LOCUS       NM_025187               2917 bp    mRNA    linear   PRI 19-SEP-2024
DEFINITION  Homo sapiens phagophore assembly factor 1 (PHAF1), transcript
            variant 1, mRNA.
ACCESSION   NM_025187
VERSION     NM_025187.5
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 2917)
  AUTHORS   Franco-Romero,A., Morbidoni,V., Milan,G., Sartori,R., Wulff,J.,
            Romanello,V., Armani,A., Salviati,L., Conte,M., Salvioli,S.,
            Franceschi,C., Buonomo,V., Swoboda,C.O., Grumati,P., Pannone,L.,
            Martinelli,S., Jefferies,H.B., Dikic,I., van der Laan,J.,
            Cabreiro,F., Millay,D.P., Tooze,S.A., Trevisson,E. and Sandri,M.
  TITLE     C16ORF70/MYTHO promotes healthy aging in C.elegans and prevents
            cellular senescence in mammals
  JOURNAL   J Clin Invest 134 (15), e165814 (2024)
   PUBMED   38869949
  REMARK    GeneRIF: C16ORF70/MYTHO promotes healthy aging in C.elegans and
            prevents cellular senescence in mammals.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2917)
  AUTHORS   Kojima,W., Yamano,K., Kosako,H., Imai,K., Kikuchi,R., Tanaka,K. and
            Matsuda,N.
  TITLE     Mammalian BCAS3 and C16orf70 associate with the phagophore assembly
            site in response to selective and non-selective autophagy
  JOURNAL   Autophagy 17 (8), 2011-2036 (2021)
   PUBMED   33499712
REFERENCE   3  (bases 1 to 2917)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   4  (bases 1 to 2917)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   5  (bases 1 to 2917)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   6  (bases 1 to 2917)
  AUTHORS   Bailey,S.D., Xie,C., Do,R., Montpetit,A., Diaz,R., Mohan,V.,
            Keavney,B., Yusuf,S., Gerstein,H.C., Engert,J.C. and Anand,S.
  CONSRTM   DREAM investigators
  TITLE     Variation at the NFATC2 locus increases the risk of
            thiazolidinedione-induced edema in the Diabetes REduction
            Assessment with ramipril and rosiglitazone Medication (DREAM) study
  JOURNAL   Diabetes Care 33 (10), 2250-2253 (2010)
   PUBMED   20628086
  REMARK    GeneRIF: Observational study of gene-disease association,
            gene-environment interaction, and pharmacogenomic / toxicogenomic.
            (HuGE Navigator)
REFERENCE   7  (bases 1 to 2917)
  AUTHORS   Hosgood,H.D. 3rd, Zhang,L., Shen,M., Berndt,S.I., Vermeulen,R.,
            Li,G., Yin,S., Yeager,M., Yuenger,J., Rothman,N., Chanock,S.,
            Smith,M. and Lan,Q.
  TITLE     Association between genetic variants in VEGF, ERCC3 and
            occupational benzene haematotoxicity
  JOURNAL   Occup Environ Med 66 (12), 848-853 (2009)
   PUBMED   19773279
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   8  (bases 1 to 2917)
  AUTHORS   Talmud,P.J., Drenos,F., Shah,S., Shah,T., Palmen,J., Verzilli,C.,
            Gaunt,T.R., Pallas,J., Lovering,R., Li,K., Casas,J.P., Sofat,R.,
            Kumari,M., Rodriguez,S., Johnson,T., Newhouse,S.J., Dominiczak,A.,
            Samani,N.J., Caulfield,M., Sever,P., Stanton,A., Shields,D.C.,
            Padmanabhan,S., Melander,O., Hastie,C., Delles,C., Ebrahim,S.,
            Marmot,M.G., Smith,G.D., Lawlor,D.A., Munroe,P.B., Day,I.N.,
            Kivimaki,M., Whittaker,J., Humphries,S.E. and Hingorani,A.D.
  CONSRTM   ASCOT investigators; NORDIL investigators; BRIGHT Consortium
  TITLE     Gene-centric association signals for lipids and apolipoproteins
            identified via the HumanCVD BeadChip
  JOURNAL   Am J Hum Genet 85 (5), 628-642 (2009)
   PUBMED   19913121
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   9  (bases 1 to 2917)
  AUTHORS   Lim,J., Hao,T., Shaw,C., Patel,A.J., Szabo,G., Rual,J.F.,
            Fisk,C.J., Li,N., Smolyar,A., Hill,D.E., Barabasi,A.L., Vidal,M.
            and Zoghbi,H.Y.
