LOCUS       NM_001077198            3770 bp    mRNA    linear   PRI 01-AUG-2024
DEFINITION  Homo sapiens autophagy related 9A (ATG9A), transcript variant 1,
            mRNA.
ACCESSION   NM_001077198
VERSION     NM_001077198.3
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 3770)
  AUTHORS   Broadbent,D., Barnaba,C. and Schmidt,J.C.
  TITLE     Tracking the transition from an ATG9A vesicle to an autophagosome
  JOURNAL   Autophagy 20 (4), 976-977 (2024)
   PUBMED   37405380
  REMARK    GeneRIF: Tracking the transition from an ATG9A vesicle to an
            autophagosome.
REFERENCE   2  (bases 1 to 3770)
  AUTHORS   Zhang,Z., Song,B., Wei,H., Liu,Y., Zhang,W., Yang,Y. and Sun,B.
  TITLE     NDRG1 overcomes resistance to immunotherapy of pancreatic ductal
            adenocarcinoma through inhibiting ATG9A-dependent degradation of
            MHC-1
  JOURNAL   Drug Resist Updat 73, 101040 (2024)
   PUBMED   38228036
  REMARK    GeneRIF: NDRG1 overcomes resistance to immunotherapy of pancreatic
            ductal adenocarcinoma through inhibiting ATG9A-dependent
            degradation of MHC-1.
REFERENCE   3  (bases 1 to 3770)
  AUTHORS   Chiduza,G.N., Garza-Garcia,A., Almacellas,E., De Tito,S., Pye,V.E.,
            van Vliet,A.R., Cherepanov,P. and Tooze,S.A.
  TITLE     ATG9B is a tissue-specific homotrimeric lipid scramblase that can
            compensate for ATG9A
  JOURNAL   Autophagy 20 (3), 557-576 (2024)
   PUBMED   37938170
  REMARK    GeneRIF: ATG9B is a tissue-specific homotrimeric lipid scramblase
            that can compensate for ATG9A.
REFERENCE   4  (bases 1 to 3770)
  AUTHORS   Liu,X., Liu,Z., Liu,Y. and Wang,N.
  TITLE     ATG9A modulated by miR-195-5p can boost the malignant progression
            of cervical cancer cells
  JOURNAL   Epigenetics 18 (1), 2257538 (2023)
   PUBMED   37782756
  REMARK    GeneRIF: ATG9A modulated by miR-195-5p can boost the malignant
            progression of cervical cancer cells.
REFERENCE   5  (bases 1 to 3770)
  AUTHORS   Kliche,J., Garvanska,D.H., Simonetti,L., Badgujar,D.,
            Dobritzsch,D., Nilsson,J., Davey,N.E. and Ivarsson,Y.
  TITLE     Large-scale phosphomimetic screening identifies phospho-modulated
            motif-based protein interactions
  JOURNAL   Mol Syst Biol 19 (7), e11164 (2023)
   PUBMED   37219487
REFERENCE   6  (bases 1 to 3770)
  AUTHORS   Zhang,X., Yang,H., Lee,J.J., Kim,E., Lippman,S.M., Khuri,F.R.,
            Spitz,M.R., Lotan,R., Hong,W.K. and Wu,X.
  TITLE     MicroRNA-related genetic variations as predictors for risk of
            second primary tumor and/or recurrence in patients with early-stage
            head and neck cancer
  JOURNAL   Carcinogenesis 31 (12), 2118-2123 (2010)
   PUBMED   20819778
  REMARK    GeneRIF: Observational study of gene-disease association and
            gene-gene interaction. (HuGE Navigator)
REFERENCE   7  (bases 1 to 3770)
  AUTHORS   Webber,J.L. and Tooze,S.A.
  TITLE     Coordinated regulation of autophagy by p38alpha MAPK through mAtg9
            and p38IP
  JOURNAL   EMBO J 29 (1), 27-40 (2010)
   PUBMED   19893488
  REMARK    GeneRIF: Manipulation of p38IP and p38alpha alters mAtg9
            localization, suggesting p38alpha regulates, through p38IP, the
            starvation-induced mAtg9 trafficking to forming autophagosomes.
            GeneRIF: ATG9A was found by co-immunoprecipitation to interact with
            FAM48A/p38IP/q8NEM7.2.
