LOCUS       NM_033388               2140 bp    mRNA    linear   PRI 01-JUN-2024
DEFINITION  Homo sapiens autophagy related 16 like 2 (ATG16L2), transcript
            variant 1, mRNA.
ACCESSION   NM_033388 XM_058426
VERSION     NM_033388.2
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 2140)
  AUTHORS   Don Wai Luu,L., Kaakoush,N.O. and Castano-Rodriguez,N.
  TITLE     The role of ATG16L2 in autophagy and disease
  JOURNAL   Autophagy 18 (11), 2537-2546 (2022)
   PUBMED   35239457
  REMARK    GeneRIF: The role of ATG16L2 in autophagy and disease.
            Review article
REFERENCE   2  (bases 1 to 2140)
  AUTHORS   Bai,H., He,Y., Lin,Y., Leng,Q., Carrillo,J.A., Liu,J., Jiang,F.,
            Chen,J. and Song,J.
  TITLE     Identification of a novel differentially methylated region adjacent
            to ATG16L2 in lung cancer cells using methyl-CpG binding domain
            protein-enriched genome sequencing
  JOURNAL   Genome 64 (5), 533-546 (2021)
   PUBMED   33113339
  REMARK    GeneRIF: Identification of a novel differentially methylated region
            adjacent to ATG16L2 in lung cancer cells using methyl-CpG binding
            domain protein-enriched genome sequencing.
REFERENCE   3  (bases 1 to 2140)
  AUTHORS   Yang,Z. and Liu,Z.
  TITLE     Potentially functional variants of autophagy-related genes are
            associated with the efficacy and toxicity of radiotherapy in
            patients with nasopharyngeal carcinoma
  JOURNAL   Mol Genet Genomic Med 7 (12), e1030 (2019)
   PUBMED   31692259
  REMARK    GeneRIF: Results found ATG16L2 rs10898880 was significantly
            associated with the occurrence of grade 3-4 oral mucositis and
            myelosuppression in nasopharyngeal carcinoma (NPC) patients treated
            with radiotherapy.
REFERENCE   4  (bases 1 to 2140)
  AUTHORS   Wen,J., Liu,H., Wang,L., Wang,X., Gu,N., Liu,Z., Xu,T., Gomez,D.R.,
            Komaki,R., Liao,Z. and Wei,Q.
  TITLE     Potentially Functional Variants of ATG16L2 Predict Radiation
            Pneumonitis and Outcomes in Patients with Non-Small Cell Lung
            Cancer after Definitive Radiotherapy
  JOURNAL   J Thorac Oncol 13 (5), 660-675 (2018)
   PUBMED   29454863
  REMARK    GeneRIF: Patients with the ATG16L2 rs10898880 CC variant genotype
            had a better LRFS, PFS, and OS (adjusted hazard ratio = 0.59, 0.64,
            and 0.64; 95% confidence interval: 0.45-0.79, 0.48-0.84, and
            0.48-0.86; p = 0.0004, 0.002, and 0.003, respectively), but a
            greater risk for development of severe RP (adjusted hazard ratio =
            1.80, 95% confidence interval: 1.04-3.12, p = 0.037) than did
            patients with AA/AC genotypes.
REFERENCE   5  (bases 1 to 2140)
  AUTHORS   Ma,T., Wu,S., Yan,W., Xie,R. and Zhou,C.
  TITLE     A functional variant of ATG16L2 is associated with Crohn's disease
            in the Chinese population
  JOURNAL   Colorectal Dis 18 (11), O420-O426 (2016)
   PUBMED   27611316
  REMARK    GeneRIF: ATG16L2 is a susceptibility gene for Crohn's disease in
            the Chinese population. The rs11235604 single nucleotide
            polymorphism is remarkably associated with downregulation of the
            expression of ATG16L2.
REFERENCE   6  (bases 1 to 2140)
  AUTHORS   Yin,L., Liu,J., Dong,H., Xu,E., Qiao,Y., Wang,L., Zhang,L., Jia,J.,
            Li,L. and Geng,X.
  TITLE     Autophagy-related gene16L2, a potential serum biomarker of multiple
            sclerosis evaluated by bead-based proteomic technology
  JOURNAL   Neurosci Lett 562, 34-38 (2014)
   PUBMED   24406150
  REMARK    GeneRIF: Atg16L2 may play an important role in autophagy of T cells
            and serve as a potential biomarker to predict clinical relapse of
            Multiple sclerosis
REFERENCE   7  (bases 1 to 2140)
  AUTHORS   Yang,S.K., Hong,M., Zhao,W., Jung,Y., Baek,J., Tayebi,N., Kim,K.M.,
            Ye,B.D., Kim,K.J., Park,S.H., Lee,I., Lee,E.J., Kim,W.H.,
            Cheon,J.H., Kim,Y.H., Jang,B.I., Kim,H.S., Choi,J.H., Koo,J.S.,
            Lee,J.H., Jung,S.A., Lee,Y.J., Jang,J.Y., Shin,H.D., Kang,D.,
            Youn,H.S., Liu,J. and Song,K.
