LOCUS       NM_001012186            4386 bp    mRNA    linear   ROD 31-MAR-2024
DEFINITION  Rattus norvegicus VPS39 subunit of HOPS complex (Vps39), mRNA.
ACCESSION   NM_001012186 XM_342500
VERSION     NM_001012186.2
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 4386)
  AUTHORS   Wartosch,L., Gunesdogan,U., Graham,S.C. and Luzio,J.P.
  TITLE     Recruitment of VPS33A to HOPS by VPS16 Is Required for Lysosome
            Fusion with Endosomes and Autophagosomes
  JOURNAL   Traffic 16 (7), 727-742 (2015)
   PUBMED   25783203
REFERENCE   2  (bases 1 to 4386)
  AUTHORS   Perini,E.D., Schaefer,R., Stoter,M., Kalaidzidis,Y. and Zerial,M.
  TITLE     Mammalian CORVET is required for fusion and conversion of distinct
            early endosome subpopulations
  JOURNAL   Traffic 15 (12), 1366-1389 (2014)
   PUBMED   25266290
REFERENCE   3  (bases 1 to 4386)
  AUTHORS   Jiang,P., Nishimura,T., Sakamaki,Y., Itakura,E., Hatta,T.,
            Natsume,T. and Mizushima,N.
  TITLE     The HOPS complex mediates autophagosome-lysosome fusion through
            interaction with syntaxin 17
  JOURNAL   Mol Biol Cell 25 (8), 1327-1337 (2014)
   PUBMED   24554770
REFERENCE   4  (bases 1 to 4386)
  AUTHORS   Graham,S.C., Wartosch,L., Gray,S.R., Scourfield,E.J., Deane,J.E.,
            Luzio,J.P. and Owen,D.J.
  TITLE     Structural basis of Vps33A recruitment to the human HOPS complex by
            Vps16
  JOURNAL   Proc Natl Acad Sci U S A 110 (33), 13345-13350 (2013)
   PUBMED   23901104
REFERENCE   5  (bases 1 to 4386)
  AUTHORS   Pols,M.S., ten Brink,C., Gosavi,P., Oorschot,V. and Klumperman,J.
  TITLE     The HOPS proteins hVps41 and hVps39 are required for homotypic and
            heterotypic late endosome fusion
  JOURNAL   Traffic 14 (2), 219-232 (2013)
   PUBMED   23167963
REFERENCE   6  (bases 1 to 4386)
  AUTHORS   Zlatic,S.A., Tornieri,K., L'Hernault,S.W. and Faundez,V.
  TITLE     Clathrin-dependent mechanisms modulate the subcellular distribution
            of class C Vps/HOPS tether subunits in polarized and nonpolarized
            cells
  JOURNAL   Mol Biol Cell 22 (10), 1699-1715 (2011)
   PUBMED   21411634
REFERENCE   7  (bases 1 to 4386)
  AUTHORS   Zhu,G.D., Salazar,G., Zlatic,S.A., Fiza,B., Doucette,M.M.,
            Heilman,C.J., Levey,A.I., Faundez,V. and L'hernault,S.W.
  TITLE     SPE-39 family proteins interact with the HOPS complex and function
            in lysosomal delivery
  JOURNAL   Mol Biol Cell 20 (4), 1223-1240 (2009)
   PUBMED   19109425
REFERENCE   8  (bases 1 to 4386)
  AUTHORS   Schroder,B., Wrocklage,C., Pan,C., Jager,R., Kosters,B.,
            Schafer,H., Elsasser,H.P., Mann,M. and Hasilik,A.
  TITLE     Integral and associated lysosomal membrane proteins
  JOURNAL   Traffic 8 (12), 1676-1686 (2007)
   PUBMED   17897319
REFERENCE   9  (bases 1 to 4386)
  AUTHORS   Richardson,S.C., Winistorfer,S.C., Poupon,V., Luzio,J.P. and
            Piper,R.C.
  TITLE     Mammalian late vacuole protein sorting orthologues participate in
            early endosomal fusion and interact with the cytoskeleton
  JOURNAL   Mol Biol Cell 15 (3), 1197-1210 (2004)
   PUBMED   14668490
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000003.1.
