LOCUS       NM_022553               2936 bp    mRNA    linear   PRI 20-SEP-2024
DEFINITION  Homo sapiens VPS52 subunit of GARP complex (VPS52), transcript
            variant 1, mRNA.
ACCESSION   NM_022553 NM_080564 XM_006715163 XM_006725495 XM_006725709
            XM_006725918 XM_006726011 XM_006726105
VERSION     NM_022553.6
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 2936)
  AUTHORS   Kim,D.K., Weller,B., Lin,C.W., Sheykhkarimli,D., Knapp,J.J.,
            Dugied,G., Zanzoni,A., Pons,C., Tofaute,M.J., Maseko,S.B.,
            Spirohn,K., Laval,F., Lambourne,L., Kishore,N., Rayhan,A.,
            Sauer,M., Young,V., Halder,H., la Rosa,N.M., Pogoutse,O.,
            Strobel,A., Schwehn,P., Li,R., Rothballer,S.T., Altmann,M.,
            Cassonnet,P., Cote,A.G., Vergara,L.E., Hazelwood,I., Liu,B.B.,
            Nguyen,M., Pandiarajan,R., Dohai,B., Coloma,P.A.R., Poirson,J.,
            Giuliana,P., Willems,L., Taipale,M., Jacob,Y., Hao,T., Hill,D.E.,
            Brun,C., Twizere,J.C., Krappmann,D., Heinig,M., Falter,C., Aloy,P.,
            Demeret,C., Vidal,M., Calderwood,M.A., Roth,F.P. and
            Falter-Braun,P.
  TITLE     A proteome-scale map of the SARS-CoV-2-human contactome
  JOURNAL   Nat Biotechnol 41 (1), 140-149 (2023)
   PUBMED   36217029
REFERENCE   2  (bases 1 to 2936)
  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   3  (bases 1 to 2936)
  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   4  (bases 1 to 2936)
  AUTHORS   Nguyen,P.M., Gandasi,N.R., Xie,B., Sugahara,S., Xu,Y. and
            Idevall-Hagren,O.
  TITLE     The PI(4)P phosphatase Sac2 controls insulin granule docking and
            release
  JOURNAL   J Cell Biol 218 (11), 3714-3729 (2019)
   PUBMED   31533953
  REMARK    GeneRIF: The Sac2 operates upstream of granule docking, since loss
            of Sac2 prevented granule tethering to the plasma membrane and
            resulted in both reduced granule density and number of exocytic
            events.
REFERENCE   5  (bases 1 to 2936)
  AUTHORS   Fragoza,R., Das,J., Wierbowski,S.D., Liang,J., Tran,T.N., Liang,S.,
            Beltran,J.F., Rivera-Erick,C.A., Ye,K., Wang,T.Y., Yao,L., Mort,M.,
            Stenson,P.D., Cooper,D.N., Wei,X., Keinan,A., Schimenti,J.C.,
            Clark,A.G. and Yu,H.
  TITLE     Extensive disruption of protein interactions by genetic variants
            across the allele frequency spectrum in human populations
  JOURNAL   Nat Commun 10 (1), 4141 (2019)
   PUBMED   31515488
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2936)
  AUTHORS   Liewen,H., Meinhold-Heerlein,I., Oliveira,V., Schwarzenbacher,R.,
            Luo,G., Wadle,A., Jung,M., Pfreundschuh,M. and Stenner-Liewen,F.
  TITLE     Characterization of the human GARP (Golgi associated retrograde
            protein) complex
  JOURNAL   Exp Cell Res 306 (1), 24-34 (2005)
   PUBMED   15878329
  REMARK    GeneRIF: Golgi associated retrograde protein complex, consisting of
            the Vps52, Vps53, and Vps54 proteins, shows significant
            conservation between various species but diversification and
            specialization result in important differences in human cells.
