LOCUS       NM_001011658            2842 bp    mRNA    linear   PRI 04-OCT-2024
DEFINITION  Homo sapiens trafficking protein particle complex subunit 2
            (TRAPPC2), transcript variant 1, mRNA.
ACCESSION   NM_001011658
VERSION     NM_001011658.4
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 2842)
  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   2  (bases 1 to 2842)
  AUTHORS   Won,J.Y., Kim,D., Park,S.Y., Lee,H.R., Lim,J.S., Park,J.H.,
            Song,M.H., Song,H.R., Kim,O.H., Kim,Y. and Cho,T.J.
  TITLE     Novel loss-of-function variants of TRAPPC2 manifesting X-linked
            spondyloepiphyseal dysplasia tarda: report of two cases
  JOURNAL   BMC Med Genet 20 (1), 70 (2019)
   PUBMED   31053099
  REMARK    GeneRIF: Novel loss-of-function variants of TRAPPC2 manifesting
            X-linked spondyloepiphyseal dysplasia tarda: report of two cases
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2842)
  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   4  (bases 1 to 2842)
  AUTHORS   Wu,X., Deng,K., Wang,C., Li,G., Lin,J., Wang,R., Wu,H. and Huang,S.
  TITLE     [Mutation analysis of the TRAPPC2 gene in a Chinese family with
            X-linked spondyloepiphyseal dysplasia tarda]
  JOURNAL   Zhonghua Yi Xue Yi Chuan Xue Za Zhi 32 (4), 476-480 (2015)
   PUBMED   26252088
  REMARK    GeneRIF: c.93+5G>A mutation in the TRAPPC2 gene is associated with
            X-linked spondyloepiphyseal dysplasia in a Chinese family.
REFERENCE   5  (bases 1 to 2842)
  AUTHORS   Milev,M.P., Hasaj,B., Saint-Dic,D., Snounou,S., Zhao,Q. and
            Sacher,M.
  TITLE     TRAMM/TrappC12 plays a role in chromosome congression, kinetochore
            stability, and CENP-E recruitment
  JOURNAL   J Cell Biol 209 (2), 221-234 (2015)
   PUBMED   25918224
REFERENCE   6  (bases 1 to 2842)
  AUTHORS   Gecz,J., Hillman,M.A., Gedeon,A.K., Cox,T.C., Baker,E. and
            Mulley,J.C.
  TITLE     Gene structure and expression study of the SEDL gene for
            spondyloepiphyseal dysplasia tarda
  JOURNAL   Genomics 69 (2), 242-251 (2000)
   PUBMED   11031107
REFERENCE   7  (bases 1 to 2842)
  AUTHORS   Gedeon,A.K., Colley,A., Jamieson,R., Thompson,E.M., Rogers,J.,
            Sillence,D., Tiller,G.E., Mulley,J.C. and Gecz,J.
  TITLE     Identification of the gene (SEDL) causing X-linked
            spondyloepiphyseal dysplasia tarda
  JOURNAL   Nat Genet 22 (4), 400-404 (1999)
   PUBMED   10431248
REFERENCE   8  (bases 1 to 2842)
  AUTHORS   Bernard,L.E., Chitayat,D., Weksberg,R., Van Allen,M.I. and
            Langlois,S.
  TITLE     Linkage analysis of two Canadian families segregating for X linked
            spondyloepiphyseal dysplasia
  JOURNAL   J Med Genet 33 (5), 432-434 (1996)
   PUBMED   8733060
REFERENCE   9  (bases 1 to 2842)
  AUTHORS   Adams,M.D., Soares,M.B., Kerlavage,A.R., Fields,C. and Venter,J.C.
  TITLE     Rapid cDNA sequencing (expressed sequence tags) from a
            directionally cloned human infant brain cDNA library
  JOURNAL   Nat Genet 4 (4), 373-380 (1993)
   PUBMED   8401585
REFERENCE   10 (bases 1 to 2842)
  AUTHORS   Tiller,G.E.
  TITLE     X-Linked Spondyloepiphyseal Dysplasia Tarda
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301324
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA344866.1, AK313736.1,
            AC003037.1 and AA770629.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_001011658.3.
            
            Summary: The protein encoded by this gene is thought to be part of
            a large multi-subunit complex involved in the targeting and fusion
            of endoplasmic reticulum-to-Golgi transport vesicles with their
            acceptor compartment. In addition, the encoded protein can bind
            c-myc promoter-binding protein 1 and block its transcriptional
            repression capability. Mutations in this gene are a cause of
            spondyloepiphyseal dysplasia tarda (SEDT). A processed pseudogene
            of this gene is located on chromosome 19, and other pseudogenes are
            found on chromosomes 8 and Y. Alternatively spliced transcript
            variants have been found for this gene. [provided by RefSeq, Mar
            2010].