REFERENCE   8  (bases 1 to 3770)
  AUTHORS   Ghosh,D., Lippert,D., Krokhin,O., Cortens,J.P. and Wilkins,J.A.
  TITLE     Defining the membrane proteome of NK cells
  JOURNAL   J Mass Spectrom 45 (1), 1-25 (2010)
   PUBMED   19946888
REFERENCE   9  (bases 1 to 3770)
  AUTHORS   Young,A.R., Chan,E.Y., Hu,X.W., Kochl,R., Crawshaw,S.G., High,S.,
            Hailey,D.W., Lippincott-Schwartz,J. and Tooze,S.A.
  TITLE     Starvation and ULK1-dependent cycling of mammalian Atg9 between the
            TGN and endosomes
  JOURNAL   J Cell Sci 119 (Pt 18), 3888-3900 (2006)
   PUBMED   16940348
  REMARK    GeneRIF: First demonstration that mammalian Atg9A, originally
            called mAtg9, is required for starvation-induced autophagy, and
            localizes to Golgi and endosomes.
REFERENCE   10 (bases 1 to 3770)
  AUTHORS   Yamada,T., Carson,A.R., Caniggia,I., Umebayashi,K., Yoshimori,T.,
            Nakabayashi,K. and Scherer,S.W.
  TITLE     Endothelial nitric-oxide synthase antisense (NOS3AS) gene encodes
            an autophagy-related protein (APG9-like2) highly expressed in
            trophoblast
  JOURNAL   J Biol Chem 280 (18), 18283-18290 (2005)
   PUBMED   15755735
  REMARK    GeneRIF: In human adult tissues APG9L1 is ubiquitously expressed.
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DC347583.1, BK004018.1 and BC065534.1.
            
            On Nov 23, 2018 this sequence version replaced NM_001077198.2.
            
            Transcript Variant: This variant (1) and variant 2 encode the same
            protein.
            
            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 :: BK004018.1, AK056595.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000361242.9/ ENSP00000355173.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-7                 DC347583.1         53-59
            8-3769              BK004018.1         1-3762
            3770-3770           BC065534.1         3701-3701
FEATURES             Location/Qualifiers
     source          1..3770
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q35"
     gene            1..3770
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /note="autophagy related 9A"
                     /db_xref="GeneID:79065"
                     /db_xref="HGNC:HGNC:22408"
                     /db_xref="MIM:612204"
     exon            1..102
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            103..154
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            155..286
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     CDS             184..2703
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /note="autophagy 9-like 1 protein; APG9-like 1; APG9
                     autophagy 9-like 1; ATG9 autophagy related 9 homolog A"
                     /codon_start=1
                     /product="autophagy-related protein 9A"
                     /protein_id="NP_001070666.1"
                     /db_xref="CCDS:CCDS42820.1"
                     /db_xref="GeneID:79065"
                     /db_xref="HGNC:HGNC:22408"
                     /db_xref="MIM:612204"
                     /translation="MAQFDTEYQRLEASYSDSPPGEEDLLVHVAEGSKSPWHHIENLD
                     LFFSRVYNLHQKNGFTCMLIGEIFELMQFLFVVAFTTFLVSCVDYDILFANKMVNHSL
                     HPTEPVKVTLPDAFLPAQVCSARIQENGSLITILVIAGVFWIHRLIKFIYNICCYWEI
                     HSFYLHALRIPMSALPYCTWQEVQARIVQTQKEHQICIHKRELTELDIYHRILRFQNY
