LOCUS       NM_016226               1531 bp    mRNA    linear   PRI 20-SEP-2024
DEFINITION  Homo sapiens VPS29 retromer complex component (VPS29), transcript
            variant 1, mRNA.
ACCESSION   NM_016226
VERSION     NM_016226.5
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 1531)
  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 1531)
  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 1531)
  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 1531)
  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 1531)
  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 1531)
  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 1531)
  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 1531)
  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 1531)
  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 1531)
  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 BC095446.1, AL832866.1 and
            AC002350.1.
            
            On May 17, 2019 this sequence version replaced NM_016226.4.
            
            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 (1) lacks two alternate exons
            compared to variant 3. The resulting isoform (1) has a shorter and
            distinct N-terminus 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 :: SRR1660803.408424.1,
                                           SRR7410570.509334.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2142680, SAMEA2162895
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000549578.6/ ENSP00000447058.1
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-989               BC095446.1         1-989
            990-1091            AL832866.1         3012-3113
            1092-1531           AC002350.1         124283-124722
FEATURES             Location/Qualifiers
     source          1..1531
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12q24.11"
     gene            1..1531
                     /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..609
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /EC_number="3.1.3.3"
                     /note="isoform 1 is encoded by transcript variant 1;
                     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 1"
                     /protein_id="NP_057310.1"
                     /db_xref="CCDS:CCDS41832.1"
                     /db_xref="GeneID:51699"
                     /db_xref="HGNC:HGNC:14340"
                     /db_xref="MIM:606932"
                     /translation="MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKE
                     SYDYLKTLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALL
                     QRQFDVDILISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTV
                     VTYVYQLIGDDVKVERIEYKKP"
     exon            64..255
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /inference="alignment:Splign:2.1.0"
     exon            256..491
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /inference="alignment:Splign:2.1.0"
     exon            492..1531
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /inference="alignment:Splign:2.1.0"
     regulatory      668..673
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="hexamer: ATTAAA"
     polyA_site      691
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="major polyA site"
     regulatory      968..973
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="hexamer: AATAAA"
     polyA_site      990
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="major polyA site"
     regulatory      1064..1069
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="hexamer: ATTAAA"
     polyA_site      1089
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
     polyA_site      1116
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
     regulatory      1145..1150
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="hexamer: AATATA"
     polyA_site      1171
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
     regulatory      1209..1214
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS29"
                     /gene_synonym="DC15; DC7; PEP11"
                     /note="hexamer: AATAAA"
     polyA_site      1230
                     /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 atgagaatct gaattatcca gaacagaaag ttgtgactgt tggacagttc
      301 aaaattggtc tgatccatgg acatcaagtt attccatggg gagatatggc cagcttagcc
      361 ctgttgcaga ggcaatttga tgtggacatt cttatctcgg gacacacaca caaatttgaa
      421 gcatttgagc atgaaaataa attctacatt aatccaggtt ctgccactgg ggcatataat
      481 gccttggaaa caaacattat tccatcattt gtgttgatgg atatccaggc ttctacagtg
      541 gtcacctatg tgtatcagct aattggagat gatgtgaaag tagaacgaat cgaatacaaa
      601 aaaccttaaa gccaggcctg tcttgatgat ttttggtttt ttttcattgt cctgttgaaa
      661 tcaagtaatt aaacatttaa gagccacaaa attgtatcac ttttataata ttttgcagta
      721 aaatataata ccatcttctc tgttaataca taattgctcc aagcttcctg taaactataa
      781 gaatatattt agtttacagt atatggattc tatgaaaaaa tgtccacaac acagtaattg
      841 gtcacttgtt aagaaaaatt tatccttgta agtatcttca aagttgatat ttggaacttt
      901 attccaaaag tagtgcatgt ggagaaagaa tctagacttt cttgtataca tttttctctt
      961 ctccagtaat aaacaattac ctttcattta tactttgata acctgtattt aatttaaaaa
     1021 aaaacataaa aatgaggaac caagtgaaac tacggatata aatattaaag tggacgagat
     1081 gacctttcag agctcttctc ttacattgtg tcataatgtt ggactcagat tttatttgct
     1141 aaataatata ccatgccgac attaacagtg attcttcaaa ctgttgctat ttccattttt
     1201 caaggtttaa taaaagtttt aaaaatacaa gtttaggggc cgggcacagt ggctcacacc
     1261 ctaatcccaa cactttggga ggctgaggca ggtggatcac ctgaggtcag gagttcaaga
     1321 ccagcctggc caacatggtg aaaccctgtc tgtactaaaa atacaaaatt agccagcatg
     1381 gtgctacatg cctgtattcc cagctactcg ggaggctgag gcagtagaat cacttgaatc
     1441 ctggagttgg aggttgcagt gagccgagat cacaccattg cactccagcc tggtcaacaa
     1501 gagcataact ccgtctcaaa aaaaaacaaa a
//