REFERENCE   7  (bases 1 to 2936)
  AUTHORS   Medeiros,R., Morais,A., Vasconcelos,A., Costa,S., Pinto,D.,
            Oliveira,J., Carvalho,R. and Lopes,C.
  TITLE     Linkage between polymorphisms in the prostate specific antigen ARE1
            gene region, prostate cancer risk, and circulating tumor cells
  JOURNAL   Prostate 53 (1), 88-94 (2002)
   PUBMED   12210484
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   8  (bases 1 to 2936)
  AUTHORS   Matsuzaka,Y., Makino,S., Okamoto,K., Oka,A., Tsujimura,A.,
            Matsumiya,K., Takahara,S., Okuyama,A., Sada,M., Gotoh,R.,
            Nakatani,T., Ota,M., Katsuyama,Y., Tamiya,G. and Inoko,H.
  TITLE     Susceptibility locus for non-obstructive azoospermia is localized
            within the HLA-DR/DQ subregion: primary role of DQB1*0604
  JOURNAL   Tissue Antigens 60 (1), 53-63 (2002)
   PUBMED   12366783
  REMARK    GeneRIF: Observational study of gene-disease association and
            gene-gene interaction. (HuGE Navigator)
REFERENCE   9  (bases 1 to 2936)
  AUTHORS   Stephens,R., Horton,R., Humphray,S., Rowen,L., Trowsdale,J. and
            Beck,S.
  TITLE     Gene organisation, sequence variation and isochore structure at the
            centromeric boundary of the human MHC
  JOURNAL   J Mol Biol 291 (4), 789-799 (1999)
   PUBMED   10452889
REFERENCE   10 (bases 1 to 2936)
  AUTHORS   Walter,L. and Gunther,E.
  TITLE     Identification of a novel highly conserved gene in the centromeric
            part of the major histocompatibility complex
  JOURNAL   Genomics 52 (3), 298-304 (1998)
   PUBMED   9790748
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DC400338.1, BC040114.1 and
            AK001725.1.
            
            On Nov 23, 2018 this sequence version replaced NM_022553.5.
            
            Summary: This gene encodes a protein that is similar to the yeast
            suppressor of actin mutations 2 gene. The yeast protein forms a
            subunit of the tetrameric Golgi-associated retrograde protein
            complex that is involved in vesicle trafficking from from both
            early and late endosomes, back to the trans-Golgi network. This
            gene is located on chromosome 6 in a head-to-head orientation with
            the gene encoding ribosomal protein S18. Alternative splicing
            results in multiple transcript variants. [provided by RefSeq, Jan
            2014].
            
            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 :: BC040114.1, SRR1660807.72670.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000445902.3/ ENSP00000409952.2
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-30                DC400338.1         49-78
            31-1020             BC040114.1         1-990
            1021-1134           AK001725.1         788-901
            1135-2936           BC040114.1         1105-2906
FEATURES             Location/Qualifiers
     source          1..2936
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="6"
                     /map="6p21.32"
     gene            1..2936
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /note="VPS52 subunit of GARP complex"
                     /db_xref="GeneID:6293"
                     /db_xref="HGNC:HGNC:10518"
                     /db_xref="MIM:603443"
     exon            1..291
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     CDS             202..2373
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /note="isoform 1 is encoded by transcript variant 1;
