LOCUS       NM_016146               1425 bp    mRNA    linear   PRI 09-FEB-2025
DEFINITION  Homo sapiens trafficking protein particle complex subunit 4
            (TRAPPC4), transcript variant 1, mRNA.
ACCESSION   NM_016146
VERSION     NM_016146.6
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 1425)
  AUTHORS   Ren,Y., Qian,Y., Ai,L., Xie,Y., Gao,Y., Zhuang,Z., Chen,J.,
            Chen,Y.X. and Fang,J.Y.
  TITLE     TRAPPC4 regulates the intracellular trafficking of PD-L1 and
            antitumor immunity
  JOURNAL   Nat Commun 12 (1), 5405 (2021)
   PUBMED   34518538
  REMARK    GeneRIF: TRAPPC4 regulates the intracellular trafficking of PD-L1
            and antitumor immunity.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1425)
  AUTHORS   Ghosh,S.G., Scala,M., Beetz,C., Helman,G., Stanley,V., Yang,X.,
            Breuss,M.W., Mazaheri,N., Selim,L., Hadipour,F., Pais,L.,
            Stutterd,C.A., Karageorgou,V., Begtrup,A., Crunk,A., Juusola,J.,
            Willaert,R., Flore,L.A., Kennelly,K., Spencer,C., Brown,M.,
            Trapane,P., Hurst,A.C.E., Lane Rutledge,S., Goodloe,D.H.,
            McDonald,M.T., Shashi,V., Schoch,K., Tomoum,H., Zaitoun,R.,
            Hadipour,Z., Galehdari,H., Pagnamenta,A.T., Mojarrad,M.,
            Sedaghat,A., Dias,P., Quintas,S., Eslahi,A., Shariati,G., Bauer,P.,
            Simons,C., Houlden,H., Issa,M.Y., Zaki,M.S., Maroofian,R. and
            Gleeson,J.G.
  CONSRTM   Undiagnosed Diseases Network
  TITLE     A relatively common homozygous TRAPPC4 splicing variant is
            associated with an early-infantile neurodegenerative syndrome
  JOURNAL   Eur J Hum Genet 29 (2), 271-279 (2021)
   PUBMED   32901138
  REMARK    GeneRIF: A relatively common homozygous TRAPPC4 splicing variant is
            associated with an early-infantile neurodegenerative syndrome.
REFERENCE   3  (bases 1 to 1425)
  AUTHORS   Van Bergen,N.J., Guo,Y., Al-Deri,N., Lipatova,Z., Stanga,D.,
            Zhao,S., Murtazina,R., Gyurkovska,V., Pehlivan,D., Mitani,T.,
            Gezdirici,A., Antony,J., Collins,F., Willis,M.J.H., Coban
            Akdemir,Z.H., Liu,P., Punetha,J., Hunter,J.V., Jhangiani,S.N.,
            Fatih,J.M., Rosenfeld,J.A., Posey,J.E., Gibbs,R.A., Karaca,E.,
            Massey,S., Ranasinghe,T.G., Sleiman,P., Troedson,C., Lupski,J.R.,
            Sacher,M., Segev,N., Hakonarson,H. and Christodoulou,J.
  TITLE     Deficiencies in vesicular transport mediated by TRAPPC4 are
            associated with severe syndromic intellectual disability
  JOURNAL   Brain 143 (1), 112-130 (2020)
   PUBMED   31794024
  REMARK    GeneRIF: Deficiencies in vesicular transport mediated by TRAPPC4
            are associated with severe syndromic intellectual disability.
            Erratum:[Brain. 2020 Mar 1;143(3):e24. doi: 10.1093/brain/awaa007..
            PMID: 32333675]
REFERENCE   4  (bases 1 to 1425)
  AUTHORS   Ai,L., Ren,Y., Li,Y., Chen,H., Qian,Y., Lu,S., Xu,A., Ren,L.,
            Zhao,S., Chen,Z., Chen,Y.X., Xu,J. and Fang,J.Y.
