LOCUS       NM_006052               3056 bp    mRNA    linear   PRI 19-SEP-2024
DEFINITION  Homo sapiens VPS26 endosomal protein sorting factor C (VPS26C),
            transcript variant 1, mRNA.
ACCESSION   NM_006052
VERSION     NM_006052.2
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 3056)
  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   2  (bases 1 to 3056)
  AUTHORS   Viard,J., Loe-Mie,Y., Daudin,R., Khelfaoui,M., Plancon,C.,
            Boland,A., Tejedor,F., Huganir,R.L., Kim,E., Kinoshita,M., Liu,G.,
            Haucke,V., Moncion,T., Yu,E., Hindie,V., Blehaut,H., Mircher,C.,
            Herault,Y., Deleuze,J.F., Rain,J.C., Simonneau,M. and
            Lepagnol-Bestel,A.M.
  TITLE     Chr21 protein-protein interactions: enrichment in proteins involved
            in intellectual disability, autism, and late-onset Alzheimer's
            disease
  JOURNAL   Life Sci Alliance 5 (12), e202101205 (2022)
   PUBMED   35914814
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3056)
  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   4  (bases 1 to 3056)
  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   5  (bases 1 to 3056)
  AUTHORS   Beetz,C., Ameziane,N., Kdissa,A., Karageorgou,V., Bauer,P.,
            Suleiman,J., Sutton,V.R. and El-Hattab,A.W.
  TITLE     VPS26C homozygous nonsense variant in two cousins with
            neurodevelopmental deficits, growth failure, skeletal
            abnormalities, and distinctive facial features
  JOURNAL   Clin Genet 97 (4), 644-648 (2020)
   PUBMED   31845315
  REMARK    GeneRIF: VPS26C homozygous nonsense variant in two cousins with
            neurodevelopmental deficits, growth failure, skeletal
            abnormalities, and distinctive facial features.
REFERENCE   6  (bases 1 to 3056)
  AUTHORS   Koumandou,V.L., Klute,M.J., Herman,E.K., Nunez-Miguel,R.,
            Dacks,J.B. and Field,M.C.
  TITLE     Evolutionary reconstruction of the retromer complex and its
            function in Trypanosoma brucei
  JOURNAL   J Cell Sci 124 (Pt 9), 1496-1509 (2011)
   PUBMED   21502137
REFERENCE   7  (bases 1 to 3056)
  AUTHORS   Aubry,L., Guetta,D. and Klein,G.
  TITLE     The arrestin fold: variations on a theme
  JOURNAL   Curr Genomics 10 (2), 133-142 (2009)
   PUBMED   19794886
REFERENCE   8  (bases 1 to 3056)
  AUTHORS   Hu,Y.H., Warnatz,H.J., Vanhecke,D., Wagner,F., Fiebitz,A.,
            Thamm,S., Kahlem,P., Lehrach,H., Yaspo,M.L. and Janitz,M.
  TITLE     Cell array-based intracellular localization screening reveals novel
            functional features of human chromosome 21 proteins
  JOURNAL   BMC Genomics 7, 155 (2006)
   PUBMED   16780588
  REMARK    Publication Status: Online-Only
REFERENCE   9  (bases 1 to 3056)
  AUTHORS   Dahmane,N., Ghezala,G.A., Gosset,P., Chamoun,Z.,
            Dufresne-Zacharia,M.C., Lopes,C., Rabatel,N.,
            Gassanova-Maugenre,S., Chettouh,Z., Abramowski,V., Fayet,E.,
            Yaspo,M.L., Korn,B., Blouin,J.L., Lehrach,H., Poutska,A.,
            Antonarakis,S.E., Sinet,P.M., Creau,N. and Delabar,J.M.
  TITLE     Transcriptional map of the 2.5-Mb CBR-ERG region of chromosome 21
            involved in Down syndrome
  JOURNAL   Genomics 48 (1), 12-23 (1998)
   PUBMED   9503011
REFERENCE   10 (bases 1 to 3056)
  AUTHORS   Nakamura,A., Hattori,M. and Sakaki,Y.
  TITLE     Isolation of a novel human gene from the Down syndrome critical
            region of chromosome 21q22.2
  JOURNAL   J Biochem 122 (4), 872-877 (1997)
   PUBMED   9399594
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AP001412.2 and AP001432.2.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_006052.1.
            
            Summary: The region of chromosome 21 between genes CBR and ERG
            (CBR-ERG region), which spans 2.5 Mb on 21q22.2, has been defined
            by analysis of patients with partial trisomy 21. It contributes
            significantly to the pathogenesis of many characteristics of Down
            syndrome, including morphological features, hypotonia, and
            cognitive disability. The DSCR3 (Down syndrome critical region gene
            3) gene is found in this region and is predictated to contain eight
            exons. DSCR3 is expressed in most tissues examined. [provided by
            RefSeq, Jul 2008].
