T.
  TITLE     Mouse Apg16L, a novel WD-repeat protein, targets to the autophagic
            isolation membrane with the Apg12-Apg5 conjugate
  JOURNAL   J Cell Sci 116 (Pt 9), 1679-1688 (2003)
   PUBMED   12665549
  REMARK    GeneRIF: In conjunction with Apg12-Apg5, Apg16L associates with the
            autophagic isolation membrane for the duration of autophagosome
            formation.
REFERENCE   10 (bases 1 to 3149)
  AUTHORS   Mizushima,N., Yamamoto,A., Hatano,M., Kobayashi,Y., Kabeya,Y.,
            Suzuki,K., Tokuhisa,T., Ohsumi,Y. and Yoshimori,T.
  TITLE     Dissection of autophagosome formation using Apg5-deficient mouse
            embryonic stem cells
  JOURNAL   J Cell Biol 152 (4), 657-668 (2001)
   PUBMED   11266458
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC159967.2, AK030983.1 and BE988512.1.
            
            On Apr 20, 2011 this sequence version replaced NM_029846.3.
            
            Transcript Variant: This variant (2, also known as Apg16Lbeta)
            lacks an exon in the coding region, but maintains the reading
            frame, compared to variant 1. The encoded isoform (2, also known as
            Apg16Lbeta) is shorter than isoform 1.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript 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 :: AK030983.1, AB087880.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-60                AC159967.2         7378-7437           c
            61-3126             AK030983.1         2-3067
            3127-3149           BE988512.1         1-23                c
FEATURES             Location/Qualifiers
     source          1..3149
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="1"
                     /map="1 44.44 cM"
     gene            1..3149
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /note="autophagy related 16 like 1"
                     /db_xref="GeneID:77040"
                     /db_xref="MGI:MGI:1924290"
     exon            1..304
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     CDS             190..2013
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /note="isoform 2 is encoded by transcript variant 2;
                     autophagy-related protein 16-1; APG16-like 1; Atg16L1
                     gamma; autophagy-related 16-like 1 gamma"
                     /codon_start=1
                     /product="autophagy-related protein 16-1 isoform 2"
                     /protein_id="NP_084122.2"
                     /db_xref="CCDS:CCDS15136.1"
                     /db_xref="GeneID:77040"
                     /db_xref="MGI:MGI:1924290"
                     /translation="MSSGLRAADFPRWKRHIAEELRRRDRLQRQAFEEIILQYTKLLE
                     KSDLHSVLTQKLQAEKHDMPNRHEISPGHDGAWNDSQLQEMAQLRIKHQEELTELHKK
                     RGELAQLVIDLNNQMQQKDKEIQMNEAKISEYLQTISDLETNCLDLRTKLQDLEVANQ
                     TLKDEYDALQITFTALEEKLRKTTEENQELVTRWMAEKAQEANRLNAENEKDSRRRQA
                     RLQKELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVRAVSRAATKRLSQPAGGLL
                     DSITNIFGRRSVSSIPVPQDIMDTHPASGKDVRVPTTASYVFDAHDGEVNAVQFSPGS
                     RLLATGGMDRRVKLWEAFGDKCEFKGSLSGSNAGITSIEFDSAGAYLLAASNDFASRI
                     WTVDDYRLRHTLTGHSGKVLSAKFLLDNARIVSGSHDRTLKLWDLRSKVCIKTVFAGS
                     SCNDIVCTEQCVMSGHFDKKIRFWDIRSESVVREMELLGKITALDLNPERTELLSCSR
                     DDLLKVIDLRTNAVKQTFSAPGFKCGSDWTRVVFSPDGSYVAAGSAEGSLYVWSVLTG
                     KVEKVLSKQHSSSINAVAWAPSGLHVVSVDKGSRAVLWAQP"
     exon            305..398
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            399..504
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            505..578
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            579..830
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            831..896
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            897..983
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            984..1040
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1041..1143
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1144..1249
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1250..1320
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1321..1392
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1393..1513
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1514..1619
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1620..1769
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1770..1817
