LOCUS       NM_024941               2910 bp    mRNA    linear   PRI 20-SEP-2024
DEFINITION  Homo sapiens trafficking protein particle complex subunit 13
            (TRAPPC13), transcript variant 2, mRNA.
ACCESSION   NM_024941
VERSION     NM_024941.4
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 2910)
  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   2  (bases 1 to 2910)
  AUTHORS   Gupta,R., Somyajit,K., Narita,T., Maskey,E., Stanlie,A., Kremer,M.,
            Typas,D., Lammers,M., Mailand,N., Nussenzweig,A., Lukas,J. and
            Choudhary,C.
  TITLE     DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of
            NHEJ and PARP Inhibitor Sensitivity
  JOURNAL   Cell 173 (4), 972-988 (2018)
   PUBMED   29656893
REFERENCE   3  (bases 1 to 2910)
  AUTHORS   Ramirez-Peinado,S., Ignashkova,T.I., van Raam,B.J., Baumann,J.,
            Sennott,E.L., Gendarme,M., Lindemann,R.K., Starnbach,M.N. and
            Reiling,J.H.
  TITLE     TRAPPC13 modulates autophagy and the response to Golgi stress
  JOURNAL   J Cell Sci 130 (14), 2251-2265 (2017)
   PUBMED   28536105
  REMARK    GeneRIF: Results lend support for the existence of a mammalian
            TRAPPIII complex containing TRAPPC13, which is important for
            autophagic flux under certain stress conditions.
REFERENCE   4  (bases 1 to 2910)
  AUTHORS   Kim,J.J., Lipatova,Z. and Segev,N.
  TITLE     TRAPP Complexes in Secretion and Autophagy
  JOURNAL   Front Cell Dev Biol 4, 20 (2016)
   PUBMED   27066478
  REMARK    Review article
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2910)
  AUTHORS   Bassik,M.C., Kampmann,M., Lebbink,R.J., Wang,S., Hein,M.Y.,
            Poser,I., Weibezahn,J., Horlbeck,M.A., Chen,S., Mann,M.,
            Hyman,A.A., Leproust,E.M., McManus,M.T. and Weissman,J.S.
  TITLE     A systematic mammalian genetic interaction map reveals pathways
            underlying ricin susceptibility
  JOURNAL   Cell 152 (4), 909-922 (2013)
   PUBMED   23394947
REFERENCE   6  (bases 1 to 2910)
  AUTHORS   Choi,C., Davey,M., Schluter,C., Pandher,P., Fang,Y., Foster,L.J.
            and Conibear,E.
  TITLE     Organization and assembly of the TRAPPII complex
  JOURNAL   Traffic 12 (6), 715-725 (2011)
   PUBMED   21453443
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DB145758.1, AK023673.1, BC117128.1, AL713699.1, N67829.1,
            BM664695.1 and AC008560.6.
            
            On Nov 22, 2018 this sequence version replaced NM_024941.3.
            
            Transcript Variant: This variant (2) uses an alternate in-frame
            splice site in the 3' coding region, compared to variant 1,
            resulting in a shorter protein (isoform 2).