  TITLE     Synbindin deficiency inhibits colon carcinogenesis by attenuating
            Wnt cascade and balancing gut microbiome
  JOURNAL   Int J Cancer 145 (1), 206-220 (2019)
   PUBMED   30561033
  REMARK    GeneRIF: Findings identify a critical role of Synbindin in gut
            microbiome composition and Wnt signaling activation in colorectal
            carcinogenesis, and highlight Synbindin as an adaptor protein with
            multifaceted roles.
REFERENCE   5  (bases 1 to 1425)
  AUTHORS   Boldt,K., van Reeuwijk,J., Lu,Q., Koutroumpas,K., Nguyen,T.M.,
            Texier,Y., van Beersum,S.E., Horn,N., Willer,J.R., Mans,D.A.,
            Dougherty,G., Lamers,I.J., Coene,K.L., Arts,H.H., Betts,M.J.,
            Beyer,T., Bolat,E., Gloeckner,C.J., Haidari,K., Hetterschijt,L.,
            Iaconis,D., Jenkins,D., Klose,F., Knapp,B., Latour,B.,
            Letteboer,S.J., Marcelis,C.L., Mitic,D., Morleo,M., Oud,M.M.,
            Riemersma,M., Rix,S., Terhal,P.A., Toedt,G., van Dam,T.J., de
            Vrieze,E., Wissinger,Y., Wu,K.M., Apic,G., Beales,P.L.,
            Blacque,O.E., Gibson,T.J., Huynen,M.A., Katsanis,N., Kremer,H.,
            Omran,H., van Wijk,E., Wolfrum,U., Kepes,F., Davis,E.E., Franco,B.,
            Giles,R.H., Ueffing,M., Russell,R.B. and Roepman,R.
  CONSRTM   UK10K Rare Diseases Group
  TITLE     An organelle-specific protein landscape identifies novel diseases
            and molecular mechanisms
  JOURNAL   Nat Commun 7, 11491 (2016)
   PUBMED   27173435
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1425)
  AUTHORS   Elstner,M., Morris,C.M., Heim,K., Lichtner,P., Bender,A., Mehta,D.,
            Schulte,C., Sharma,M., Hudson,G., Goldwurm,S., Giovanetti,A.,
            Zeviani,M., Burn,D.J., McKeith,I.G., Perry,R.H., Jaros,E.,
            Kruger,R., Wichmann,H.E., Schreiber,S., Campbell,H., Wilson,J.F.,
            Wright,A.F., Dunlop,M., Pistis,G., Toniolo,D., Chinnery,P.F.,
            Gasser,T., Klopstock,T., Meitinger,T., Prokisch,H. and
            Turnbull,D.M.
  TITLE     Single-cell expression profiling of dopaminergic neurons combined
            with association analysis identifies pyridoxal kinase as
            Parkinson's disease gene
  JOURNAL   Ann Neurol 66 (6), 792-798 (2009)
   PUBMED   20035503
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   7  (bases 1 to 1425)
  AUTHORS   Fan,S., Wei,Z., Xu,H. and Gong,W.
  TITLE     Crystal structure of human synbindin reveals two conformations of
            longin domain
  JOURNAL   Biochem Biophys Res Commun 378 (3), 338-343 (2009)
   PUBMED   18466758
  REMARK    GeneRIF: The three-dimensional structure of human synbindin, which
            contains a longin domain and an atypical PDZ domain is presented.
REFERENCE   8  (bases 1 to 1425)
  AUTHORS   Kim,Y.G., Raunser,S., Munger,C., Wagner,J., Song,Y.L., Cygler,M.,
            Walz,T., Oh,B.H. and Sacher,M.