  TITLE     Genome-wide association study of Crohn's disease in Koreans
            revealed three new susceptibility loci and common attributes of
            genetic susceptibility across ethnic populations
  JOURNAL   Gut 63 (1), 80-87 (2014)
   PUBMED   23850713
  REMARK    GeneRIF: Three novel risk loci including ATG16L2 were discovered by
            genome-wide association study in the Korean Crohn's disease
            population, of which two showed patterns of association in the
            International Inflammatory Bowel Disease Genetics Consortium
            dataset.
REFERENCE   8  (bases 1 to 2140)
  AUTHORS   Yamazaki,K., Umeno,J., Takahashi,A., Hirano,A., Johnson,T.A.,
            Kumasaka,N., Morizono,T., Hosono,N., Kawaguchi,T., Takazoe,M.,
            Yamada,T., Suzuki,Y., Tanaka,H., Motoya,S., Hosokawa,M.,
            Arimura,Y., Shinomura,Y., Matsui,T., Matsumoto,T., Iida,M.,
            Tsunoda,T., Nakamura,Y., Kamatani,N. and Kubo,M.
  TITLE     A genome-wide association study identifies 2 susceptibility Loci
            for Crohn's disease in a Japanese population
  JOURNAL   Gastroenterology 144 (4), 781-788 (2013)
   PUBMED   23266558
REFERENCE   9  (bases 1 to 2140)
  AUTHORS   Otomo,C., Metlagel,Z., Takaesu,G. and Otomo,T.
  TITLE     Structure of the human ATG12 ATG5 conjugate required for LC3
            lipidation in autophagy
  JOURNAL   Nat Struct Mol Biol 20 (1), 59-66 (2013)
   PUBMED   23202584
REFERENCE   10 (bases 1 to 2140)
  AUTHORS   Hattori,A., Okumura,K., Nagase,T., Kikuno,R., Hirosawa,M. and
            Ohara,O.
  TITLE     Characterization of long cDNA clones from human adult spleen
  JOURNAL   DNA Res 7 (6), 357-366 (2000)
   PUBMED   11214971
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BQ929430.1, BC069189.1, BC036713.2, AK024423.1, AK090597.1 and
            AL832974.1.
            
            On Nov 23, 2018 this sequence version replaced NM_033388.1.
            
            Transcript Variant: This variant (1) encodes the longer 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 :: AK093017.1, BC137489.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000321297.10/ ENSP00000326340.5
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-23                BQ929430.1         17-39
            24-353              BC069189.1         41-370
            354-801             BC036713.2         88-535
            802-859             AK024423.1         835-892
            860-922             AK024423.1         1991-2053
            923-1280            AK024423.1         2665-3022
            1281-1401           AK024423.1         3136-3256
            1402-1657           AK024423.1         3621-3876
            1658-1745           AK024423.1         4097-4184
            1746-1980           BC036713.2         1480-1714
            1981-2099           AK090597.1         2097-2215
            2100-2138           AK090597.1         2220-2258
            2139-2140           AL832974.1         1755-1756
FEATURES             Location/Qualifiers
     source          1..2140
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11q13.4"
     gene            1..2140
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /note="autophagy related 16 like 2"
                     /db_xref="GeneID:89849"
                     /db_xref="HGNC:HGNC:25464"
                     /db_xref="MIM:618716"
     exon            1..153
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     CDS             36..1895
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /note="isoform 1 is encoded by transcript variant 1;
                     autophagy-related protein 16-2; APG16-like 2; protein
                     Atg16l2; WD repeat-containing protein 80; ATG16 autophagy
                     related 16-like 2"
                     /codon_start=1
                     /product="protein Atg16l2 isoform 1"
                     /protein_id="NP_203746.1"
                     /db_xref="CCDS:CCDS31634.1"
                     /db_xref="GeneID:89849"
                     /db_xref="HGNC:HGNC:25464"
                     /db_xref="MIM:618716"
                     /translation="MAGPGVPGAPAARWKRHIVRQLRLRDRTQKALFLELVPAYNHLL
                     EKAELLDKFSKKLQPEPNSVTPTTHQGPWEESELDSDQVPSLVALRVKWQEEEEGLRL
                     VCGEMAYQVVEKGAALGTLESELQQRQSRLAALEARVAQLREARAQQAQQVEEWRAQN
                     AVQRAAYEALRAHVGLREAALRRLQEEARDLLERLVQRKARAAAERNLRNERRERAKQ
                     ARVSQELKKAAKRTVSISEGPDTLGDGMRERRETLALAPEPEPLEKEACEKWKRPFRS
                     ASATSLTLSHCVDVVKGLLDFKKRRGHSIGGAPEQRYQIIPVCVAARLPTRAQDVLDA
