LOCUS       NM_018289               3024 bp    mRNA    linear   PRI 21-SEP-2024
DEFINITION  Homo sapiens VPS53 subunit of GARP complex (VPS53), transcript
            variant 2, mRNA.
ACCESSION   NM_018289
VERSION     NM_018289.4
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 3024)
  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   2  (bases 1 to 3024)
  AUTHORS   Ilyas,M., Efthymiou,S., Salpietro,V., Noureen,N., Zafar,F.,
            Rauf,S., Mir,A. and Houlden,H.
  TITLE     Novel variants underlying autosomal recessive intellectual
            disability in Pakistani consanguineous families
  JOURNAL   BMC Med Genet 21 (1), 59 (2020)
   PUBMED   32209057
  REMARK    GeneRIF: Novel and deleterious variants in VPS53, GLB1, and MLC1,
            genes previously associated with variable neurodevelopmental
            anomalies, were found to segregate with intellectual disabilities
            in the three families.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3024)
  AUTHORS   Hausman-Kedem,M., Ben-Shachar,S., Menascu,S., Geva,K., Sagie,L. and
            Fattal-Valevski,A.
  TITLE     VPS53 gene is associated with a new phenotype of complicated
            hereditary spastic paraparesis
  JOURNAL   Neurogenetics 20 (4), 187-195 (2019)
   PUBMED   31418091
  REMARK    GeneRIF: VPS53 gene is associated with a new phenotype of
            complicated hereditary spastic paraparesis.
REFERENCE   4  (bases 1 to 3024)
  AUTHORS   Xie,X.H., Chen,Y.R., Jin,S., Ma,Y.S., Tian,X.D. and Yang,Y.M.
  TITLE     HCCS1 inhibits the stemness of human pancreatic cancer stem-like
            cells
  JOURNAL   Eur Rev Med Pharmacol Sci 23 (5), 2125-2131 (2019)
   PUBMED   30915757
  REMARK    GeneRIF: HCCS1 inhibits the stemness of human pancreatic cancer
            stem-like cells.
REFERENCE   5  (bases 1 to 3024)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Paulo,J.A., Cannon,J.R., Ting,L.,
            Baltier,K., Colby,G., Gebreab,F., Gygi,M.P., Parzen,H., Szpyt,J.,
            Tam,S., Zarraga,G., Pontano-Vaites,L., Swarup,S., White,A.E.,
            Schweppe,D.K., Rad,R., Erickson,B.K., Obar,R.A., Guruharsha,K.G.,
            Li,K., Artavanis-Tsakonas,S., Gygi,S.P. and Harper,J.W.
  TITLE     Architecture of the human interactome defines protein communities
            and disease networks
  JOURNAL   Nature 545 (7655), 505-509 (2017)
   PUBMED   28514442
REFERENCE   6  (bases 1 to 3024)
  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 3024)
  AUTHORS   Wan,D., Gong,Y., Qin,W., Zhang,P., Li,J., Wei,L., Zhou,X., Li,H.,
            Qiu,X., Zhong,F., He,L., Yu,J., Yao,G., Jiang,H., Qian,L., Yu,Y.,
            Shu,H., Chen,X., Xu,H., Guo,M., Pan,Z., Chen,Y., Ge,C., Yang,S. and
            Gu,J.
  TITLE     Large-scale cDNA transfection screening for genes related to cancer
            development and progression
  JOURNAL   Proc Natl Acad Sci U S A 101 (44), 15724-15729 (2004)
   PUBMED   15498874
  REMARK    Erratum:[Proc Natl Acad Sci U S A. 2004 Dec 14:101(50):17565]
REFERENCE   8  (bases 1 to 3024)
  AUTHORS   Cardoso,C., Leventer,R.J., Ward,H.L., Toyo-Oka,K., Chung,J.,
            Gross,A., Martin,C.L., Allanson,J., Pilz,D.T., Olney,A.H.,
            Mutchinick,O.M., Hirotsune,S., Wynshaw-Boris,A., Dobyns,W.B. and
            Ledbetter,D.H.
  TITLE     Refinement of a 400-kb critical region allows genotypic
            differentiation between isolated lissencephaly, Miller-Dieker
            syndrome, and other phenotypes secondary to deletions of 17p13.3
  JOURNAL   Am J Hum Genet 72 (4), 918-930 (2003)
   PUBMED   12621583
REFERENCE   9  (bases 1 to 3024)
  AUTHORS   Zhao,X., He,M., Wan,D., Ye,Y., He,Y., Han,L., Guo,M., Huang,Y.,
            Qin,W., Wang,M.W., Chong,W., Chen,J., Zhang,L., Yang,N., Xu,B.,
            Wu,M., Zuo,L. and Gu,J.
  TITLE     The minimum LOH region defined on chromosome 17p13.3 in human
            hepatocellular carcinoma with gene content analysis
  JOURNAL   Cancer Lett 190 (2), 221-232 (2003)
   PUBMED   12565177
REFERENCE   10 (bases 1 to 3024)
  AUTHORS   Canestri,F.