  TITLE     The architecture of the multisubunit TRAPP I complex suggests a
            model for vesicle tethering
  JOURNAL   Cell 127 (4), 817-830 (2006)
   PUBMED   17110339
REFERENCE   9  (bases 1 to 1425)
  AUTHORS   Gavin,A.C., Bosche,M., Krause,R., Grandi,P., Marzioch,M., Bauer,A.,
            Schultz,J., Rick,J.M., Michon,A.M., Cruciat,C.M., Remor,M.,
            Hofert,C., Schelder,M., Brajenovic,M., Ruffner,H., Merino,A.,
            Klein,K., Hudak,M., Dickson,D., Rudi,T., Gnau,V., Bauch,A.,
            Bastuck,S., Huhse,B., Leutwein,C., Heurtier,M.A., Copley,R.R.,
            Edelmann,A., Querfurth,E., Rybin,V., Drewes,G., Raida,M.,
            Bouwmeester,T., Bork,P., Seraphin,B., Kuster,B., Neubauer,G. and
            Superti-Furga,G.
  TITLE     Functional organization of the yeast proteome by systematic
            analysis of protein complexes
  JOURNAL   Nature 415 (6868), 141-147 (2002)
   PUBMED   11805826
REFERENCE   10 (bases 1 to 1425)
  AUTHORS   Ethell,I.M., Hagihara,K., Miura,Y., Irie,F. and Yamaguchi,Y.
  TITLE     Synbindin, A novel syndecan-2-binding protein in neuronal dendritic
            spines
  JOURNAL   J Cell Biol 151 (1), 53-68 (2000)
   PUBMED   11018053
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AF105025.1 and AP003392.2.
            
            On May 17, 2019 this sequence version replaced NM_016146.5.
            
            Transcript Variant: This variant (1) encodes the longest 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 :: AK290520.1, SRR1803616.451998.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000533632.6/ ENSP00000436005.1
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-395               AF105025.1         236-630
            396-396             AP003392.2         111230-111230
            397-965             AF105025.1         632-1200
            966-1425            AP003392.2         114740-115199
FEATURES             Location/Qualifiers
     source          1..1425
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="11"
                     /map="11q23.3"
     gene            1..1425
                     /gene="TRAPPC4"
                     /gene_synonym="CGI-104; HSPC172; NEDESBA; PTD009; SBDN;
                     SYNBINDIN; TRS23"
                     /note="trafficking protein particle complex subunit 4"
                     /db_xref="GeneID:51399"
                     /db_xref="HGNC:HGNC:19943"
                     /db_xref="MIM:610971"
     exon            1..205
                     /gene="TRAPPC4"
                     /gene_synonym="CGI-104; HSPC172; NEDESBA; PTD009; SBDN;
                     SYNBINDIN; TRS23"
                     /inference="alignment:Splign:2.1.0"
     CDS             31..690
                     /gene="TRAPPC4"
                     /gene_synonym="CGI-104; HSPC172; NEDESBA; PTD009; SBDN;
                     SYNBINDIN; TRS23"
                     /note="isoform 1 is encoded by transcript variant 1; TRS23
                     homolog; hematopoietic stem/progenitor cell protein 172;
                     trafficking protein particle complex 4"
                     /codon_start=1
                     /product="trafficking protein particle complex subunit 4
                     isoform 1"
                     /protein_id="NP_057230.1"
                     /db_xref="CCDS:CCDS8407.1"
                     /db_xref="GeneID:51399"
                     /db_xref="HGNC:HGNC:19943"
                     /db_xref="MIM:610971"
                     /translation="MAIFSVYVVNKAGGLIYQLDSYAPRAEAEKTFSYPLDLLLKLHD
                     ERVLVAFGQRDGIRVGHAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPR
                     LTSNEKLMLASMFHSLFAIGSQLSPEQGSSGIEMLETDTFKLHCYQTLTGIKFVVLAD
