LOCUS       NM_001282151            1295 bp    mRNA    linear   PRI 22-SEP-2024
DEFINITION  Homo sapiens VPS29 retromer complex component (VPS29), transcript
            variant 4, mRNA.
ACCESSION   NM_001282151
VERSION     NM_001282151.2
KEYWORDS    RefSeq.
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 1295)
  AUTHORS   Yao,Y.Q. and Lv,J.L.
  TITLE     Potential functions and causal associations of VPS29 in
            hepatocellular carcinoma: a bioinformatic and Mendelian
            randomization study
  JOURNAL   Eur Rev Med Pharmacol Sci 27 (20), 9586-9600 (2023)
   PUBMED   37916325
  REMARK    GeneRIF: Potential functions and causal associations of VPS29 in
            hepatocellular carcinoma: a bioinformatic and Mendelian
            randomization study.
REFERENCE   2  (bases 1 to 1295)
  AUTHORS   Healy,M.D., McNally,K.E., Butkovic,R., Chilton,M., Kato,K.,
            Sacharz,J., McConville,C., Moody,E.R.R., Shaw,S.,
            Planelles-Herrero,V.J., Yadav,S.K.N., Ross,J., Borucu,U.,
            Palmer,C.S., Chen,K.E., Croll,T.I., Hall,R.J., Caruana,N.J.,
            Ghai,R., Nguyen,T.H.D., Heesom,K.J., Saitoh,S., Berger,I.,
            Schaffitzel,C., Williams,T.A., Stroud,D.A., Derivery,E.,
            Collins,B.M. and Cullen,P.J.
  TITLE     Structure of the endosomal Commander complex linked to
            Ritscher-Schinzel syndrome
  JOURNAL   Cell 186 (10), 2219-2237 (2023)
   PUBMED   37172566
REFERENCE   3  (bases 1 to 1295)
  AUTHORS   Cho,N.H., Cheveralls,K.C., Brunner,A.D., Kim,K., Michaelis,A.C.,
            Raghavan,P., Kobayashi,H., Savy,L., Li,J.Y., Canaj,H., Kim,J.Y.S.,
            Stewart,E.M., Gnann,C., McCarthy,F., Cabrera,J.P., Brunetti,R.M.,
            Chhun,B.B., Dingle,G., Hein,M.Y., Huang,B., Mehta,S.B.,
            Weissman,J.S., Gomez-Sjoberg,R., Itzhak,D.N., Royer,L.A., Mann,M.
            and Leonetti,M.D.
  TITLE     OpenCell: Endogenous tagging for the cartography of human cellular
            organization
  JOURNAL   Science 375 (6585), eabi6983 (2022)
   PUBMED   35271311
REFERENCE   4  (bases 1 to 1295)
  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   5  (bases 1 to 1295)
  AUTHORS   Crawley-Snowdon,H., Yang,J.C., Zaccai,N.R., Davis,L.J.,
            Wartosch,L., Herman,E.K., Bright,N.A., Swarbrick,J.S.,
            Collins,B.M., Jackson,L.P., Seaman,M.N.J., Luzio,J.P., Dacks,J.B.,
            Neuhaus,D. and Owen,D.J.
  TITLE     Mechanism and evolution of the Zn-fingernail required for
            interaction of VARP with VPS29
  JOURNAL   Nat Commun 11 (1), 5031 (2020)
   PUBMED   33024112
  REMARK    GeneRIF: Mechanism and evolution of the Zn-fingernail required for
            interaction of VARP with VPS29.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1295)
  AUTHORS   Verges,M., Luton,F., Gruber,C., Tiemann,F., Reinders,L.G.,
            Huang,L., Burlingame,A.L., Haft,C.R. and Mostov,K.E.
  TITLE     The mammalian retromer regulates transcytosis of the polymeric
            immunoglobulin receptor
  JOURNAL   Nat Cell Biol 6 (8), 763-769 (2004)
   PUBMED   15247922
REFERENCE   7  (bases 1 to 1295)
  AUTHORS   Haft,C.R., de la Luz Sierra,M., Bafford,R., Lesniak,M.A., Barr,V.A.
            and Taylor,S.I.
  TITLE     Human orthologs of yeast vacuolar protein sorting proteins Vps26,
            29, and 35: assembly into multimeric complexes
  JOURNAL   Mol Biol Cell 11 (12), 4105-4116 (2000)
   PUBMED   11102511
REFERENCE   8  (bases 1 to 1295)
  AUTHORS   Edgar,A.J. and Polak,J.M.
  TITLE     Human homologues of yeast vacuolar protein sorting 29 and 35
  JOURNAL   Biochem Biophys Res Commun 277 (3), 622-630 (2000)
   PUBMED   11062004
REFERENCE   9  (bases 1 to 1295)
  AUTHORS   Simpson,J.C., Wellenreuther,R., Poustka,A., Pepperkok,R. and
            Wiemann,S.
  TITLE     Systematic subcellular localization of novel proteins identified by
            large-scale cDNA sequencing
  JOURNAL   EMBO Rep 1 (3), 287-292 (2000)
   PUBMED   11256614
REFERENCE   10 (bases 1 to 1295)
  AUTHORS   Seaman,M.N., McCaffery,J.M. and Emr,S.D.
  TITLE     A membrane coat complex essential for endosome-to-Golgi retrograde
            transport in yeast
  JOURNAL   J Cell Biol 142 (3), 665-681 (1998)
   PUBMED   9700157
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AB578892.1, CB158821.1,
            AL832866.1 and AC002350.1.
            
