LOCUS       NM_001399318            3160 bp    mRNA    linear   ROD 28-MAR-2024
DEFINITION  Rattus norvegicus VPS41 subunit of HOPS complex (Vps41), mRNA.
ACCESSION   NM_001399318 XM_039095719
VERSION     NM_001399318.1
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 3160)
  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 3160)
  AUTHORS   Asensio,C.S., Sirkis,D.W., Maas,J.W. Jr., Egami,K., To,T.L.,
            Brodsky,F.M., Shu,X., Cheng,Y. and Edwards,R.H.
  TITLE     Self-assembly of VPS41 promotes sorting required for biogenesis of
            the regulated secretory pathway
  JOURNAL   Dev Cell 27 (4), 425-437 (2013)
   PUBMED   24210660
REFERENCE   3  (bases 1 to 3160)
  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   4  (bases 1 to 3160)
  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   5  (bases 1 to 3160)
  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   6  (bases 1 to 3160)
  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   7  (bases 1 to 3160)
  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   8  (bases 1 to 3160)
  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
REFERENCE   9  (bases 1 to 3160)
  AUTHORS   McVey Ward,D., Radisky,D., Scullion,M.A., Tuttle,M.S., Vaughn,M.
            and Kaplan,J.
  TITLE     hVPS41 is expressed in multiple isoforms and can associate with
            vesicles through a RING-H2 finger motif
  JOURNAL   Exp Cell Res 267 (1), 126-134 (2001)
   PUBMED   11412045
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000017.1.
            
            On Jan 6, 2022 this sequence version replaced XM_039095719.1.
            
            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 :: FQ221883.1, FQ223450.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA5760383,
                                           SAMEA5760434 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-38                JAXUCZ010000017.1  50923092-50923129   c
            39-77               JAXUCZ010000017.1  50915432-50915470   c
            78-182              JAXUCZ010000017.1  50902737-50902841   c
            183-260             JAXUCZ010000017.1  50896933-50897010   c
            261-335             JAXUCZ010000017.1  50855192-50855266   c
            336-398             JAXUCZ010000017.1  50845902-50845964   c
            399-464             JAXUCZ010000017.1  50843010-50843075   c
            465-584             JAXUCZ010000017.1  50822865-50822984   c
            585-731             JAXUCZ010000017.1  50821707-50821853   c
            732-798             JAXUCZ010000017.1  50819383-50819449   c
            799-896             JAXUCZ010000017.1  50808436-50808533   c
            897-1026            JAXUCZ010000017.1  50804177-50804306   c
            1027-1142           JAXUCZ010000017.1  50802368-50802483   c
            1143-1199           JAXUCZ010000017.1  50800786-50800842   c
            1200-1261           JAXUCZ010000017.1  50797015-50797076   c
            1262-1343           JAXUCZ010000017.1  50793382-50793463   c
            1344-1436           JAXUCZ010000017.1  50792202-50792294   c
            1437-1564           JAXUCZ010000017.1  50791155-50791282   c
            1565-1709           JAXUCZ010000017.1  50789742-50789886   c
            1710-1751           JAXUCZ010000017.1  50782344-50782385   c
            1752-1802           JAXUCZ010000017.1  50781733-50781783   c
            1803-1940           JAXUCZ010000017.1  50778935-50779072   c
            1941-1995           JAXUCZ010000017.1  50772731-50772785   c
            1996-2136           JAXUCZ010000017.1  50770319-50770459   c
            2137-2273           JAXUCZ010000017.1  50769178-50769314   c
            2274-2373           JAXUCZ010000017.1  50762515-50762614   c
            2374-2418           JAXUCZ010000017.1  50762367-50762411   c
            2419-2498           JAXUCZ010000017.1  50760939-50761018   c
            2499-3160           JAXUCZ010000017.1  50758739-50759400   c
FEATURES             Location/Qualifiers
     source          1..3160
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="17"