  TITLE     A proposed clinical application of a model of CO2 laser radiation
            induced damage craters
  JOURNAL   J Med Eng Technol 12 (3), 112-117 (1988)
   PUBMED   3172165
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK092532.1, AK290343.1,
            AK001841.1 and AC015853.8.
            
            On May 31, 2019 this sequence version replaced NM_018289.3.
            
            Transcript Variant: This variant (2) has multiple differences in
            the coding region and uses a different segment for its 3' UTR but
            maintains the reading frame, compared to variant 1. The resulting
            protein (isoform 2) has a shorter and distinct C-terminus when it
            is compared to isoform 2.
            
            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 :: AK290343.1, BC006116.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-3                 AK092532.1         18-20
            4-2652              AK290343.1         1-2649
            2653-2677           AK001841.1         1651-1675
            2678-3024           AC015853.8         38560-38906         c
FEATURES             Location/Qualifiers
     source          1..3024
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="17"
                     /map="17p13.3"
     gene            1..3024
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /note="VPS53 subunit of GARP complex"
                     /db_xref="GeneID:55275"
                     /db_xref="HGNC:HGNC:25608"
                     /db_xref="MIM:615850"
     exon            1..217
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     CDS             131..2143
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /note="isoform 2 is encoded by transcript variant 2;
                     vacuolar protein sorting-associated protein 53 homolog;
                     VPS53, GARP complex subunit; hepatocellular carcinoma
                     suppressor 1"
                     /codon_start=1
                     /product="vacuolar protein sorting-associated protein 53
                     homolog isoform 2"
                     /protein_id="NP_060759.2"
                     /db_xref="CCDS:CCDS10995.1"
                     /db_xref="GeneID:55275"
                     /db_xref="HGNC:HGNC:25608"
                     /db_xref="MIM:615850"
                     /translation="MMEEEELEFVEELEAVLQLTPEVQLAIEQVFPSQDPLDRADFNA
                     VEYINTLFPTEQSLANIDEVVNKIRLKIRRLDDNIRTVVRGQTNVGQDGRQVKEITRD
                     IKQLDHAKRHLTTSITTLNHLHMLAGGVDSLEAMTRRRQYGEVANLLQGVMNVLEHFH
                     KYMGIPQIRQLSERVKAAQTELGQQILADFEEAFPSQGTKRPGGPSNVLRDACLVANI
                     LDPRIKQEIIKKFIKQHLSEYLVLFQENQDVAWLDKIDRRYAWIKRQLVDYEEKYGRM
                     FPREWCMAERIAVEFCHVTRAELAKIMRTRAKEIEVKLLLFAIQRTTNFEGFLAKRFS
                     GCTLTDGTLKKLESPPPSTNPFLEDEPTPEMEELATEKGDLDQPKKPKAPDNPFHGIV
                     SKCFEPHLYVYIESQDKNLGELIDRFVADFKAQGPPKPNTDEGGAVLPSCADLFVYYK
                     KCMVQCSQLSTGEPMIALTTIFQKYLREYAWKILSGNLPKTTTSSGGLTISSLLKEKE
                     GSEVAKFTLEELCLICNILSTAEYCLATTQQLEEKLKEKVDVSLIERINLTGEMDTFS
                     TVISSSIQLLVQDLDAACDPALTAMSKMQWQNVEHVGDQSPYVTSVILHIKQNVPIIR
                     DNLASTRKYFTQFCVKFANSFIPKFITHLFKCKPISMVGAEQVRWT"
     exon            218..298
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            299..348
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            349..415
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            416..531
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            532..651
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            652..730
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            731..874
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            875..1017
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            1018..1159
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            1160..1261
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            1262..1356
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            1357..1599
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            1600..1747
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            1748..1830
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            1831..1909