  TITLE     A protein-protein interaction network for human inherited ataxias
            and disorders of Purkinje cell degeneration
  JOURNAL   Cell 125 (4), 801-814 (2006)
   PUBMED   16713569
REFERENCE   10 (bases 1 to 2917)
  AUTHORS   Setou,M., Nakagawa,T., Seog,D.H. and Hirokawa,N.
  TITLE     Kinesin superfamily motor protein KIF17 and mLin-10 in NMDA
            receptor-containing vesicle transport
  JOURNAL   Science 288 (5472), 1796-1802 (2000)
   PUBMED   10846156
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC074143.5, HY121038.1, BC004556.2 and AA127668.1.
            
            On May 17, 2019 this sequence version replaced NM_025187.4.
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longer isoform (a). Variants 1, 2, 3,
            and 4 all encode the same isoform (a).
            
            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 :: SRR3476690.1094037.1, BC004556.2
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000219139.8/ ENSP00000219139.3
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-51                AC074143.5         78577-78627
            52-71               HY121038.1         2-21
            72-2912             BC004556.2         1-2841
            2913-2917           AA127668.1         26-30               c
FEATURES             Location/Qualifiers
     source          1..2917
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="16"
                     /map="16q22.1"
     gene            1..2917
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /note="phagophore assembly factor 1"
                     /db_xref="GeneID:80262"
                     /db_xref="HGNC:HGNC:29564"
     exon            1..299
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     CDS             236..1504
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /note="isoform a is encoded by transcript variant 1;
                     UPF0183 protein C16orf70; macro-autophagy and youth
                     optimizer; phagosome assembly factor 1"
                     /codon_start=1
                     /product="phagosome assembly factor 1 isoform a"
                     /protein_id="NP_079463.2"
                     /db_xref="CCDS:CCDS10828.1"
                     /db_xref="GeneID:80262"
                     /db_xref="HGNC:HGNC:29564"
                     /translation="MLDLEVVPERSLGNEQWEFTLGMPLAQAVAILQKHCRIIKNVQV
                     LYSEQSPLSHDLILNLTQDGIKLMFDAFNQRLKVIEVCDLTKVKLKYCGVHFNSQAIA
                     PTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQLDSWTEAPKYEPNFAHGLASL
                     QIPHGATVKRMYIYSGNSLQDTKAPMMPLSCFLGNVYAESVDVLRDGTGPAGLRLRLL
                     AAGCGPGLLADAKMRVFERSVYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQ
                     VPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTNYPGHYNFNIYHRCEFKIPLAIK
                     KENADGQTETCTTYSKWDNIQELLGHPVEKPVVLHRSSSPNNTNPFGSTFCFGLQRMI
                     FEVMQNNHIASVTLYGPPRPGSHLRTAELP"
     exon            300..382
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            383..466
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            467..510
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            511..590
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            591..685
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            686..783
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            784..896
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            897..1030
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            1031..1114
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            1115..1197
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            1198..1241
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            1242..1285
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            1286..1344
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            1345..1417
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     exon            1418..2917
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /inference="alignment:Splign:2.1.0"