                     vacuolar protein sorting-associated protein 52 homolog;
                     SAC2 suppressor of actin mutations 2-like protein;
                     vacuolar protein sorting 52 homolog; VPS52, GARP complex
                     subunit"
                     /codon_start=1
                     /product="vacuolar protein sorting-associated protein 52
                     homolog isoform 1"
                     /protein_id="NP_072047.4"
                     /db_xref="CCDS:CCDS4770.2"
                     /db_xref="GeneID:6293"
                     /db_xref="HGNC:HGNC:10518"
                     /db_xref="MIM:603443"
                     /translation="MAAAATMAAAARELVLRAGTSDMEEEEGPLAGGPGLQEPLQLGE
                     LDITSDEFILDEVDVHIQANLEDELVKEALKTGVDLRHYSKQVELELQQIEQKSIRDY
                     IQESENIASLHNQITACDAVLERMEQMLGAFQSDLSSISSEIRTLQEQSGAMNIRLRN
                     RQAVRGKLGELVDGLVVPSALVTAILEAPVTEPRFLEQLQELDAKAAAVREQEARGTA
                     ACADVRGVLDRLRVKAVTKIREFILQKIYSFRKPMTNYQIPQTALLKYRFFYQFLLGN
                     ERATAKEIRDEYVETLSKIYLSYYRSYLGRLMKVQYEEVAEKDDLMGVEDTAKKGFFS
                     KPSLRSRNTIFTLGTRGSVISPTELEAPILVPHTAQRGEQRYPFEALFRSQHYALLDN
                     SCREYLFICEFFVVSGPAAHDLFHAVMGRTLSMTLKHLDSYLADCYDAIAVFLCIHIV
                     LRFRNIAAKRDVPALDRYWEQVLALLWPRFELILEMNVQSVRSTDPQRLGGLDTRPHY
                     ITRRYAEFSSALVSINQTIPNERTMQLLGQLQVEVENFVLRVAAEFSSRKEQLVFLIN
                     NYDMMLGVLMERAADDSKEVESFQQLLNARTQEFIEELLSPPFGGLVAFVKEAEALIE
                     RGQAERLRGEEARVTQLIRGFGSSWKSSVESLSQDVMRSFTNFRNGTSIIQGALTQLI
                     QLYHRFHRVLSQPQLRALPARAELINIHHLMVELKKHKPNF"
     exon            292..376
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            377..429
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            430..505
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            506..573
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            574..749
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            750..900
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            901..1001
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1002..1134
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1135..1192
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1193..1326
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1327..1482
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1483..1601
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1602..1725
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1726..1821
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1822..1929
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1930..1995
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            1996..2107
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            2108..2226
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     exon            2227..2936
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2914..2919
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /note="hexamer: AATAAA"
     polyA_site      2936
                     /gene="VPS52"
                     /gene_synonym="ARE1; dJ1033B10.5; SAC2; SACM2L"
                     /note="major polyA site"
ORIGIN      
        1 agtttgtgtt tcagacttcc atatttccat ttgcagttgg gtgaagtggt tagagctgaa
       61 aggggacagc tggagtcaaa caacttaact caaatatctg ggaacgattt cgcgctgagg
      121 aagacccttt gggacttgta gctccactcc ggggaacgga ctcgccggga ctgacagttg