            
            Transcript Variant: This variant (1) encodes the shorter isoform
            (1). Variants 1 and 2 encode the same isoform.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: SRR3476690.338880.1,
                                           SRR1660809.193340.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2467148 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000380579.6/ ENSP00000369953.1
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-45                DA344866.1         16-60
            46-680              AK313736.1         1-635
            681-2648            AC003037.1         15613-17580         c
            2649-2842           AA770629.1         13-206              c
FEATURES             Location/Qualifiers
     source          1..2842
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xp22.2"
     gene            1..2842
                     /gene="TRAPPC2"
                     /gene_synonym="hYP38334; MIP2A; SEDL; SEDT; TRAPPC2P1;
                     TRS20; ZNF547L"
                     /note="trafficking protein particle complex subunit 2"
                     /db_xref="GeneID:6399"
                     /db_xref="HGNC:HGNC:23068"
                     /db_xref="MIM:300202"
     exon            1..96
                     /gene="TRAPPC2"
                     /gene_synonym="hYP38334; MIP2A; SEDL; SEDT; TRAPPC2P1;
                     TRS20; ZNF547L"
                     /inference="alignment:Splign:2.1.0"
     exon            97..238
                     /gene="TRAPPC2"
                     /gene_synonym="hYP38334; MIP2A; SEDL; SEDT; TRAPPC2P1;
                     TRS20; ZNF547L"
                     /inference="alignment:Splign:2.1.0"
     exon            239..350
                     /gene="TRAPPC2"
                     /gene_synonym="hYP38334; MIP2A; SEDL; SEDT; TRAPPC2P1;
                     TRS20; ZNF547L"
                     /inference="alignment:Splign:2.1.0"
     CDS             258..680
                     /gene="TRAPPC2"
                     /gene_synonym="hYP38334; MIP2A; SEDL; SEDT; TRAPPC2P1;
                     TRS20; ZNF547L"
                     /note="isoform 1 is encoded by transcript variant 1;
                     sedlin; trafficking protein particle complex 2"
                     /codon_start=1
                     /product="trafficking protein particle complex subunit 2
                     isoform 1"
                     /protein_id="NP_001011658.1"
                     /db_xref="CCDS:CCDS48082.1"
                     /db_xref="GeneID:6399"
                     /db_xref="HGNC:HGNC:23068"
                     /db_xref="MIM:300202"
                     /translation="MSGSFYFVIVGHHDNPVFEMEFLPAGKAESKDDHRHLNQFIAHA
                     ALDLVDENMWLSNNMYLKTVDKFNEWFVSAFVTAGHMRFIMLHDIRQEDGIKNFFTDV
                     YDLYIKFSMNPFYEPNSPIRSSAFDRKVQFLGKKHLLS"
     exon            351..495
                     /gene="TRAPPC2"
                     /gene_synonym="hYP38334; MIP2A; SEDL; SEDT; TRAPPC2P1;
                     TRS20; ZNF547L"
                     /inference="alignment:Splign:2.1.0"
     exon            496..581
                     /gene="TRAPPC2"
                     /gene_synonym="hYP38334; MIP2A; SEDL; SEDT; TRAPPC2P1;
                     TRS20; ZNF547L"
                     /inference="alignment:Splign:2.1.0"
     exon            582..2842
                     /gene="TRAPPC2"
                     /gene_synonym="hYP38334; MIP2A; SEDL; SEDT; TRAPPC2P1;
                     TRS20; ZNF547L"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2824..2829
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRAPPC2"
                     /gene_synonym="hYP38334; MIP2A; SEDL; SEDT; TRAPPC2P1;
                     TRS20; ZNF547L"
                     /note="hexamer: AATAAA"