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1818..1919
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1920..3132
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3103..3108
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /note="hexamer: AAGAAA"
     polyA_site      3129
                     /gene="Atg16l1"
                     /gene_synonym="1500009K01Rik; Apg16l; Atg16l; WDR30"
                     /note="major polyA site"
ORIGIN      
        1 ggccttctcc agaataattt ccggcagaga ccggaaaatc ttcccggatc gcctccgggt
       61 gccctgtgtg ggaaggtgag gttccggcgg ccggcttctg ttcgctggcg gctggcagca
      121 cgctgcagcc tgcagccccc cagtgtcggc acggatcggc cgccctgagg cgccggggca
      181 gcgttcggca tgtcgtcggg cctgcgcgcc gcagactttc cccgctggaa gcgtcacatc
      241 gcggaggaac tgaggcgccg ggaccgactg cagaggcagg cgttcgagga gatcattctg
      301 cagtatacca agttgctgga aaagtcagat cttcattcag tattgaccca gaaactacaa
      361 gcagaaaagc atgacatgcc aaataggcat gaaataagtc ctggacatga tggtgcgtgg
      421 aatgatagtc aactacaaga aatggcccag ttgaggatca aacaccagga agagctgacc
      481 gaactgcaca agaagcgtgg ggagttagct cagttggtga ttgacctgaa caaccaaatg
      541 cagcagaagg acaaggagat acagatgaat gaagcaaaga tttcggagta tttacagacc
      601 atctctgacc tggagacaaa ctgcctggac ctgcgcacca aactgcagga cctcgaggta
      661 gccaaccaga ccctgaagga tgagtatgac gccctgcaga ttacttttac tgccctagaa
      721 gagaaactga ggaaaactac tgaggagaac caggaactgg tcaccagatg gatggctgag
      781 aaggcccaag aagccaatcg cctcaatgca gagaatgaga aggactccag gaggcgtcaa
      841 gcacggctgc agaaggagct tgcagaagca gcaaaggaac ctctacctgt tgaacaggat
      901 gatgacattg aagtcattgt ggatgagacc tcagaccaca cagaagagac ctctcccgtc
      961 cgagctgtca gcagagcagc tactaagcga ctctcgcagc ctgctggagg ccttctggat
     1021 tctatcacta atatctttgg gagacgctct gtctcttcca tcccagtccc ccaggatatc
     1081 atggacactc atcctgcttc tggtaaagat gtgagagtcc caactactgc ctcgtatgtc
     1141 ttcgatgcgc atgacggaga ggtcaacgca gtgcagttca gtccaggctc ccggttgctg
     1201 gccactggag gcatggaccg cagggtgaaa ctttgggaag cattcggaga taaatgtgaa
     1261 ttcaagggct ccctgtctgg cagtaatgct ggaattacaa gcattgaatt tgatagtgct
     1321 ggagcttacc tattagcagc ttcaaatgat tttgcaagcc gaatctggac tgtggatgat
     1381 tatcgattac ggcacacact cacaggccac agcgggaaag tcctctctgc caagttcctg
     1441 ctggacaatg cacggattgt ctcaggaagt cacgaccgga ccctcaaact ctgggatctc
     1501 cgcagcaaag tctgcataaa aacagtgttt gcaggatcca gctgcaatga cattgtttgc
     1561 actgaacaat gtgtaatgag tggacatttt gacaagaaaa ttcgtttctg ggatatccgg
     1621 tcagagagtg tggtccgaga gatggaactg ttagggaaga tcactgctct ggacctaaac
     1681 cctgagagaa ctgagctcct gagctgctcc cgtgatgacc tgctaaaagt catcgacctc
     1741 cggacaaatg cagtcaaaca gacattcagt gcgcctggat tcaaatgcgg ctctgactgg
     1801 acccgggttg tcttcagccc tgatggcagt tacgtggcag caggctcagc cgagggttct
     1861 ctttatgtct ggagtgtgct gacagggaaa gtggagaagg ttctttcaaa acagcacagc
     1921 tcttctatca atgcggtggc gtgggccccc tcgggcttac atgttgtcag tgtggacaaa
     1981 ggaagcagag ctgtgctgtg ggcacagcct tgatgctgca cccttaggag caccgtggga
     2041 ccccacggcc catcttggag aatgatgtgt cctcccagaa aagagctgaa gccatgtggt
     2101 gccgtagctt tcttgagaac tttgacttaa ggtctctaat ggctgagaag aaccaacact
     2161 gaaccaaact gactctgcaa gtccctagca gaggttcaga tttttgtctg catttgggtg
     2221 ggaaacacta ctaactctga ccttccatac ctcatgggga gtacagggtc cctgctgggt
     2281 ctccccactg gacacagtgc caaggacaac cccacacacc gggtattggg tcccctgtgc
     2341 tcttcccatc tttccaaagt ctgttgtagc ctgatgctcg ccccctttct gtggagtcac
     2401 ttacccaggg ggctcactgt aggcactggg tcagtggaaa ccaaatccgg gcctgtcctc
     2461 ctgtgacaaa ggatgggtgg agctgttttc agggctggtg gtatgtctgg tctcactgct
     2521 gaaacctgca tcttcagctg gccctcagaa ccctgaactc ccttcctgcc aacacttgca
     2581 catagctttg tgtgtgtgtg aggaaaggac tgtgccaacc tttccctgtc tggtagaatt
     2641 tgcagcagag gtgagaaaca catctttacc ctgcatcact gcacgtgcac agcaggtggc
     2701 cgagcactca cctggagcag agagtggtga ggccagccac tgcctgtgcg tgcagtgcag
     2761 tgttggtaag agaagcctac ctaggagctg gtgatgatga aggctgggct gggaaagcat
     2821 tctctgtcct gctcgcccgt gcacatggtc tgagcgccac gtttgtctgt cacacttact
     2881 ttgcacttta ttttttgctt ccacactgtt ctctggacag cagggacaac atgagtgctg
     2941 gagctcggga agagggacag cagttctgcc tgccctgccc gaaacccacc tgttgctttg
     3001 ctcccagaga gtttgtggcg ttggaagttg agattcgctg gccagggcac atcttttatt
     3061 tatttaatta tgtgtcccaa cagaacttga ttgtaaataa agaagaaatt ctgttatata
     3121 cttttcaaac tcaaaaaaaa aaaaaaaaa
//
