LOCUS       NM_030803               3298 bp    mRNA    linear   PRI 24-SEP-2024
DEFINITION  Homo sapiens autophagy related 16 like 1 (ATG16L1), transcript
            variant 1, mRNA.
ACCESSION   NM_030803
VERSION     NM_030803.7
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 3298)
  AUTHORS   Gubas,A., Attridge,E., Jefferies,H.B., Nishimura,T., Razi,M.,
            Kunzelmann,S., Gilad,Y., Mercer,T.J., Wilson,M.M., Kimchi,A. and
            Tooze,S.A.
  TITLE     WIPI2b recruitment to phagophores and ATG16L1 binding are regulated
            by ULK1 phosphorylation
  JOURNAL   EMBO Rep 25 (9), 3789-3811 (2024)
   PUBMED   39152217
  REMARK    GeneRIF: WIPI2b recruitment to phagophores and ATG16L1 binding are
            regulated by ULK1 phosphorylation.
REFERENCE   2  (bases 1 to 3298)
  AUTHORS   Liao,F.X., Yang,S., Liu,Z.H., Bo,K.D., Xu,P.F. and Chang,J.
  TITLE     Estrogen receptor is involved in the osteoarthritis mediated by
            Atg16L1-NLRP3 activation
  JOURNAL   Jt Dis Relat Surg 35 (3), 513-520 (2024)
   PUBMED   39189559
  REMARK    GeneRIF: Estrogen receptor is involved in the osteoarthritis
            mediated by Atg16L1-NLRP3 activation.
REFERENCE   3  (bases 1 to 3298)
  AUTHORS   Cui,Y., Yu,X., Bao,J., Ping,X., Shi,S., Huang,Y., Yin,Q., Yang,H.,
            Chen,R., Yao,K., Chen,X. and Shentu,X.
  TITLE     Lens autophagy protein ATG16L1: a potential target for cataract
            treatment
  JOURNAL   Theranostics 14 (10), 3984-3996 (2024)
   PUBMED   38994020
  REMARK    GeneRIF: Lens autophagy protein ATG16L1: a potential target for
            cataract treatment.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3298)
  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   5  (bases 1 to 3298)
  AUTHORS   Schreurs,R.R.C.E., Koulis,A., Booiman,T., Boeser-Nunnink,B.,
            Cloherty,A.P.M., Rader,A.G., Patel,K.S., Kootstra,N.A. and
            Ribeiro,C.M.S.
  TITLE     Autophagy-enhancing ATG16L1 polymorphism is associated with
            improved clinical outcome and T-cell immunity in chronic HIV-1
            infection
  JOURNAL   Nat Commun 15 (1), 2465 (2024)
   PUBMED   38548722
  REMARK    GeneRIF: Autophagy-enhancing ATG16L1 polymorphism is associated
            with improved clinical outcome and T-cell immunity in chronic HIV-1
            infection.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3298)
  AUTHORS   Rioux,J.D., Xavier,R.J., Taylor,K.D., Silverberg,M.S., Goyette,P.,
            Huett,A., Green,T., Kuballa,P., Barmada,M.M., Datta,L.W.,
            Shugart,Y.Y., Griffiths,A.M., Targan,S.R., Ippoliti,A.F.,
            Bernard,E.J., Mei,L., Nicolae,D.L., Regueiro,M., Schumm,L.P.,
            Steinhart,A.H., Rotter,J.I., Duerr,R.H., Cho,J.H., Daly,M.J. and
            Brant,S.R.
  TITLE     Genome-wide association study identifies new susceptibility loci
            for Crohn disease and implicates autophagy in disease pathogenesis
  JOURNAL   Nat Genet 39 (5), 596-604 (2007)
   PUBMED   17435756
REFERENCE   7  (bases 1 to 3298)
  AUTHORS   Hampe,J., Franke,A., Rosenstiel,P., Till,A., Teuber,M., Huse,K.,
            Albrecht,M., Mayr,G., De La Vega,F.M., Briggs,J., Gunther,S.,
            Prescott,N.J., Onnie,C.M., Hasler,R., Sipos,B., Folsch,U.R.,
            Lengauer,T., Platzer,M., Mathew,C.G., Krawczak,M. and Schreiber,S.