            
            On Sep 11, 2008 this sequence version replaced NM_001012186.1.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26643289.10478.1,
                                           SRR26643429.12965.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA5760383,
                                           SAMEA5760386 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-221               JAXUCZ010000003.1  127758422-127758642 c
            222-287             JAXUCZ010000003.1  127755579-127755644 c
            288-352             JAXUCZ010000003.1  127751976-127752040 c
            353-395             JAXUCZ010000003.1  127751245-127751287 c
            396-490             JAXUCZ010000003.1  127749891-127749985 c
            491-589             JAXUCZ010000003.1  127748714-127748812 c
            590-682             JAXUCZ010000003.1  127747823-127747915 c
            683-866             JAXUCZ010000003.1  127745015-127745198 c
            867-987             JAXUCZ010000003.1  127742062-127742182 c
            988-1108            JAXUCZ010000003.1  127741846-127741966 c
            1109-1238           JAXUCZ010000003.1  127737002-127737131 c
            1239-1381           JAXUCZ010000003.1  127731907-127732049 c
            1382-1525           JAXUCZ010000003.1  127729306-127729449 c
            1526-1667           JAXUCZ010000003.1  127728722-127728863 c
            1668-1754           JAXUCZ010000003.1  127728520-127728606 c
            1755-1828           JAXUCZ010000003.1  127727980-127728053 c
            1829-1927           JAXUCZ010000003.1  127727592-127727690 c
            1928-2045           JAXUCZ010000003.1  127727019-127727136 c
            2046-2174           JAXUCZ010000003.1  127726472-127726600 c
            2175-2277           JAXUCZ010000003.1  127725274-127725376 c
            2278-2323           JAXUCZ010000003.1  127725035-127725080 c
            2324-2473           JAXUCZ010000003.1  127724112-127724261 c
            2474-2608           JAXUCZ010000003.1  127723858-127723992 c
            2609-2700           JAXUCZ010000003.1  127723576-127723667 c
            2701-4386           JAXUCZ010000003.1  127721076-127722761 c
FEATURES             Location/Qualifiers
     source          1..4386
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="3"
                     /map="3q35"
     gene            1..4386
                     /gene="Vps39"
                     /note="VPS39 subunit of HOPS complex"
                     /db_xref="GeneID:362199"
                     /db_xref="RGD:1304858"
     exon            1..221
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     CDS             149..2776
                     /gene="Vps39"
                     /note="Vam6; vacuolar protein sorting 39 homolog; VPS39
                     HOPS complex subunit"
                     /codon_start=1
                     /product="vam6/Vps39-like protein"
                     /protein_id="NP_001012186.2"
                     /db_xref="GeneID:362199"
                     /db_xref="RGD:1304858"
                     /translation="MHDAFEPVPILEKLPLQIDCLAAWEEWLLVGTKQGHLLLYRIRK
                     DVGCNRFEVTLEKSNKNFSKKIQQIHVVSQFKILVSLLENNIYVHDLLTFQQITTVSK
                     AKGASLFTCDLQHTETGEEVLRMCVAVRKKLQLYFWKDREFHELQGDFSVPDVPKSMA
                     WCENSICVGFKRDYYLIRVDAKGSIKELFPTGKQLEPLVAPLADGKVAVGQDDLTVVL
                     NEEGICTQKCALNWTDIPVAMEHQPPYIVAVLPRYVEIRTLEPRLLVQSIELQRPRFI
                     TSGGSNIIYVASNHFVWRLIPVPMATQIQQLLQDKQFELALQLAEMKDDSDSEKQQQI
                     HHIKNLYAFNLFCQKRFDESMQVFAKLGTDPTHVMGLYPDLLPTDYRKQLQYPNPLPT
                     LSGAELEKAHLALIDYLTQKRSQLVKKLNDSDHQSSTSPLMEGTPTIKSKQKLLQIID
                     TTLLKCYLHTNVALVAPLLRLENNHCHIEESEHVLKKAHKYSELIILYEKKGLHEKAL
                     QVLVDQSKKANSPLKGHERTVQYLQHLGTENLHLIFSYSIWVLRDFPEDGLKIFTEDL