     polyA_site      2597
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
     regulatory      2850..2855
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /note="hexamer: AATAAA"
     polyA_site      2870
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /note="major polyA site"
     polyA_site      2917
                     /gene="PHAF1"
                     /gene_synonym="C16orf6; C16orf70; lin-10; LIN10; MYTHO"
                     /note="major polyA site"
ORIGIN      
        1 gcagtcgcgc ccgccgccgt cgttgccccc gctgccgcgg ctgctgcagg tgaggtgaag
       61 tgaggtgagg tgtggtgttg ggccggtgct gctgccgctg ccgccgggga ggaggtggaa
      121 agcggggctg tggcgggccg gcgggggcgg cctgtcagcc gctgctttgt ctccttagct
      181 cgggtccctt ctgcgctgcc gcagggaggc cgcccgggcc aggcgagccg aaccaatgct
      241 ggacctggag gtagtgcccg aacgctctct ggggaacgag caatgggaat tcacgctggg
      301 aatgcctctg gctcaggcag tagccattct tcagaagcac tgtcgcatca tcaaaaacgt
      361 ccaggttctc tacagtgaac agtctcctct aagccatgac ctcattctta acctgactca
      421 ggacgggatc aaactaatgt ttgatgcttt caatcagaga cttaaggtga tcgaagtatg
      481 tgatttgact aaagtaaagt taaaatattg tggcgtgcat tttaattctc aggccatagc
      541 tcctaccatt gaacagattg accagtcttt tggcgcaacc catcctggag tgtacaactc
      601 cgctgagcag ctcttccatc tcaacttcag aggactgtct ttctcttttc agttagactc
      661 atggactgag gctccaaagt atgagcccaa ttttgcccat ggcctggctt ctctccagat
      721 accccatgga gcaactgtaa aacgaatgta catctacagt ggcaacagcc tgcaggatac
      781 caaggctccc atgatgcctc tgagctgttt cctgggcaat gtctatgctg agagtgtaga
      841 tgttcttcga gatggaactg gacctgcagg tttacgactt cgcctacttg ctgcaggttg
      901 tggacctggc ctattagcag atgccaagat gcgggtattt gaacgttcag tgtattttgg
      961 tgattcctgc caagatgttc ttagcatgct tggctctcca cacaaagtct tctataaatc
     1021 agaagacaag atgaaaattc attctccttc ccctcataaa caagttccat cgaagtgtaa
     1081 tgactacttt tttaactact tcactcttgg agtggacatc ctctttgatg cgaatacaca
     1141 caaagtgaag aagtttgttc tacacaccaa ttaccctggg cattataatt tcaacattta
     1201 tcatcgctgt gagttcaaga tcccactagc cataaagaaa gaaaacgcag atggtcagac
     1261 agaaacatgc acgacctaca gcaagtggga caacatccag gagctcctgg gccaccctgt
     1321 ggagaagcct gttgtcctgc acaggtcttc ctccccaaac aacaccaacc catttggttc
     1381 cacattctgc tttggtcttc agcgaatgat ctttgaggtc atgcagaaca accacattgc
     1441 ctcggtgacc ctgtatggcc cccccaggcc tggtagccac ctgagaacag cggaactccc
     1501 ctagggacac caccacccat gcccctctgt cccgtggaac tgtgcatcac atcctgctca
     1561 gtgggcctct gtaccaccct gtgggttttc ttggacacct ggccagtgct gaagggctgt
     1621 tgtgatgttc tgaggttggg ctcaggctgg gtgctctgcc atgggctgag tggcccagat
     1681 attcttctgt ccatctttgg cctgctggtg ccagcagggg acacagactg caaagagaag
     1741 cacaaagttt gagccttgat tcctggaccc aggagctctc aactaacaag gaggcaggag
     1801 aggtcaaccc ttgtcccatg cacattggga agacttgggg ctctttctgt gactgaggac
     1861 acaggcaccc aggataagga caaggtcctg cctttggctc cacattgcca catgaccctt
     1921 aaggcaagca ggtagcgtgt ccatagtact tggttgcgac atttgcacta catccacttt
     1981 agttacttga tgagctggct gtggccaggg tggcccacct gcccttccct gttcctttct
     2041 tgcacgcgct ccctgcctgg gcacaccaaa ctggttgaaa cacagctttc taccatccag
     2101 gtacatgccc aggcctggtt ctcacccctg ttggagtcag ctttcaagat tgcctgtgcc
     2161 cctgctctgc cccatcctgg ctggcagggc tgcatgtttc catcctgttt gcctctttta
     2221 tttaatgcca aagttttagc caaagacatc ttcctacttt tgttgtgttt cagcattctg
     2281 ttctgcactg tgggctggct ctctgcccca accctgggca ctggcccctg gctgggccat
     2341 ttcatggctc aaagcctctg ggggctcaag gaaggctggg ctgctcagtc ccttcatggg
     2401 tcttgctaat ggaaagtagc atatatgtgc tttaaaaata ttaatccttt tgaaaagaac
     2461 tgagaagaaa aatgtataat tttatcccat ttttaatatt ttggtctagc aacttgtgat
     2521 acatagatga caattttgtg agtttttcaa atgtgtgtac agatttttgt aaatatgact
     2581 cttttgtaat taactcatgt acagcctcat cctgtatagt ttaatgatga atgtgcaggg
     2641 gacctgtctc aggctcctat atggttcctg ggccttatag ccaggtttgt gtggcgctcc
     2701 cgacttttgt gactgactgg tgtcttccca tttggactgt ggcctggcca gagccccttg
     2761 catatcccca ctgtcagggg cagccaggac tgttcccatc ctcctggaat gggggaacct
     2821 tccttatccc ctgcccacat cccctctcca ataaagcacc tgtgccctca gcaatggcct
     2881 gccatgtgct gttgctggga tgtttgtatt aaggtaa
//