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR3476690.664281.1, AK023673.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000399438.8/ ENSP00000382367.3
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-18                DB145758.1         295-312
            19-220              AK023673.1         2-203
            221-580             BC117128.1         154-513
            581-1877            AK023673.1         564-1860
            1878-2746           AL713699.1         1214-2082
            2747-2802           N67829.1           2-57                c
            2803-2804           BM664695.1         18-19               c
            2805-2910           AC008560.6         16854-16959         c
FEATURES             Location/Qualifiers
     source          1..2910
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q12.3"
     gene            1..2910
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /note="trafficking protein particle complex subunit 13"
                     /db_xref="GeneID:80006"
                     /db_xref="HGNC:HGNC:25828"
     exon            1..80
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /inference="alignment:Splign:2.1.0"
     CDS             35..1288
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /note="isoform 2 is encoded by transcript variant 2;
                     UPF0533 protein C5orf44; Trs65-related; REV7-interacting
                     novel NHEJ regulator 1; trafficking protein particle
                     complex 13"
                     /codon_start=1
                     /product="trafficking protein particle complex subunit 13
                     isoform 2"
                     /protein_id="NP_079217.2"
                     /db_xref="CCDS:CCDS47222.1"
                     /db_xref="GeneID:80006"
                     /db_xref="HGNC:HGNC:25828"
                     /translation="MEVNPPKQEHLLALKVMRLTKPTLFTNIPVTCEEKDLPGDLFNQ
                     LMRDDPSTVNGAEVLMLGEMLTLPQNFGNIFLGETFSSYISVHNDSNQVVKDILVKAD
                     LQTSSQRLNLSASNAAVAELKPDCCIDDVIHHEVKEIGTHILVCAVSYTTQAGEKMYF
                     RKFFKFQVLKPLDVKTKFYNAESDLSSVTDEVFLEAQIQNMTTSPMFMEKVSLEPSIM
                     YNVTELNSVSQAGECVSTFGSRAYLQPMDTRQYLYCLKPKNEFAEKAGIIKGVTVIGK
                     LDIVWKTNLGERGRLQTSQLQRMAPGYGDVRLSLEAIPDTVNLEEPFHITCKITNCSE
                     RTMDLVLEMCNTNSIHWCGISGRQLGKLHPSSSLCLALTLLSSVQGLQSISGLRLTDT
                     FLKRTYEYDDIAQVCVVSSAIKVES"
     exon            81..149
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /inference="alignment:Splign:2.1.0"
     exon            150..249
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /inference="alignment:Splign:2.1.0"
     exon            250..334
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /inference="alignment:Splign:2.1.0"
     exon            335..462
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /inference="alignment:Splign:2.1.0"
     exon            463..535
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /inference="alignment:Splign:2.1.0"
     exon            536..580
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /inference="alignment:Splign:2.1.0"
     exon            581..598
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /inference="alignment:Splign:2.1.0"
     exon            599..732
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /inference="alignment:Splign:2.1.0"
     exon            733..931
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /inference="alignment:Splign:2.1.0"
     exon            932..1032
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /inference="alignment:Splign:2.1.0"
     exon            1033..1180
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /inference="alignment:Splign:2.1.0"
     exon            1181..2910
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1421..1426
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /note="hexamer: ATTAAA"
     polyA_site      1443
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /note="major polyA site"
     regulatory      2586..2591
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /note="hexamer: ATTAAA"
     polyA_site      2604
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /note="major polyA site"
     regulatory      2724..2729