                     MVALVNKSLLPLRFRLPGLGEAVFFTRGLKYNFELILFWGPGSLFLNEWSLKAEYKRG
                     GQRLELAQRLSNRILWIGIANFLLCPLILIWQILYAFFSYAEVLKREPGALGARCWSL
                     YGRCYLRHFNELEHELQSRLNRGYKPASKYMNCFLSPLLTLLAKNGAFFAGSILAVLI
                     ALTIYDEDVLAVEHVLTTVTLLGVTVTVCRSFIPDQHMVFCPEQLLRVILAHIHYMPD
                     HWQGNAHRSQTRDEFAQLFQYKAVFILEELLSPIVTPLILIFCLRPRALEIIDFFRNF
                     TVEVVGVGDTCSFAQMDVRQHGHPQWLSAGQTEASVYQQAEDGKTELSLMHFAITNPG
                     WQPPRESTAFLGFLKEQVQRDGAAASLAQGGLLPENALFTSIQSLQSESEPLSLIANV
                     VAGSSCRGPPLPRDLQGSRHRAEVASALRSFSPLQPGQAPTGRAHSTMTGSGVDARTA
                     SSGSSVWEGQLQSLVLSEYASTEMSLHALYMHQLHKQQAQAEPERHVWHRRESDESGE
                     SAPDEGGEGARAPQSIPRSASYPCAAPRPGAPETTALHGGFQRRYGGITDPGTVPRVP
                     SHFSRLPLGGWAEDGQSASRHPEPVPEEGSEDELPPQVHKV"
     exon            287..330
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            331..395
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            396..557
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            558..699
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            700..1448
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            1449..1602
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            1603..1782
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            1783..2031
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            2032..2210
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            2211..2328
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            2329..2551
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            2552..2697
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     exon            2698..3770
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3748..3753
                     /regulatory_class="polyA_signal_sequence"
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /note="hexamer: AATAAA"
     polyA_site      3770
                     /gene="ATG9A"
                     /gene_synonym="APG9L1; mATG9; MGD3208"
                     /note="major polyA site"
ORIGIN      
        1 gagtggcaga cacccggcct agcgccgcgg gtcgcgccga gccgagccga gccgagcgga
       61 gccggcggag cctctggaat cacccgggtc gctgttcctg agcagctgca gagcatcgag
      121 ggctggagag gagcacatac tgtccatgga gctggtggtc aaggtggaca gggggcggtg
      181 gtgatggcgc agtttgacac tgaataccag cgcctagagg cctcctatag tgattcaccc
      241 ccaggggagg aggacctgtt ggtgcacgtc gccgagggga gcaagtcacc ttggcaccat
      301 attgaaaacc ttgacctctt cttctctcga gtttataatc tgcaccagaa gaatggcttc
      361 acatgtatgc tcatcgggga gatctttgag ctcatgcagt tcctctttgt ggttgccttc
      421 actaccttcc tggtcagctg cgtggactat gacatcctat ttgccaacaa gatggtgaac
      481 cacagtcttc accctactga acccgtcaag gtcactctgc cagacgcctt tttgcctgct
      541 caagtctgta gtgccaggat tcaggaaaat ggctccctta tcaccatcct ggtcattgct
      601 ggtgtcttct ggatccaccg gcttatcaag ttcatctata acatttgctg ctactgggag
      661 atccactcct tctacctgca cgctctgcgc atccctatgt ctgcccttcc gtattgcacg
      721 tggcaagaag tgcaggcccg gatcgtgcag acgcagaagg agcaccagat ctgcatccac
      781 aaacgtgagc tgacagaact ggacatctac caccgcatcc tccgtttcca gaactacatg
      841 gtggcactgg ttaacaaatc cctcctgcct ctgcgcttcc gcctgcctgg cctcggggaa
      901 gctgtcttct tcacccgtgg tctcaagtac aactttgagc tgatcctctt ctggggacct
      961 ggctctctgt ttctcaatga atggagcctc aaggccgagt acaaacgtgg ggggcaacgg