            On Aug 14, 2020 this sequence version replaced NM_001282151.1.
            
            Summary: This gene belongs to a group of vacuolar protein sorting
            (VPS) genes that, when functionally impaired, disrupt the efficient
            delivery of vacuolar hydrolases. The protein encoded by this gene
            is a component of a large multimeric complex, termed the retromer
            complex, which is involved in retrograde transport of proteins from
            endosomes to the trans-Golgi network. This VPS protein may be
            involved in the formation of the inner shell of the retromer coat
            for retrograde vesicles leaving the prevacuolar compartment.
            Alternative splice variants encoding different isoforms and
            representing non-protein coding transcripts have been found for
            this gene. [provided by RefSeq, Aug 2013].
            
            Transcript Variant: This variant (4) lacks several alternate exons
            compared to variant 3. The resulting isoform (4) has shorter and
            distinct N- and C-termini compared to isoform 3.
            
            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 :: CB158821.1, SRR14243140.2326322.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1966682,
                                           SAMEA1968540 [ECO:0006172]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-37                AB578892.1         30-66
            38-425              CB158821.1         1-388
            426-855             AL832866.1         2684-3113
            856-1295            AC002350.1         124283-124722
FEATURES             Location/Qualifiers
     source          1..1295
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12q24.11"
     gene            1..1295
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="VPS29 retromer complex component"
                     /db_xref="GeneID:51699"
                     /db_xref="HGNC:HGNC:14340"
                     /db_xref="MIM:606932"
     exon            1..63
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /inference="alignment:Splign:2.1.0"
     CDS             61..336
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /EC_number="3.1.3.3"
                     /note="isoform 4 is encoded by transcript variant 4;
                     vacuolar sorting protein VPS29/PEP11; retromer protein; x
                     007 protein; vacuolar protein sorting-associated protein
                     29; hVPS29; PEP11 homolog; vesicle protein sorting 29;
                     vacuolar protein sorting 29 homolog; epididymis secretory
                     sperm binding protein"
                     /codon_start=1
                     /product="vacuolar protein sorting-associated protein 29
                     isoform 4"
                     /protein_id="NP_001269080.1"
                     /db_xref="GeneID:51699"
                     /db_xref="HGNC:HGNC:14340"
                     /db_xref="MIM:606932"
                     /translation="MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKE
                     SYDYLKTLAGDVHIVRGDFDEKHYSIICVDGYPGFYSGHLCVSANWR"
     exon            64..255
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /inference="alignment:Splign:2.1.0"
     exon            256..1295
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /inference="alignment:Splign:2.1.0"
     regulatory      432..437
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="hexamer: ATTAAA"
     polyA_site      455
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="major polyA site"
     regulatory      732..737
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="hexamer: AATAAA"
     polyA_site      754
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="major polyA site"
     regulatory      828..833
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="hexamer: ATTAAA"
     polyA_site      853
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
     polyA_site      880
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
     regulatory      909..914
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="hexamer: AATATA"
     polyA_site      935
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
     regulatory      973..978
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="hexamer: AATAAA"
     polyA_site      994
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
ORIGIN      
        1 gaggagcctg aggaagaggg cggcgacggt ggtggtgact gagcggagcc cggtgacagg
       61 atgttggtgt tggtattagg agatctgcac atcccacacc ggtgcaacag tttgccagct
      121 aaattcaaaa aactcctggt gccaggaaaa attcagcaca ttctctgcac aggaaacctt
      181 tgcaccaaag agagttatga ctatctcaag actctggctg gtgatgttca tattgtgaga
      241 ggagacttcg atgagaaaca ttattccatc atttgtgttg atggatatcc aggcttctac
      301 agtggtcacc tatgtgtatc agctaattgg agatgatgtg aaagtagaac gaatcgaata
      361 caaaaaacct taaagccagg cctgtcttga tgatttttgg ttttttttca ttgtcctgtt
      421 gaaatcaagt aattaaacat ttaagagcca caaaattgta tcacttttat aatattttgc
      481 agtaaaatat aataccatct tctctgttaa tacataattg ctccaagctt cctgtaaact
      541 ataagaatat atttagttta cagtatatgg attctatgaa aaaatgtcca caacacagta
      601 attggtcact tgttaagaaa aatttatcct tgtaagtatc ttcaaagttg atatttggaa
      661 ctttattcca aaagtagtgc atgtggagaa agaatctaga ctttcttgta tacatttttc
      721 tcttctccag taataaacaa ttacctttca tttatacttt gataacctgt atttaattta
      781 aaaaaaaaca taaaaatgag gaaccaagtg aaactacgga tataaatatt aaagtggacg
      841 agatgacctt tcagagctct tctcttacat tgtgtcataa tgttggactc agattttatt
      901 tgctaaataa tataccatgc cgacattaac agtgattctt caaactgttg ctatttccat
      961 ttttcaaggt ttaataaaag ttttaaaaat acaagtttag gggccgggca cagtggctca
     1021 caccctaatc ccaacacttt gggaggctga ggcaggtgga tcacctgagg tcaggagttc
     1081 aagaccagcc tggccaacat ggtgaaaccc tgtctgtact aaaaatacaa aattagccag
     1141 catggtgcta catgcctgta ttcccagcta ctcgggaggc tgaggcagta gaatcacttg
     1201 aatcctggag ttggaggttg cagtgagccg agatcacacc attgcactcc agcctggtca
     1261 acaagagcat aactccgtct caaaaaaaaa caaaa
//