      181 ccggaagtga ggctgcgggg aatggccgcc gctgcgacca tggcggctgc ggcccgggaa
      241 ctggtgttgc gggctgggac ctcagatatg gaggaggaag agggcccgct ggcgggtggt
      301 cctgggctcc aggaaccact gcaacttggg gagttggata tcacttctga tgaattcatc
      361 ctggatgaag tggatgttca cattcaggca aatctggagg atgagttagt aaaggaagct
      421 cttaaaacgg gtgtagatct ccgtcactat tcaaagcaag ttgagctgga gctacagcag
      481 attgaacaga aatccattcg ggattatatt caagagagtg agaatatagc atctctacac
      541 aaccagatca cagcctgtga tgctgtcctg gagcgaatgg agcagatgtt gggagctttt
      601 cagagtgacc tcagctccat cagctctgag atccggacac tgcaggaaca gtcaggagcc
      661 atgaacattc gacttcgaaa tcgccaggca gttcggggga aacttgggga gcttgttgat
      721 ggtctggtgg tgccttctgc tctggtcacg gcaattctgg aggctccagt gacagagccc
      781 aggttcttgg agcagctaca ggagctggat gccaaggcag ccgcagtcag agagcaggaa
      841 gctagaggca cagcagcctg cgcagatgtc agaggcgtgc tcgatcggct ccgggtcaag
      901 gcagtgacga agatccgaga gtttatcctc cagaagattt attccttcag gaaacccatg
      961 accaactatc agatccccca gacggccctg ctgaagtaca ggttcttcta tcagtttctg
     1021 ctgggcaatg aacgagcaac agcaaaggag atcagggatg aatatgtgga gacgctgagc
     1081 aagatttacc tgtcttacta ccgctcttac ctggggcggc tcatgaaggt gcagtatgag
     1141 gaagtcgctg agaaagatga tctaatgggt gtggaagata cagcaaagaa aggattcttc
     1201 tcaaagccat cgctccgcag caggaacacc attttcaccc taggaacccg cggctctgtc
     1261 atctccccca ctgaacttga ggcccccatc ctggtgcctc acacagcgca gcgcggagag
     1321 cagaggtatc catttgaggc cctcttccgc agccagcact acgccctcct agacaattcc
     1381 tgccgcgaat accttttcat ctgtgaattt tttgttgtgt ctggcccagc tgcacacgac
     1441 ctgttccatg ctgtcatggg ccgtacactc agcatgaccc tgaaacacct ggattcttat
     1501 ctagctgact gctacgatgc cattgctgtt tttctctgta tccacattgt tctccggttc
     1561 cgtaacattg cagcaaagag ggatgttcct gccctggaca ggtactggga acaggtgctt
     1621 gccttgctat ggccacggtt tgaactgatc ctggagatga atgttcagag cgtccgaagc
     1681 actgaccccc agcgcctagg ggggttggat actcggcccc actatatcac acgccgctat
     1741 gcagagttct cctccgctct tgtcagtatc aaccagacaa ttcctaatga acggaccatg
     1801 caattgctgg gacagctgca ggtggaggtg gagaattttg tcctccgagt ggcagctgag
     1861 ttctcctcaa ggaaggagca gcttgtgttt ctgatcaaca actatgacat gatgctgggt
     1921 gtgctgatgg agcgggctgc agatgacagc aaagaggttg agagcttcca gcagctgctc
     1981 aatgctcgga cacaggaatt cattgaagag ttgctgtctc ccccttttgg gggtttagtg
     2041 gcatttgtga aggaggctga ggctttgatt gagcgtggac aggctgagcg acttcgaggg
     2101 gaagaagccc gggtaactca gctgatccgt ggctttggta gttcctggaa atcatcagtg
     2161 gaatctctga gtcaggatgt aatgcggagt ttcaccaact tcagaaatgg caccagtatc
     2221 attcagggag cgctgaccca gctgatccag ctctatcatc gcttccaccg ggtgctgtcc
     2281 cagccgcagc tccgagccct ccctgcccgg gctgagctca tcaacattca ccaccttatg
     2341 gtggagctca agaagcataa gcccaacttc tgatgtgcca gaaaccgccc tgagatctgc
     2401 cggtcatctc catggacttc tgcaccccat tccataccct tcttcacctg gggtacccct
     2461 tccagttttc cccttgcttc ccaggccctt gacatggctt acctgccttc actcccagca
     2521 ccttgcccaa caggataagc tggatcccct tggccttctg aatatcccag tgtcttcagg
     2581 tttcccaaga ccacttccct gtgggcttcc aaaatggcct ttatcatttc tccagtctgt
     2641 caccctcctt tcctgctccc atacacccaa ggcttgtttc ttcccctgta aaaaccactg
     2701 cctcaatctc tggttcactc aactagtcac catgtcctga ggcatgaagc ctcctcagct
     2761 cttggaattg ctggcaaggg gtgactgcct ctgagtcatt gtgtttttca aagtgatttc
     2821 ttttctgtag ctttttgacc taagatctca gcaatttgaa cactaacctc tcccctcctg
     2881 gctcaagaat tactccgaag tcagtctgca gaaaataaat atttagtatg acatga
//