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /note="hexamer: AATAAA"
     polyA_site      2751
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /note="major polyA site"
     regulatory      2779..2784
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /note="hexamer: ATTAAA"
     polyA_site      2808
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
     regulatory      2888..2893
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
                     /note="hexamer: AGTAAA"
     polyA_site      2910
                     /gene="TRAPPC13"
                     /gene_synonym="C5orf44; SHLD3"
ORIGIN      
        1 ccccgtaggc tgtgggtcaa aagtgccggt caaaatggaa gtgaatcccc ctaaacagga
       61 gcacctgctg gcgctaaaag tgatgcggct gactaagcct actttattca ccaatatccc
      121 agtaacatgt gaagagaaag acttacctgg agatctcttt aaccagctga tgagagatga
      181 tccttcaacc gttaatggtg cagaagtttt aatgttggga gaaatgctga ctttaccaca
      241 gaattttggg aatatatttt tgggagagac cttttccagt tatatcagcg ttcataatga
      301 tagcaatcaa gttgtaaaag acatattagt aaaagctgat cttcagacaa gttctcagcg
      361 tttaaatctt tcagcctcca atgctgcagt ggctgaactt aaaccggatt gttgtattga
      421 tgatgtcata catcatgaag tcaaagaaat tggaacacac atcttggtat gtgctgtgag
      481 ttatacaact caggctggag aaaaaatgta tttcagaaaa ttcttcaaat ttcaggttct
      541 caaaccattg gatgtgaaaa ccaaatttta caatgcagag agtgacctca gttctgtgac
      601 tgatgaagta tttctggaag cccagattca gaatatgaca acctcaccta tgtttatgga
      661 gaaggtttca ctggagccat ctattatgta caatgtaaca gaattaaatt cagtcagcca
      721 agctggagaa tgtgtgtcta cgtttgggtc aagagcatat ttgcaaccaa tggatacacg
      781 ccagtactta tactgcctaa agccaaagaa tgaatttgca gaaaaagcag gcatcattaa
      841 gggagtaaca gtaattggaa aattggatat agtatggaaa acaaatctag gtgaaagggg
      901 aaggttacag accagccaac ttcaaagaat ggctccaggt tatggagatg ttaggttgtc
      961 tttggaggca ataccagata ccgtaaacct tgaagaacct tttcatatta cctgtaaaat
     1021 aacaaactgc agtgaaagga ctatggatct ggttttggaa atgtgcaata ccaattccat
     1081 ccactggtgt ggaatttcag gaagacagct gggaaagctg catccaagtt cttcgctctg
     1141 tcttgccctt actctgcttt cttcagtaca gggactgcaa agcatctctg gcttaagact
     1201 aacagacaca ttcttaaaga gaacatatga atatgatgac atcgcacaag tctgtgtggt
     1261 atcttctgcc attaaagtgg aaagctgaag gaaacttcca atgttaggct tttcatttag
     1321 tttcacagaa ctgctctttt tgttaccttt gtaaaatgat gacgtcaaca acgaagtaaa
     1381 tatgttactt aaattttctt tcctgtaaaa tggttaaaat attaaatatt tgttttgaag
     1441 agatctgatt ttatcttgta atttatattt gaaatgaaca tgtgtatatt ttctacacct
     1501 attatttaat ttcatttcat tttagatgac cattggactt tgttctccaa aagctgtgta
     1561 tctgagacca tttgtcccta gcaagttatc tagaacacga gtcagcacac tttttatgta
     1621 aggtacaaga tactaaatat tttaggcttt gcaggccgta aggtttctgt cacaaatact
     1681 gaactctgcc atcgtacttc aagagcagcc agtaggcaaa aaaagtacag tggtgtacac
     1741 aaaaagaagc agttggactc gggaagctga ggcaggagaa tcacttgaac cggggaggca
     1801 gaggttgcag ttaagccgag atcatgctac tgcactctag cctgagcgac agagtgagac
     1861 tctgtctcaa aaaaaaagag gcagctgggc agatttggcc tgcagggtat agttggctga
     1921 cctcaatcta gaagatagag ttgtttctta gaactttgta atattttggt tagaaatatt
     1981 tcagttaact ccagtttttt cctagctatt cggtcagcag aaaaagtttg cttaaaacaa
     2041 agggggtagt cctcttataa cctgatattt gtcaacacag tataagcttt ctagttgttt
     2101 tcaaaattac tgtaatggtt tgtgtctgta tttgtatatt atacctacaa acatacatat
     2161 ctttcagcta ctgaacacat cagaattggt tttacttttt aggttgttga ttttttttaa
     2221 ttaactatta actaagaata atacttattt tctaattata agccaaaaac ccctgggttt
     2281 ttttctcatt gattaagcca cttattttta taaggtatat ttaaataatt cccatcttct
     2341 gatatgattt taaactctaa atcatgtgtt actgttacaa aactttctct ctccatgtaa
     2401 tcacacttag ttatgagcaa agcagtgaga aagttgaggt gataaacaac tttgcagcat
     2461 taatgtaaca aaaagtttca gtatttgtca ggaaaacaaa agcttaggct gttaaataaa
     2521 agctattcta ttttggtaag ttgaaattca agaatgtata tataatttct taaatgtaag
     2581 agtgcattaa atcaaataca aaaattggtt tttcaatgca tcattattta ttgccataac
     2641 aaattgtttg gtccaaaatg aaagctatat tcagaaggtt tgcacctcaa aattgagtaa
     2701 taattaatga aatgtctgta caaaataaag tgcaagcagt gtaaaattga agtctgtctt
     2761 tgtttcaaaa tgattaagat taaatgatga aataatattt tatagccact gcattggata
     2821 cttggattgt ttttcaagca tcttcttatg actaaatctt ctgtttcatt ctgttttaaa
     2881 tctaaaaagt aaaatgatgg tcacttggaa
//