                     HLSEVNAVRFGPNSSLLATGGADRLIHLWNVVGSRLEANQTLEGAGGSITSVDFDPSG
                     YQVLAATYNQAAQLWKVGEAQSKETLSGHKDKVTAAKFKLTRHQAVTGSRDRTVKEWD
                     LGRAYCSRTINVLSYCNDVVCGDHIIISGHNDQKIRFWDSRGPHCTQVIPVQGRVTSL
                     SLSHDQLHLLSCSRDNTLKVIDLRVSNIRQVFRADGFKCGSDWTKAVFSPDRSYALAG
                     SCDGALYIWDVDTGKLESRLQGPHCAAVNAVAWCYSGSHMVSVDQGRKVVLWQ"
     exon            154..253
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            254..353
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            354..427
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            428..679
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            680..745
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            746..859
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            860..922
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            923..1031
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            1032..1137
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            1138..1208
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            1209..1280
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            1281..1401
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            1402..1507
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            1508..1657
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            1658..1705
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            1706..1807
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     exon            1808..2140
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /inference="alignment:Splign:2.1.0"
     polyA_site      2140
                     /gene="ATG16L2"
                     /gene_synonym="ATG16B; WDR80"
                     /note="major polyA site"
ORIGIN      
        1 gggaggaacg cgccgctagg cgggagagcg cggccatggc ggggccgggc gtccccggtg
       61 cccccgcagc gcgctggaaa cgccacatcg tgcggcagct gcggcttcgg gaccgtacgc
      121 aaaaggcgct tttcctggag ctggtgccgg cctataacca tctcttagag aaggctgagc
      181 tgctggacaa gttctcaaag aagctgcagc cggagccaaa cagtgtcact cccaccaccc
      241 accagggccc ctgggaggag tcagagcttg actcagacca agtcccatca ctggtcgcac
      301 tgagggtgaa gtggcaggag gaggaggagg ggctccggct ggtctgtggt gagatggcct
      361 accaggtggt ggagaagggc gcggccctgg gcacgctgga gtcggagctg cagcagaggc
      421 aaagcaggct ggcagccctg gaggcccgcg tggcgcagct gcgagaggcg cgggcgcagc
      481 aggcccagca ggtggaggag tggcgggcgc agaatgcggt gcagcgggca gcctacgagg
      541 cgctgcgcgc gcacgtcggg ctccgggagg cggcactgcg caggctccag gaagaggcgc
      601 gcgacctgct ggagaggctc gtgcagcgca aggcgcgcgc cgcggccgag cgcaacctgc
      661 gcaacgagcg ccgggagcgg gccaagcagg cgcgggtgtc ccaggagctg aagaaggctg
      721 ccaagcggac cgtgagcatc agcgagggcc cggacaccct aggcgatggg atgagggaga
      781 gaagggagac tctggctctg gcccctgagc cagagcccct ggagaaggaa gcttgtgaga
      841 agtggaagag gcccttcagg tctgcctcag ccacctccct gacgctgtcc cactgtgtgg
      901 atgtggtgaa ggggcttctg gattttaaga agaggagagg tcactcaatt gggggagccc
      961 ctgagcagcg ataccagatc atccctgtgt gtgtggctgc ccgacttcct acccgggctc
     1021 aggatgtgct ggatgcccac ctctctgagg tcaatgctgt tcgttttggc cccaacagca
     1081 gcctcctggc cactggaggg gctgaccgcc tgatccacct ctggaatgtt gtgggaagtc
     1141 gcctggaggc caaccagacc ctggagggag ctggtggcag catcaccagt gtggactttg
     1201 acccctcggg ctaccaggtt ttagcagcaa cttacaacca ggctgcccag ctctggaagg
     1261 tgggggaggc acagtccaag gagacactgt ctggacacaa ggataaggtg acagctgcca
     1321 aattcaagct aacgaggcac caggcagtga ctgggagccg cgaccggaca gtgaaggagt
     1381 gggacctcgg ccgtgcctat tgctccagga ccatcaatgt cctttcctac tgtaatgacg
     1441 tggtgtgtgg ggaccatatc atcattagtg gccacaatga ccagaagatc cggttctggg
     1501 acagcagggg gccccactgc acccaggtca tccctgtgca gggccgggtc acctccctga
     1561 gcctcagcca cgaccaactg cacctgctca gctgttcccg agacaacaca ctcaaggtca
     1621 tcgacctgcg tgtcagcaac atccgccagg tgttcagggc cgatggcttc aagtgtggtt
     1681 ctgactggac caaagctgtg ttcagcccgg acagaagcta tgcactggca ggctcctgtg
     1741 atggggccct ttacatctgg gatgtggaca ccgggaaact ggagagcaga ctacagggac
     1801 cccattgcgc tgccgtcaac gccgtggcct ggtgctactc cgggagccac atggtgagcg
     1861 tggaccaggg caggaaggtt gtgctctggc agtagggcca cgacctgcct gcctgggctg
     1921 gagctcttgc ccgaagcctg aagcttcctt cggcgccatg caggggttgg ggttgggact
     1981 ggagctggcc ttgggattta atggggaaga aggcctggca ggacctggcc tgtttgttta
     2041 aaaatgaagt atgggttggg ggattacgct agtttttctt tgtattttta tctctatctc
     2101 ctcacttttt ctcccaaagt agaaaaaaat gatatctgaa
//