     polyA_site      2842
                     /gene="TRAPPC2"
                     /gene_synonym="hYP38334; MIP2A; SEDL; SEDT; TRAPPC2P1;
                     TRS20; ZNF547L"
                     /note="major polyA site"
ORIGIN      
        1 gcgagaactg cttcggcgtt ctggctacag gttcggggcg cgggtctctt ccgcggaaac
       61 tgacattgcg tttccgttgt cggcctccca ctgcagtatc accttctccc ccaagtgtga
      121 caaccaaaga tgtctccaga tattgccaga tgtcctcttg gaagcaagat cgctccgggt
      181 tgagatccac agagctaaac gttttagagt accaaccatt gtgtgctgtg aggtaaagga
      241 gccatatatt gaagaccatg tctgggagct tctactttgt aattgttggc caccatgata
      301 atccagtttt tgaaatggag tttttgccag ctgggaaggc agaatccaaa gacgaccatc
      361 gtcatctgaa ccagttcata gctcatgctg ctctcgacct cgtagatgag aacatgtggc
      421 tatcgaacaa catgtacttg aaaactgtgg acaagttcaa cgagtggttt gtgtcggcat
      481 ttgtcactgc ggggcatatg aggtttatta tgcttcatga cataagacaa gaagatggaa
      541 taaagaactt ctttactgat gtttatgatt tatatataaa gttttcaatg aatccatttt
      601 atgaacccaa ttctcctatt cgatcaagtg catttgacag aaaagttcag tttcttggga
      661 agaaacacct tttaagctga atgcagaaaa ttccaaaata aatgatgtca ccacaatggt
      721 gtatactcag gaatgtgtac attgtaagtt acttgattaa atagcctgga aaacttttgt
      781 gtattctcag cttatctaaa cctaatgaaa ttccttttat atttaaaaat agtacattct
      841 gtctcatgtc acgtatcaat agatcaattg gtatttcctt gtgaacagtg ttatttataa
      901 agagttcatt atcaataatc atgttttttt tttttttttt tttctgatac agagtctcac
      961 tctgttgcca ggctggagtg cagtggcgca atcttggctc actgcaacct ccgcctccca
     1021 ggttcaggcg attctcctgc ctcagcctcc aagtagctgg gactacaggc gcgtgccacc
     1081 acgcccggct aatttttgta tttttagtag agacagggtt tcaccatatt ggtcaggctg
     1141 gtcttgaact cctgacctcg tgatctgccc gccttggcct cccaaagtac tgggattaca
     1201 ggcgtgagcc accgtgccca accatgaaat atttttactt aaaaattggg aataagctcg
     1261 cttttttttt ttttgagatg gagtcttgct cctgttgtgc aggctgtagt gcagtggcac
     1321 gatcttggct cactgcaacc tccacctccc gggttcaagc aattctcctt cttcagcctc
     1381 ccgagtagct gagattatag gcgtgcacca ccacacctgg ctaatttttg tatttttagt
     1441 agagacaggg tttcaccata ttggtcaggc tggtcttgaa ctcctgacct cgtgatccac
     1501 ccacctcagg aagtgctggg attacaggcg tgtgagccac cacgcccggc catgaaatat
     1561 ttttacttaa aaattgggaa taagcttttt ggttttttgt gggtttttgt ttttgttttt
     1621 tgttttttgt ttttttgaga tggagtcttg ctcctgttgt gcaggctgga gtgcagtggc
     1681 acagtcttgg ctcactgcaa cctccacctc ctgggttcaa gcaattctcc ttcttcagcc
     1741 tcccgagtag ctgggattac aggcatgcac caccacacct ggctaatttt tgtgttttta
     1801 gtagagacgg ggtttcgcta ttttggccgg gctggtttca aactcctgac ctcagttgat
     1861 ccacccgcct cagcctccca aagtgctagg attacaggca tgaaccaccg tgcccggcca
     1921 ggaataagct tttgacttac ccaattcaga taggttgatc tttggggttt tttttttttt
     1981 tttgagatgg agtttcgctc tgttgtccag gctggagtgc aatggcagtt gtttcaccgt
     2041 aacctctgcc tcctgacttc aagcaattct cctgcctcag cctcccaaag tgctgggatt
     2101 acaggtgtga gccaccgtgc ccggcccaga taggttgatc ttaatgtaac aacccaaaaa
     2161 taaatgtcat agtcaagatt tggtagataa atttaaaatt aaaatattct gcagttggga
     2221 gtgaaatgtg atagcacata cgttgacatt atgcatttag agatgttata aaaatgtata
     2281 ggcagtatac acagcactac tcaagaagcc aaagaaacac ttgtgcagtg ctaagtgtca
     2341 catgtctgct tccaccagag gctaggaata gtgatcctgc tataatgtga gaacccaaat
     2401 catgtttata aaataggacg ctgggagcag ttgcaggcca cagtgaagtg tgttgcttct
     2461 gtcactttat attcttatat ttcctttccc tcagacagta aactgttgat actcgtactt
     2521 gtaaaaaatt gtaaggcaat ttttagtatt gttgtcaaag aaaagcttgg attacattaa
     2581 catttgtatt cagtctttta ggtgatacac cagagggggc tgggaattgt ctctttgttc
     2641 ctataagtag atcttaatgt aaaatagtaa atgtccattg aaaagcaagt aatacagcct
     2701 gtgctaattg ggagcacttg aacaattttg ttccattctg agtaactttt gagcaagtaa
     2761 ttctaagctt tgtcttgtat ccttgtgtga aattgcataa tttttaccct atttgatttc
     2821 ttaaataaag atgtttgctc aa
//