                     PEVESLPRDRVLNFLIENFKALAIPYLEHIIHVWEETGTRFHNCLIQLYCEKVQNLMK
                     DYLLSLPTGKSPVPAGEEAGELGESRQKLLTFLEISSSYDPGRLICDFPFDGLLEERA
                     LLLGRMGKHEQALFIYVHVLKDTKMAKEYCHKHYDQNKEGNKDVYLSLLRMYLSPPSI
                     HCLGPIKLELLEPQANLQAALQVLELHYSKLDTTKAINLLPANTQINDIRIFLEKVLE
                     ENAQKKRFNQVLKNLLHAEFLRVQEERILHQQVKCIITEEKVCMVCKKKIGNSAFARY
                     PNGVVVHYFCSKEVNSADT"
     exon            222..287
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            288..352
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            353..395
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            396..490
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            491..589
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            590..682
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            683..866
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            867..987
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            988..1108
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            1109..1238
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            1239..1381
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            1382..1525
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            1526..1667
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            1668..1754
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            1755..1828
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            1829..1927
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            1928..2045
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            2046..2174
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            2175..2277
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            2278..2323
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            2324..2473
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            2474..2608
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            2609..2700
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
     exon            2701..4386
                     /gene="Vps39"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 agcaggaagt ccggcggcaa ggatggaggt gttgctgaag gccctgtaag cggggtccct
       61 ggtgggatcc gggtcttccc tgttttcttg gtcagcaggc tcctcccagt agcaggggcg
      121 ggacggcagc ggcgaagctc ccgcagccat gcatgacgct tttgagccgg tgccgatcct
      181 ggagaagctt ccactgcaga ttgactgcct ggctgcctgg gaggaatggc ttcttgttgg
      241 aaccaagcaa gggcatcttc ttctctacag gattcggaag gatgttggtt gtaacaggtt
      301 tgaggtaaca ctagagaagt ccaataagaa cttttccaaa aagatccagc agatccatgt
      361 ggtttcccag tttaagattc tagtcagctt gttagaaaac aacatttatg tccatgactt
      421 actgacattt caacaaatca ctacagtttc aaaggctaaa ggagcatcac tgttcacctg
      481 tgacctccag cacactgaga cgggtgagga ggtgttgcgg atgtgtgtgg cggtgaggaa
      541 gaagctgcag ttgtacttct ggaaggatag agaattccat gaactgcagg gagactttag
      601 tgtacccgat gtgcccaagt ccatggcatg gtgtgaaaat tctatctgtg ttggcttcaa
      661 gagagactac tacctgatta gggtggatgc aaaggggtct atcaaagagc tcttcccaac
      721 aggaaagcag ctggagccct tagttgcccc tctggcagat ggaaaagtag ccgtgggtca
      781 ggatgatctg actgtggtgc tcaacgagga aggcatctgc actcagaaat gcgccctgaa
      841 ctggacagac atcccggtgg ccatggagca ccagcctccg tacattgtcg cagtgttgcc
      901 aagatacgtg gagatccgaa cacttgaacc aaggcttctg gtccagagca tagagttgca
      961 aaggccccgc ttcattacat cagggggatc aaacattatc tatgtggcca gcaatcattt
     1021 tgtttggaga ctcattcctg tccccatggc aacccaaatc caacagcttc tccaggacaa
     1081 gcagtttgaa ttggctctgc agctagcgga aatgaaagat gactcagaca gtgaaaagca
     1141 gcagcaaatc catcacatta agaacttgta tgccttcaac ctcttctgtc agaagcgctt
     1201 tgatgagtcc atgcaggtct ttgctaaact tggcacagat cccacccacg tgatgggctt
     1261 gtaccccgac ctgctgccca cggactacag gaagcaactg cagtacccca acccgctgcc