  TITLE     A genome-wide association scan of nonsynonymous SNPs identifies a
            susceptibility variant for Crohn disease in ATG16L1
  JOURNAL   Nat Genet 39 (2), 207-211 (2007)
   PUBMED   17200669
  REMARK    GeneRIF: A genome-wide association scan of nonsynonymous SNPs
            identifies a susceptibility variant for Crohn disease in ATG16L1.
            GeneRIF: Observational study and genome-wide association study of
            gene-disease association and gene-gene interaction. (HuGE
            Navigator)
REFERENCE   8  (bases 1 to 3298)
  AUTHORS   Zheng,H., Ji,C., Li,J., Jiang,H., Ren,M., Lu,Q., Gu,S., Mao,Y. and
            Xie,Y.
  TITLE     Cloning and analysis of human Apg16L
  JOURNAL   DNA Seq 15 (4), 303-305 (2004)
   PUBMED   15620219
  REMARK    GeneRIF: Contains a coiled-coil domain and a motif with seven WD
            repeats, which are also shared by mouse Apg16L.
REFERENCE   9  (bases 1 to 3298)
  AUTHORS   Bouwmeester,T., Bauch,A., Ruffner,H., Angrand,P.O., Bergamini,G.,
            Croughton,K., Cruciat,C., Eberhard,D., Gagneur,J., Ghidelli,S.,
            Hopf,C., Huhse,B., Mangano,R., Michon,A.M., Schirle,M., Schlegl,J.,
            Schwab,M., Stein,M.A., Bauer,A., Casari,G., Drewes,G., Gavin,A.C.,
            Jackson,D.B., Joberty,G., Neubauer,G., Rick,J., Kuster,B. and
            Superti-Furga,G.
  TITLE     A physical and functional map of the human TNF-alpha/NF-kappa B
            signal transduction pathway
  JOURNAL   Nat Cell Biol 6 (2), 97-105 (2004)
   PUBMED   14743216
  REMARK    Erratum:[Nat Cell Biol. 2004 May;6(5):465]
REFERENCE   10 (bases 1 to 3298)
  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
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DB084962.1, AC013726.7,
            AY398617.1, BC117337.1 and AA809053.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_030803.6.
            
            Summary: The protein encoded by this gene is part of a large
            protein complex that is necessary for autophagy, the major process
            by which intracellular components are targeted to lysosomes for
            degradation. Defects in this gene are a cause of susceptibility to
            inflammatory bowel disease type 10 (IBD10). Several transcript
            variants encoding different isoforms have been found for this
            gene.[provided by RefSeq, Jun 2010].
            
            Transcript Variant: This variant (1) encodes isoform 1.
            
            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 :: AY398617.1, SRR1803613.75084.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000392017.9/ ENSP00000375872.4
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-26                DB084962.1         103-128
            27-27               AC013726.7         168663-168663       c
            28-1052             AY398617.1         19-1043
            1053-2529           BC117337.1         817-2293
            2530-3096           AC013726.7         124895-125461       c
            3097-3298           AA809053.1         28-229              c
FEATURES             Location/Qualifiers
     source          1..3298
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q37.1"
     gene            1..3298
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /note="autophagy related 16 like 1"
                     /db_xref="GeneID:55054"
                     /db_xref="HGNC:HGNC:21498"
                     /db_xref="MIM:610767"
     exon            1..270
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     CDS             156..1979