                     /map="17q11"
     gene            1..3160
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /note="VPS41 subunit of HOPS complex"
                     /db_xref="GeneID:306991"
                     /db_xref="RGD:1560511"
     exon            1..38
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     CDS             18..2579
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /note="Vam2; vacuolar protein sorting 41 homolog; VPS41
                     HOPS complex subunit"
                     /codon_start=1
                     /product="vacuolar protein sorting-associated protein 41
                     homolog"
                     /protein_id="NP_001386247.1"
                     /db_xref="GeneID:306991"
                     /db_xref="RGD:1560511"
                     /translation="MAEAEEQETESLEESTDESEEESEEEPKLKYERLSNGVTEILQK
                     DAASCMTVHDKFLALGTHYGKVYLLDVQGNITQKFDVSPVKINQISLDESGEHMGVCS
                     EDGKLQVFGLYSGEEFHETFDCPIKIVAVHPQFVRSSCKQFVTGGKKLLLFERTWMNR
                     WKSSVLHEGEGNIRSVKWRGHLIAWANNMGVKIFDITSKQRITNVPRDDISLRPDMYP
                     CSLCWKDAVTLIIGWGTSIKICSVKERHASEMRDLPSRYVEIVSQFETEFYISGLAPL
                     CDQLVVLSYVKEVSEKTEREYCARPRLDIIQPLPETCEEISSDALTVRGFQENECRDY
                     HLEYSEGESLFYVVSPRDVVVAKERDQDDHIDWLLEKKKYEEALMAAEISHRNIKRHK
                     ILEIGLAYVNHLVERGEYDMAARKCQKILGKNASLWEYEVYKFKEIGQLKAISPYLPR
                     GDPVLKPLIYEMILHEFLESDYEGFATLIREWPGDLYNNSVIVQAVRDHLKKDSQNKT
                     LLKTLAELYTYDKNYGNALEIYLTLRHKDVFQLIHKHNLFSSIKDKIVLLMDFDSEKA
                     VDMLLDNEDKISIKKVVEELEDRPELQHVYLHKLFKRDHHKGQRYHEKQISLYAEYDR
                     PNLLPFLRDSTHCPLEKALEICQQRNFVEETVYLLSRMGNSRSALKMIMEELHDVDKA
                     IEFAKEQDDGELWEDLILYSIDKPPFITGLLNNIGTHVDPILLIHRIKEGMEIPNLRD
                     SLVKILQDYNLQILLREGCKKILVADSLSLLKKMHRTQMKGVLVDEENICESCLSPIL
                     PTDAAKPFSVVVFHCRHMFHKECLPMPSLNAPAQYCNICSAKNRGPGSAILEMKK"
     exon            39..77
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            78..182
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            183..260
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            261..335
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            336..398
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            399..464
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            465..584
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            585..731
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            732..798
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            799..896
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            897..1026
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            1027..1142
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            1143..1199
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            1200..1261
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            1262..1343
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            1344..1436
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            1437..1564
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            1565..1709
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            1710..1751
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            1752..1802
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            1803..1940
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            1941..1995
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            1996..2136
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            2137..2273
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            2274..2373
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            2374..2418
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            2419..2498
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
     exon            2499..3160
                     /gene="Vps41"