            
            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 :: SRR3476690.892867.1,
                                           SRR1660807.239745.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000309117.11/ ENSP00000311399.6
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-97                AP001412.2         12433-12529         c
            98-241              AP001432.2         87714-87857         c
            242-391             AP001432.2         85678-85827         c
            392-472             AP001432.2         80580-80660         c
            473-547             AP001432.2         79595-79669         c
            548-698             AP001432.2         75441-75591         c
            699-851             AP001432.2         74872-75024         c
            852-3056            AP001432.2         70640-72844         c
FEATURES             Location/Qualifiers
     source          1..3056
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="21"
                     /map="21q22.13"
     gene            1..3056
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
                     /note="VPS26 endosomal protein sorting factor C"
                     /db_xref="GeneID:10311"
                     /db_xref="HGNC:HGNC:3044"
                     /db_xref="MIM:605298"
     exon            1..97
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
                     /inference="alignment:Splign:2.1.0"
     CDS             41..934
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
                     /note="isoform 1 is encoded by transcript variant 1; Down
                     syndrome critical region protein A; Down syndrome critical
                     region protein 3; Down syndrome critical region gene 3;
                     Down syndrome critical region 3; DSCR3 arrestin fold
                     containing; vacuolar protein sorting-associated protein
                     26C"
                     /codon_start=1
                     /product="vacuolar protein sorting-associated protein 26C
                     isoform 1"
                     /protein_id="NP_006043.1"
                     /db_xref="CCDS:CCDS33553.1"
                     /db_xref="GeneID:10311"
                     /db_xref="HGNC:HGNC:3044"
                     /db_xref="MIM:605298"
                     /translation="MGTALDIKIKRANKVYHAGEVLSGVVVISSKDSVQHQGVSLTME
                     GTVNLQLSAKSVGVFEAFYNSVKPIQIINSTIEMVKPGKFPSGKTEIPFEFPLHLKGN
                     KVLYETYHGVFVNIQYTLRCDMKRSLLAKDLTKTCEFIVHSAPQKGKFTPSPVDFTIT
                     PETLQNVKERALLPKFLLRGHLNSTNCVITQPLTGELVVESSEAAIRSVELQLVRVET
                     CGCAEGYARDATEIQNIQIADGDVCRGLSVPIYMVFPRLFTCPTLETTNFKVEFEVNI
                     VVLLHPDHLITENFPLKLCRI"
     exon            98..241
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
                     /inference="alignment:Splign:2.1.0"
     exon            242..391
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
                     /inference="alignment:Splign:2.1.0"
     exon            392..472
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
                     /inference="alignment:Splign:2.1.0"
     exon            473..547
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
                     /inference="alignment:Splign:2.1.0"
     exon            548..698
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
                     /inference="alignment:Splign:2.1.0"
     exon            699..851
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
                     /inference="alignment:Splign:2.1.0"
     exon            852..3056
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1056..1061
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
                     /note="hexamer: AATGAA"
     polyA_site      1078
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
     regulatory      3032..3037
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
                     /note="hexamer: AATAAA"