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /note="isoform 1 is encoded by transcript variant 1; WD
                     repeat domain 30; autophagy-related protein 16-1; APG16L
                     beta; ATG16 autophagy related 16-like 1"
                     /codon_start=1
                     /product="autophagy-related protein 16-1 isoform 1"
                     /protein_id="NP_110430.5"
                     /db_xref="CCDS:CCDS2503.2"
                     /db_xref="GeneID:55054"
                     /db_xref="HGNC:HGNC:21498"
                     /db_xref="MIM:610767"
                     /translation="MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLE
                     KSDLHSVLAQKLQAEKHDVPNRHEISPGHDGTWNDNQLQEMAQLRIKHQEELTELHKK
                     RGELAQLVIDLNNQMQRKDREMQMNEAKIAECLQTISDLETECLDLRTKLCDLERANQ
                     TLKDEYDALQITFTALEGKLRKTTEENQELVTRWMAEKAQEANRLNAENEKDSRRRQA
                     RLQKELAEAAKEPLPVEQDDDIEVIVDETSDHTEETSPVRAISRAATKRLSQPAGGLL
                     DSITNIFGRRSVSSFPVPQDNVDTHPGSGKEVRVPATALCVFDAHDGEVNAVQFSPGS
                     RLLATGGMDRRVKLWEVFGEKCEFKGSLSGSNAGITSIEFDSAGSYLLAASNDFASRI
                     WTVDDYRLRHTLTGHSGKVLSAKFLLDNARIVSGSHDRTLKLWDLRSKVCIKTVFAGS
                     SCNDIVCTEQCVMSGHFDKKIRFWDIRSESIVREMELLGKITALDLNPERTELLSCSR
                     DDLLKVIDLRTNAIKQTFSAPGFKCGSDWTRVVFSPDGSYVAAGSAEGSLYIWSVLTG
                     KVEKVLSKQHSSSINAVAWSPSGSHVVSVDKGCKAVLWAQY"
     exon            271..364
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            365..470
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            471..544
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            545..796
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            797..862
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            863..949
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            950..1006
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1007..1109
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1110..1215
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1216..1286
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1287..1358
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1359..1479
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1480..1585
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1586..1735
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1736..1783
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1784..1885
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     exon            1886..3298
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3273..3278
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /note="hexamer: AAGAAA"
     polyA_site      3298
                     /gene="ATG16L1"
                     /gene_synonym="APG16L; ATG16A; ATG16L; IBD10; WDR30"
                     /note="major polyA site"
ORIGIN      
        1 agaccgtccc ggatggcctc ggggactgcc agtgtgtgga ggtgagctcc gggattgccg
       61 gcattcccgc ttctgctggt tgcttcatgc tgcaggctgc ggccgtcagc cctcgctcgc
      121 attggtggcg ctgaggtgcc ggggcagcaa gtgacatgtc gtcgggcctc cgcgccgctg
      181 acttcccccg ctggaagcgc cacatctcgg agcaactgag gcgccgggac cggctgcaga
      241 gacaggcgtt cgaggagatc atcctgcagt ataacaaatt gctggaaaag tcagatcttc
      301 attcagtgtt ggcccagaaa ctacaggctg aaaagcatga cgtaccaaac aggcacgaga
      361 taagtcccgg acatgatggc acatggaatg acaatcagct acaagaaatg gcccaactga
      421 ggattaagca ccaagaggaa ctgactgaat tacacaagaa acgtggggag ttagctcaac