     1321 cacactctct ggtgctgagc tggagaaggc tcacttagcg ctcattgact acctgacaca
     1381 gaagcggagc cagttggtaa agaagctgaa tgactcggac caccagtcca gcacctcccc
     1441 actcatggag ggcactccca ccatcaagtc caagcagaag ctgctgcaga tcatcgacac
     1501 cactctactc aagtgctacc tccatacaaa tgtggccctg gtggctccct tgctgcgcct
     1561 ggagaacaac cactgtcaca tcgaggagag tgagcatgtg ctgaagaagg ctcacaagta
     1621 cagtgagctg atcatcctgt atgagaagaa ggggctccat gagaaagctc tgcaggtgct
     1681 agtggaccag tccaagaaag caaactcacc tctgaaaggc catgaaagga cggtgcagta
     1741 cctacagcat ttgggcacag aaaacctaca tttgattttt tcctactcga tctgggtgct
     1801 gagagacttc ccagaagatg gcctgaagat attcactgaa gacctcccgg aggtggagtc
     1861 tctgccacga gatcgcgtgc tcaacttctt gatagagaat ttcaaggccc tggccattcc
     1921 ttacctggag cacatcatcc acgtgtggga ggagacaggc acacggttcc acaattgcct
     1981 aatccagctg tactgtgaga aagtgcagaa tctgatgaaa gactacctcc tgtcactacc
     2041 cacaggcaaa agtccagtcc ctgctggcga ggaagcagga gaactgggag aatcccgaca
     2101 gaagctgctc acgttcctgg agatttccag ctcctacgat cccggccggc tcatctgtga
     2161 ttttcccttc gatggcctct tagaagaaag agctctcctg ttgggacgca tggggaagca
     2221 cgaacaagct ctcttcatct atgtccatgt cttgaaggac acaaagatgg ctaaggagta
     2281 ctgccacaaa cactacgacc aaaacaaaga aggcaacaaa gatgtatatc tgtccctgct
     2341 tcggatgtac ctgtcgcctc caagcattca ctgcctgggg ccaatcaaac tagagctcct
     2401 ggagccacag gccaacctcc aggctgccct gcaggtccta gagctgcact acagcaaatt
     2461 agacaccacc aaggcaatca accttctgcc agcaaacact cagatcaatg acatacgaat
     2521 cttcctagaa aaggtcttag aagaaaatgc acaaaagaaa cggttcaatc aagtgcttaa
     2581 gaatcttctc catgcggagt ttctcagggt tcaggaagag cggattttac accagcaggt
     2641 gaagtgcatc atcactgagg agaaggtgtg catggtgtgc aagaagaaga ttgggaacag
     2701 tgcatttgca agatacccca atggagtggt tgtgcactac ttctgctcca aagaagttaa
     2761 ctcagccgac acctgagccc ggcatcccaa gcactcagca gtggacagct cagcttccca
     2821 gagagttgaa ggagcggcca ccctaggaac tagggactgc taccataaag tgtctccctc
     2881 atttgggcgt tgctggctac cttgctctct ggagcatctc tgaatcaact ggacttgtga
     2941 cctggcattg caggcttttt actagaagaa gagattaggc atatccttcg ctgttatgtt
     3001 gcagacaatt ccaggaattt aacccctgcc tggacaggag gaaatgcacc gtcttgcctt
     3061 tgtataccaa tcacctggac aaggagattt catctcaagt gtttgtaccc atggggttgt
     3121 tgactgcgag ttttctatta cagtaactac acggcttcac cagacccctg caggcagcct
     3181 ggagagtccc atgggagcct ggtactagag ctttccagcc ccactggccg caggctgctt
     3241 gtactctgac ggttctccac aggagctgtg ccctgtgtcc tgcttatccc tttaatattc
     3301 agtctccttt tctttctcac tatttatttt acccccaatc tcttctcttg taccatcctc
     3361 tcccactctg tagactgggc ggtagggagt aactaatatt taaatgtggc aacatgggag
     3421 gcacagtcta ggtttccagg agtggactga tgagcaggtg tcacatacat tgtatgaagg
     3481 ttctcaggag ctgaactttt ctactaagat gtgtaggaga gcacaagtct ctgtaggcgt
     3541 aggctttggt aggtagctct ctggggcagc actgggcagg gcgtgtggtc taggcaggat
     3601 ctctgcagaa gtgcctgctt cagccactca ccagctgctt ggacaggtca ttgagccttc
     3661 gttggtgagc tctttgagct ctgagcagct ttctccactc tagccacttt ctgtcctgtt
     3721 gctttcatgg ccatagttgt tccctggcct tttttgcaag actggaggat ttcactagga
     3781 tatcttggta atgggtgtct gccctgcaca cagggaacag ttgaccagaa actgacagcc
     3841 atgagatgcc gggtatgttt gtgaggcact gagcaaaggg taatgcagga gcggatggac
     3901 ttagagctta ctgctggctc tgttgagcat gtcagggagc ctgcaggagg tatgcaggaa
     3961 cttctggcat tggaggctgt aggcaccagg cacacatgca cagtcatata tgcaggcagc
     4021 acacccacac acaaagttta aaaaaaaatg accagtgctg cttcaacagc ttaaaatgca
     4081 cttcctcagg agtggccctg gaatgctggg cagctcccca taggacagga ccggtacttg
     4141 tgccgtccat gagtcctgcc ctctcacctg gtaggcttgt agcatccctt cttatgaact
     4201 gtgtttgaag cagtagaata aaacctgtat tttctcctgg atggtgtaca tccttaattc
     4261 tatttcccca aactccatcc tttcttccct ggatcctgcc ctccgtagag ggttggggag
     4321 gggaacagat agctccagcc tgaggatgct ggagggctgc ttcccaataa acaagcgaaa
     4381 caccaa
//