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            1910..2058
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     exon            2059..3024
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2217..2222
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /note="hexamer: AATAAA"
     polyA_site      2262
                     /gene="VPS53"
                     /gene_synonym="HCCS1; hVps53L; PCH2E; pp13624"
                     /note="major polyA site"
ORIGIN      
        1 gacagagcgg ctgacggagc cgggctcacc aggtcgctgc cgcgagggag ttgctgtgct
       61 ggggcctggg tggcggctgg aggcctgagt tgggctcgcg gcgggggtcg gcagggggcc
      121 gggtggcgga atgatggagg aggaggaact ggagttcgtg gaggagctgg aagccgtgct
      181 gcagctcacg cccgaggtgc agctggccat cgagcaggtg tttccaagcc aggaccctct
      241 agatcgagca gatttcaatg ctgttgagta tatcaatacc ctgttcccaa ccgagcaatc
      301 tctggcgaac atagacgaag tcgtgaacaa aattaggctg aaaataagga gactggatga
      361 caatattcga actgttgtaa gaggtcagac gaacgtgggg caggatggac ggcaagtgaa
      421 agaaatcacc cgtgatatta agcaattaga tcacgccaaa cgccacctga ccacctcaat
      481 caccacactg aaccacctgc acatgctggc aggaggtgtc gactccctcg aagccatgac
      541 caggcgaaga caatacggag aagttgctaa tctccttcag ggtgtgatga atgtcctgga
      601 gcacttccac aagtatatgg ggattccgca gatccggcag ctttccgaaa gagtgaaggc
      661 tgcacagact gagttaggac agcaaatcct ggcagatttt gaagaagcgt ttccttccca
      721 gggcaccaag agaccaggag gacccagcaa tgttctacga gatgcatgtc tggttgctaa
      781 tattctagat cccaggatca aacaggaaat catcaaaaag tttattaaac agcatctgtc
      841 agagtatctg gtactttttc aagaaaacca agatgttgcc tggctggaca aaatcgacag
      901 acgctatgcc tggataaaac gccagcttgt ggactatgag gagaaatacg gccgcatgtt
      961 tccacgtgag tggtgcatgg ctgagaggat tgcggtggaa ttttgccatg tgacaagggc
     1021 agaacttgcc aagattatgc gtaccagagc gaaggaaatt gaagtgaaat tgcttctttt
     1081 tgctattcaa agaacaacta actttgaggg gtttcttgca aaacgcttct ccggctgcac
     1141 cctgaccgat gggaccctga aaaagcttga gtctccaccc ccatctacca atcccttcct
     1201 ggaagatgag ccaacaccag agatggagga actggcaacg gagaaaggag atttagatca
     1261 accaaagaag cctaaagccc cagacaatcc atttcatggc attgtttcca agtgttttga
     1321 gcctcatctc tacgtgtata tcgaatccca agacaagaac ctcggagagc tgatagatcg
     1381 gtttgtggct gatttcaaag cccaggggcc acctaagccc aacactgatg aagggggtgc
     1441 cgtgctcccc agctgcgccg acctctttgt ctactacaag aagtgcatgg tgcaatgctc
     1501 tcagctcagt actggggagc ccatgatcgc cctgaccacc attttccaga agtacctccg
     1561 agaatacgcc tggaaaatcc tctctggcaa cctgcccaaa accacaacca gcagtggagg
     1621 actgactatc agcagcctcc tcaaggaaaa ggagggctca gaagtagcca agttcactct
     1681 ggaggagctc tgcctcatct gtaacatcct gagcacggca gagtactgtc tggccaccac
     1741 ccagcagcta gaagaaaaac tcaaagaaaa agtggatgta agtctgattg aacgaatcaa
     1801 tctgactgga gagatggaca cgttcagcac cgtcatctcc agcagtattc agctgctggt
     1861 tcaggatctg gatgctgcct gtgatcctgc cctgactgcc atgagcaaga tgcagtggca
     1921 gaacgtggag cacgttggtg accagagccc ctacgtcacc tctgtcattc tgcacatcaa
     1981 gcagaacgtc cccatcatcc gtgacaacct ggcttccaca cgcaagtact tcactcagtt
     2041 ctgcgttaaa tttgcaaact ccttcattcc caaattcatc acccacctct tcaagtgcaa
     2101 gccaattagc atggtgggag cagaacaggt gagatggacg tagtatcagg catttgcctg
     2161 gcagcttttg ttgtagatca agcacatatt cttctagtcc agatctactt ggcaggaata
     2221 aaattgatga tgtcccctgt ttggggacag tataatgact cacccggaag gtttcttaat
     2281 tcgttcttcc atttattttt aaaaattttg tttgaacgcc tactaagttc tgggtgcagg
     2341 gtataacaca gcaagcacca tggaaaggtc cctgctccta gtgctcacac tccaataaga
     2401 agaagtggct gggccgggca cagcggctca cgctgtaacc ccagcatttc gggaggcctg
     2461 ggcaggcaga tcacctgggg taaggaattt gagagcagcc tggccaacat ggtgaaatcc
     2521 catctctact aaaaatacaa aaattagctg ggcatggggg caggctactg gggaggctga
     2581 ggcaggagaa tcacttgaac ccgggaggtg gaggttgcag tgagccgata tcacaccact
     2641 gcactccagc ctgggtgaca aagtgagact ccatctcaaa aaaacaaaca aacaaaaaaa
     2701 ctagcaaaaa acttggaata ttggccgggc atggtggctc acgtctgtaa tcctagcact
     2761 ttgggaggcc caggcaggcg gatcatctga ggtcaggagt tcgagaccag cctggctaac
     2821 atggtgaacc ctgtctctac taataataca aaaaattagc cgggcgtgat ggtgggcgcc
     2881 tgtaatccca gctactcggg aggctgaggc agaattgctt caacccagga ggtggaggtt
     2941 gcagtgagct gagatcacac cactgtactc cagcctgggc aacaagagcg aaactccatc
     3001 tcaaaaaaaa aaaaaaaaaa aaaa
//