                     PRQAGIDSLLRKIYEIYSDFALKNPFYSLEMPIRCELFDQNLKLALEVAEKAGTFGPG
                     S"
     exon            206..380
                     /gene="TRAPPC4"
                     /gene_synonym="CGI-104; HSPC172; NEDESBA; PTD009; SBDN;
                     SYNBINDIN; TRS23"
                     /inference="alignment:Splign:2.1.0"
     exon            381..484
                     /gene="TRAPPC4"
                     /gene_synonym="CGI-104; HSPC172; NEDESBA; PTD009; SBDN;
                     SYNBINDIN; TRS23"
                     /inference="alignment:Splign:2.1.0"
     exon            485..611
                     /gene="TRAPPC4"
                     /gene_synonym="CGI-104; HSPC172; NEDESBA; PTD009; SBDN;
                     SYNBINDIN; TRS23"
                     /inference="alignment:Splign:2.1.0"
     exon            612..1425
                     /gene="TRAPPC4"
                     /gene_synonym="CGI-104; HSPC172; NEDESBA; PTD009; SBDN;
                     SYNBINDIN; TRS23"
                     /inference="alignment:Splign:2.1.0"
     regulatory      934..939
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRAPPC4"
                     /gene_synonym="CGI-104; HSPC172; NEDESBA; PTD009; SBDN;
                     SYNBINDIN; TRS23"
                     /note="hexamer: AATAAA"
     polyA_site      965
                     /gene="TRAPPC4"
                     /gene_synonym="CGI-104; HSPC172; NEDESBA; PTD009; SBDN;
                     SYNBINDIN; TRS23"
                     /note="major polyA site"
     regulatory      1086..1091
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TRAPPC4"
                     /gene_synonym="CGI-104; HSPC172; NEDESBA; PTD009; SBDN;
                     SYNBINDIN; TRS23"
                     /note="hexamer: AATGAA"
     polyA_site      1111
                     /gene="TRAPPC4"
                     /gene_synonym="CGI-104; HSPC172; NEDESBA; PTD009; SBDN;
                     SYNBINDIN; TRS23"
ORIGIN      
        1 gaataccagt ttccgagcgg caaggcagcg atggcgattt ttagtgtgta tgtggtgaac
       61 aaagctggcg gcttgattta ccagttggac agctacgcgc cacgggctga ggctgagaaa
      121 actttcagtt atccgctgga tctgctgctc aagctacacg atgagcgtgt gttggttgct
      181 ttcggccagc gggacggcat ccgagtgggt catgcagtgc tggccatcaa tggcatggac
      241 gtgaatggca ggtacacggc cgacgggaaa gaggtgctgg agtatctggg taaccctgct
      301 aattacccgg tgtccattcg atttggccgg ccccgcctca cttctaatga gaagcttatg
      361 ctggcctcca tgttccactc gctctttgcc atcggctccc agctgtctcc tgaacaggga
      421 agctcaggca ttgagatgct ggagacagac acattcaaat tgcactgcta ccagacactg
      481 acagggatca agtttgtggt tctagcagat cctaggcaag ctggaataga ttctcttctc
      541 cgaaagattt atgagattta ctcagacttt gccctcaaga atccattcta ttccttagaa
      601 atgcctatca ggtgtgagct ctttgaccag aacctgaagc tagctctgga ggtggcagag
      661 aaggctggaa cttttggacc tgggtcatag gctgaacctg ttatggaccc ccaaattctg
      721 agagttcctg caacaagaat actgctgttg acactccagt ggaaatccca gcagccttgt
      781 tagtgcactt gaaagtggga gaatgctgac cctgatgact tgtactgatt cctgagcctt
      841 aacactgtgc tctttccttc tgtatatacc atggtcttac tttccaactc tgtacagatt
      901 tatttatgga ggagctaggt ccataaatgt tgtaataaat attcctttga tcttggtgtt
      961 tgcaatctgt cttaatcgat ggttttgggg gaaagataca ggaagtgagt caaaaatggt
     1021 tagggaattc tgggaagatg attatgtgct agtaaaaaac ataacaaata tgtgttcatt
     1081 aaataaatga acataagatt ttgaagcatg agcattggat ctagtcccag aattgctgct
     1141 gatttcctgg ggtcctgggg tggtggcagc agtggtggtg gctgttatga tgatgatgat
     1201 gatggaacat atttcaagca cttacagcca ggcattcctg ctttatctca cttgatcttc
     1261 accctaactc cagggggtac attctgttac agataagaga tttagcagac tttctgcctc
     1321 aaagtttcca agctagttac tgacagtctg ggtttgaacc aggctttctg gctacacact
     1381 cagtaaacca ctgttacact tcttccctcc atcaagttat ttaat
//