      481 tggtgattga cctgaataac caaatgcagc ggaaggacag ggagatgcag atgaatgaag
      541 caaaaattgc agaatgtttg cagactatct ctgacctgga gacggagtgc ctagacctgc
      601 gcactaagct ttgtgacctt gaaagagcca accagaccct gaaggatgaa tatgatgccc
      661 tgcagatcac ttttactgcc ttggagggaa aactgaggaa aactacggaa gagaaccagg
      721 agctggtcac cagatggatg gctgagaaag cccaggaagc caatcggctt aatgcagaga
      781 atgaaaaaga ctccaggagg cggcaagccc ggctgcagaa agagcttgca gaagcagcaa
      841 aggaacctct accagtcgaa caggatgatg acattgaggt cattgtggat gaaacttctg
      901 atcacacaga agagacctct cctgtgcgag ccatcagcag agcagccact aagcgactct
      961 cgcagcctgc tggaggcctt ctggattcta tcactaatat ctttgggaga cgctctgtct
     1021 cttccttccc agtcccccag gacaatgtgg atactcatcc tggttctggt aaagaagtga
     1081 gggtaccagc tactgccttg tgtgtcttcg atgcacatga tggggaagtc aacgctgtgc
     1141 agttcagtcc aggttcccgg ttactggcca ctggaggcat ggaccgcagg gttaagcttt
     1201 gggaagtatt tggagaaaaa tgtgagttca agggttccct atctggcagt aatgcaggaa
     1261 ttacaagcat tgaatttgat agtgctggat cttacctctt agcagcttca aatgattttg
     1321 caagccgaat ctggactgtg gatgattatc gattacggca cacactcacg ggacacagtg
     1381 ggaaagtgct gtctgctaag ttcctgctgg acaatgcgcg gattgtctca ggaagtcacg
     1441 accggactct caaactctgg gatctacgca gcaaagtctg cataaagaca gtgtttgcag
     1501 gatccagttg caatgatatt gtctgcacag agcaatgtgt aatgagtgga cattttgaca
     1561 agaaaattcg tttctgggac attcgatcag agagcatagt tcgagagatg gagctgttgg
     1621 gaaagattac tgccctggac ttaaacccag aaaggactga gctcctgagc tgctcccgtg
     1681 atgacttgct aaaagttatt gatctccgaa caaatgctat caagcagaca ttcagtgcac
     1741 ctgggttcaa gtgcggctct gactggacca gagttgtctt cagccctgat ggcagttacg
     1801 tggcggcagg ctctgctgag ggctctctgt atatctggag tgtgctcaca gggaaagtgg
     1861 aaaaggttct ttcaaagcag cacagctcat ccatcaatgc ggtggcgtgg tcgccctctg
     1921 gctcgcacgt tgtcagtgtg gacaaaggat gcaaagctgt gctgtgggca cagtactgac
     1981 ggggctctca gggctgggag gaccccagtg ccctcctcag aagaagcaca tgggctcctg
     2041 cagccctgtc ctggcaggtg atgtgctggg tatagcatgg acctcccaga gaagctcaag
     2101 ctatgtggca ctgtagcttt gccgtgaatg ggatttctga agatttgact gaggtctctc
     2161 ttggcctgga agaataacac tgaaaaaacc tgacgctgcg gtcacttagc agaggctcag
     2221 gttcttgcct tgggaaacac tactagctct gaccttccat acctcacttg ggggagcaca
     2281 gggccccgct gggcctcctc accaacggca gtgccaaaat cagcccccac atcaaggtgg
     2341 tgttctctgt gctttctctc gtccttccaa agtcggttct ggcctaacgc atgtcccaac
     2401 accttgggtt catttgcccg gtgaactcac tttaagcatt ggattaacgg aaactcccga
     2461 actacagacc cctccctggt gggttgcatg aatgtgtctc attactgctg aaatgtcctc
     2521 acatctcttt cactgttctt cagagctttc tggctctctt tcccccacaa aattcgacat
     2581 atttaaaaat ctccgtgtgg ctttaaaaaa tggttttttg tttttttgtt tttttgaggt
     2641 gggagaggat gtgtgaaaat cttttccagg gaaatgggtt cgctgcagag gtaaggatgt
     2701 gttcctgtat cgatctgcag acacccagaa ggtgggtgca cactgcatgc ttgggggtgc
     2761 caagggattc gagacctcca acatacttgt ctgaaggtgg tgattctggc catggcccct
     2821 ctgccaagcc tgtgtgcgat gcccttggtg ctttagtgca agaagcctag gctcagaagc
     2881 acagcagcgc catctttccg tttcaggggt tgtgatgaag gccaaggaaa aacatttatc
     2941 tttactattt tacctacgta taaagtttta gttcattggg tgtgcgaaac acccttttta
     3001 tcacttttaa atttgcactt tatttttttt cttccatgct tgttctctgg acatttgggg
     3061 atgtgagtgt tagagctggt gagagaggag tcaggtggcc ttcccaccga tggtcctggc
     3121 ctccacctgc cctctcttcc ctgcctgatc accgctttcc aatttgccct tcagagaact
     3181 taagtcaagg agagttgaaa ttcacaggcc agggcacatc ttttatttat ttcattatgt
     3241 tggccaacag aacttgattg taaataataa taaagaaatc tgttatatac ttttcaaa
//