                     /gene_synonym="RGD1560511"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gactctcaga ctgagctatg gcggaagcag aggagcagga aactgagtct cttgaagaat
       61 ctacagatga gtcagaggaa gagagtgaag aggaacccaa actgaagtat gaaaggcttt
      121 ctaatggggt gacagagatt cttcagaaag atgcagcaag ctgtatgacg gtccatgaca
      181 agtttttggc actgggcaca cactatggca aggtttattt actggacgtc cagggaaaca
      241 tcactcagaa gtttgatgta agtcctgtga agataaacca gatcagcttg gatgaaagcg
      301 gagaacatat gggcgtgtgc tcggaggatg gcaagctgca ggtctttgga ctgtactctg
      361 gagaagaatt ccatgagact ttcgactgtc ccattaaaat cgttgctgtg cacccccagt
      421 tcgtgagatc cagttgtaag cagttcgtga ctggtgggaa aaagttgctg ctatttgaac
      481 ggacgtggat gaacagatgg aagtcttctg tcctgcacga aggggaaggg aacataagga
      541 gcgtgaagtg gagaggccat ctgattgcct gggccaacaa catgggtgtg aagatttttg
      601 acatcacctc aaagcaaaga atcaccaacg ttccccgaga tgatataagt cttcgcccag
      661 atatgtatcc ctgcagcctc tgctggaagg atgctgtgac actgattatc ggctggggaa
      721 cttccatcaa gatatgctca gtgaaggaac gccatgccag tgagatgagg gatctgccaa
      781 gtcgatacgt tgaaatagtg tctcaatttg aaactgaatt ctacattagt ggacttgcac
      841 ctctctgtga tcagcttgtt gtactttcct acgtaaagga ggtttcggaa aaaacggaaa
      901 gagaatactg tgcaagaccg agactggaca tcatccagcc acttccagag acttgtgaag
      961 agatctcatc tgatgctttg acagtcagag gttttcagga gaatgaatgt agggattacc
     1021 acctagaata ctctgaaggg gaatcactct tctacgtcgt gagtccaaga gatgtcgtcg
     1081 tagccaagga gcgagaccag gatgatcata tcgactggct ccttgagaag aagaaatatg
     1141 aagaagcttt gatggcagct gaaattagcc acaggaacat taaaagacat aagattctgg
     1201 agatcgggtt ggcatatgta aaccacctgg tggagagagg cgagtacgac atggccgcac
     1261 gaaaatgcca gaaaattctt gggaaaaatg catccctctg ggaatacgaa gtttacaaat
     1321 ttaaagaaat tggacagctt aaagcaatta gtccctattt acctcgaggg gaccccgttc
     1381 tgaaaccact catctatgaa atgattttgc acgaatttct ggaaagtgat tatgagggct
     1441 ttgccacatt gatcagagaa tggcctggag atctgtataa caattctgtg atagttcaag
     1501 cagttcgaga ccacctgaag aaggacagtc agaacaagac tttattgaaa acactggcag
     1561 aattgtatac ctatgacaaa aattatggca atgctctgga aatatactta acgttaagac
     1621 ataaagatgt tttccaactg atacacaagc ataatctttt cagctccatc aaggataaaa
     1681 ttgttttatt aatggacttt gattcagaga aagctgttga catgcttttg gacaatgaag
     1741 ataaaatttc aattaaaaaa gtggtagaag aattagaaga caggccagag ctgcagcatg
     1801 tgtatttgca caagctcttc aagagagacc atcataaggg acagcgctac catgaaaaac
     1861 agatcagtct gtatgccgaa tatgatcgac caaacctact gccctttctc cgagacagta
     1921 cccattgccc actagaaaag gctcttgaga tctgtcaaca aagaaacttt gtagaagaga
     1981 cagtttacct tctgagccga atgggaaaca gtcgaagtgc cctgaagatg attatggagg
     2041 aattgcatga tgttgataaa gcaattgagt ttgccaagga acaagatgat ggagagctct
     2101 gggaagatct gattctatat tccattgaca aaccaccatt tatcactggc ttgttgaaca
     2161 acattggcac acacgtagac ccgattctac tcattcaccg aattaaggaa ggaatggaga
     2221 ttcccaattt gagagattcc ttggttaaaa ttctgcaaga ttataactta cagattctgc
     2281 ttcgggaagg ctgcaagaaa atcctcgtag ctgactcttt gtcattgctg aaaaaaatgc
     2341 accgaaccca aatgaaaggc gttctggttg acgaggagaa tatctgtgaa tcgtgccttt
     2401 ctcccatcct tccaacagat gcagcgaagc ccttcagcgt ggtggtcttc cattgtcggc
     2461 acatgttcca caaggagtgc ctacctatgc caagcctgaa tgctcctgca cagtactgta
     2521 acatctgtag tgctaagaac cgtgggcctg gaagtgccat cctggagatg aagaagtagg
     2581 cctgcctgcc attaccactc tactctggtg accgttggac cacagccgct agctatgtca
     2641 aggccaatgc tgttctgtga tgtgttcagg gctactctgt gttccacatc agttgttcct
     2701 ccagaccttc cttccagaag ctgttcttgt cactgatgga gaagtcagag ctgttcccat
     2761 gccatgaaat atttggattg acaatcaata tttcatgatt tgtttatttg gcttatttag
     2821 gcaacagatg aacccaagtc tcagagtgac ttcattagac cctagttaca ccaccaggca
     2881 tgaaccgcac tgccgagaac actgccagct gcagacagcc gaaagttctg ctggtaacag
     2941 ttctagcatg cctggctata ctgtttgtca tcagcttcct agtatgcatt tggtgaaaca
     3001 ctggaaactg tcactcgttc aatgacgtgt gggaatacca ttatctgatg tcatgcaacc
     3061 ttatgcttgc tacgtacatg ctatgcattc tgactaatcg agttatctga ccccattagg
     3121 taatcaatat ctgttgagta aataaacatt gcccttctca
//