     1021 ctagagctgg cccagcgcct cagcaaccgc atcctgtgga ttggcatcgc taacttcctg
     1081 ctgtgccccc tcatcctcat atggcaaatc ctctatgcct tcttcagcta tgctgaggtg
     1141 ctgaagcggg agccgggggc cctgggagca cgctgctggt cactctatgg ccgctgctac
     1201 ctccgccact tcaacgagct ggagcacgag ctgcagtccc gcctcaaccg tggctacaag
     1261 cccgcctcca agtacatgaa ttgcttcttg tcacctcttt tgacactgct ggccaagaat
     1321 ggagccttct tcgctggctc catcctggct gtgcttattg ccctcaccat ttatgacgaa
     1381 gatgtgttgg ctgtggaaca tgtgctgacc accgtcacac tcctgggggt caccgtgacc
     1441 gtgtgcaggt cctttatccc ggaccagcac atggtgttct gccctgagca gctgctccgc
     1501 gtgatcctcg ctcacatcca ctacatgcct gaccactggc agggtaatgc ccaccgctcg
     1561 cagacccggg acgagtttgc ccagctcttc cagtacaagg cagtgttcat tttggaagag
     1621 ttgctgagcc ccattgtcac acccctcatc ctcatcttct gcctgcgccc acgggccctg
     1681 gagattatag acttcttccg aaacttcacc gtggaggtcg ttggtgtggg agatacctgc
     1741 tcctttgctc agatggatgt tcgccagcat ggtcatcccc agtggctatc tgctgggcag
     1801 acagaggcct cagtgtacca gcaagctgag gatggaaaga cagagttgtc actcatgcac
     1861 tttgccatca ccaaccctgg ctggcagcca ccacgtgaga gcacagcctt cctaggcttc
     1921 ctcaaggagc aggttcagcg ggatggagca gctgctagcc tcgcccaagg gggtctgctc
     1981 cctgaaaatg ccctctttac gtctatccag tccttacaat ctgagtctga gcccctgagc
     2041 cttatcgcaa atgtggtagc tggctcatcc tgccggggcc ctccactgcc cagagacctg
     2101 cagggctcca ggcacagggc tgaagtcgcc tctgccctgc gctccttctc cccgctgcaa
     2161 cccgggcagg cgcccacagg ccgggctcac agcaccatga caggctctgg ggtggatgcc
     2221 aggacagcca gctccgggag cagcgtgtgg gaaggacagc tgcagagcct ggtgctgtca
     2281 gaatatgcat ccacagagat gagcctgcat gccctctata tgcaccagct ccacaagcag
     2341 caggcccagg ctgaacctga gcggcatgta tggcaccgcc gggagagtga tgagagtgga
     2401 gaaagcgccc ctgatgaagg gggagagggc gcccgggccc cccagtctat ccctcgctct
     2461 gctagctatc cctgtgcagc accccggcct ggagctcctg agaccactgc cctgcatggg
     2521 ggcttccaga ggcgctacgg tggcatcaca gatcctggca cagtgcccag ggttccctct
     2581 catttctctc ggctgcctct tggagggtgg gcagaagatg ggcagtcggc atcaaggcac
     2641 cctgagcccg tgcccgaaga gggctcggag gatgagctac cccctcaggt gcacaaggta
     2701 tagacaaggc tgagcagggt tcctgtggcc caggatggag gccaccgctg ccctgccatc
     2761 ccgtctgcct gccatgggac ggctcctctg agtgttccct ggccccacgt gtgtggtgtt
     2821 tgtgtgtctg tgcctggcca agggaggtgc caacactggg cttgccacag ccccaggaga
     2881 ggaatttggg gcctaggaac cgagggcaca cgggactcta gcctcatccc caggaccccc
     2941 ttggctcaga gtgtggtgct agaaactggc ccccagccca gccccagtac tgccaccttt
     3001 acacctaccc ctgcaagtcc ccagagggct gcccacgata gaagctgcca agcagggaga
     3061 acctgtgcca actgtggagt ggggaggttg ggcctggacc ctcaacccct gcaaccttcc
     3121 ctagccccct caatagatga gcaggtcagg ctgtggccct tacctcaccc gcagttctcg
     3181 cccagtgctg cagccggctc acctctctcc gcttcttgca catcactggc ctgtgtgtgc
     3241 tgcttgctcc tgttctgttc gcttgctccc gttccgttcg gcttttgctt tgcgttaggg
     3301 tgaagaccct agcgtccagc tcccctcaac gctatatttt gacactaaaa aagaaggttt
     3361 ctaaattgta ggagcaggat ggaaatactt tgctgccctt gccatctttt aggatgggcc
     3421 cccaggagac tgaggtcttc ctgggccctc attgctgctt atcgtacccc ccatcacctg
     3481 cacatgggac agaccgggct ggagggtgac cttggctgtg tgcgtcccag caaaagagct
     3541 ctggcccgca tctcgctgtg ccctgaaggg ggatgaaggg cgatgcctcg cccgaggctt
     3601 tgggctgctg cactgcatgc tgggactgct cctactctct gtcccacccc tcacccagct
     3661 gtggtccggc tttgggagag tggtgaattg cgctgcccga actcggagcg gagcagggta
     3721 gggaccgtgt acagcttgat aacccttaat aaaaagggag tttgaccaga
//