     polyA_site      3056
                     /gene="VPS26C"
                     /gene_synonym="DCRA; DSCR3; DSCRA"
                     /note="major polyA site"
ORIGIN      
        1 acgcgcagcc ggaagtggcg gctgctgcgg agaattggag atggggaccg ccctggacat
       61 caagattaaa agagcgaata aagtttatca cgccggggaa gtgctctctg gcgtggtggt
      121 catatcgagt aaggattcag tccaacacca gggagtgtct ttgaccatgg aaggaactgt
      181 aaacctccag ctcagtgcca aaagtgtggg tgtgtttgaa gctttttata attctgttaa
      241 gcctatccag attatcaaca gcaccataga aatggtgaag ccggggaaat ttcccagcgg
      301 caaaacagaa atcccttttg aatttcctct gcacttgaag ggtaacaaag ttctgtatga
      361 gacgtatcat ggcgtgtttg tcaacattca gtatacactg cgctgtgaca tgaagcggtc
      421 tctgttggcc aaggacttga caaagacctg tgaatttatc gttcactccg ctcctcagaa
      481 ggggaagttt actcccagtc ccgtggactt cacgattaca cctgaaacct tacagaacgt
      541 caaagagaga gctttgcttc ccaaatttct ccttcgagga catctcaact caacaaactg
      601 tgtcatcacg cagccactaa cgggagagct ggtggtggag agctcggaag ccgccatcag
      661 aagcgtggag ctgcagctgg tgcgcgtgga gacgtgcggg tgtgcagaag gctatgcccg
      721 cgacgccacg gagattcaga acattcagat cgccgacggg gatgtgtgca ggggcctctc
      781 tgtccccatc tacatggtct tccctaggct gttcacctgc cctacactgg agaccaccaa
      841 cttcaaagtg gaatttgagg ttaacatcgt ggtgctgctt caccctgacc acctcatcac
      901 ggagaacttc ccgctgaagc tctgcaggat atagcccgga ggagggaagc atagagaacg
      961 ggagtggcca tctggaaatc cagctggtta tccaaatcct aaggggagct acagccagcg
     1021 gcatatactt gtttttgtga ttattctgta tcagaaatga aacagaccct caaattaact
     1081 ttccttcctc atttcttgag gcttctgctt ccaacaggca cctctaatca gaccttttct
     1141 ttgaaattca acaagatttc ttaatgctat ttgccaagac catttcacag aaaacattga
     1201 ctgtggctct tgccttatct gttccttttt aggtacagta aaacaattgt gacagcagtt
     1261 tgagcttgct ggagagtggc atcatgggga caaaaggaaa cctctgactt gctaatggat
     1321 gtagccaggg actccccata gcaaagggtc tgtggccagt tgacatccag gatggctgca
     1381 agcgcacttg atggtcagga agtttgcaga tactcgccaa ggcagagcgc aaagtgctag
     1441 ccactggaaa tgcatgactt ccctccaccc ctactctatt ctgtagtttt ttggttttgt
     1501 ttctgagacg gagtctcagt ctgtcaccca ggctggagtg atctcagctc actgcaacct
     1561 ccacctccca ggttcaagcg actctcctgc ctcagcctcc cgagtagttg ggattacagg
     1621 tgactgccac cgtgcccggc taatgtttgt atttttagta gagacggggc ttcaccatct
     1681 tggccaggct ggtcttgaac tcctgacctc gtgacccacc cgccttggcc tcccaaagtg
     1741 ctgggattac aggtgtgagc caccacaccc agcctctgta gttcttttta caacattttt
     1801 cattataact ttaaattttt taagcaactg gaaaagtgtt ccttgctctc ttggggggat
     1861 ttggctggtg ccgaagtgtt tctgaagtct caagaactgc cataaaatct cacgctgcca
     1921 tttccctgaa cagatacata catagagaga gacagttttc caaactgtgt cacgcaggct
     1981 gagtgcactg gcaggatcac agctcacggc agcctcaacc tccctggctc aagcgatccc
     2041 tcccctcagc ctcctgagta gctgagacta caggtgagtg ccaccacact cagctaattt
     2101 tcaaattttt tgtagacagg gtctccctat gttgcccagg ctggtcttga actcctagac
     2161 tcaagtgatc ctcctgtctt ggcctcccaa agtgctgaga ttacaggtgt gagccactgt
     2221 gcccagcagt ttcccagaat atatttaaat gcaaagttac atgaggggaa aacatgtatg
     2281 tttgctcctg ttgttactgg gtaggttctg aacagcagaa acccatgtgc agggtgggct
     2341 ggtgaaggcc cctctccgca aggtggtagc aggaaaaggt ccttgacttg atgaatttgg
     2401 tctgcctctg agccactgga ggaagctgtt ttgagccagg gttttttggc ctaaagccag
     2461 catttcctca gtctcccttt gtggttcgaa ggatatggac tattgcaata catttcttcc
     2521 ttcaaatcct gccactgttt tgttggccca caactaatag gacctcaaaa taagccatgc
     2581 tgctttgcac acacactagc cttcttttgt acttttcatt ctggatgggc ttggccaaaa
     2641 caggctcagg ccaaagacct cccaagctgt atgtacttcc agtatcctga aacagtgttt
     2701 ggtgacataa tgccaagggt aaacaagcct gatttaggca ctgctttatc caggggcttc
     2761 acccatgaaa ttaataaaac ttatctgagt cacttgaaac ttggttccca gaaaacacat
     2821 ttctggttta taatctcctt ttatgctcac ctgacattaa ttatctatcc ttgatgatgt
     2881 gtttaaactg agtagcagaa aacagaggcc acactttctg ggaaatttta aaggaagaaa
     2941 ccatttttaa tgagatgaaa atatttaacg aatttaaaaa gctaatgaca attttgagaa
     3001 aaggtttggg atgtatattg ctatgtaatt taataaactg attttatgga tataaa
//
