LOCUS       NM_001399656            3109 bp    mRNA    linear   ROD 27-MAR-2024
DEFINITION  Rattus norvegicus VPS35 endosomal protein sorting factor like
            (Vps35l), transcript variant 1, mRNA.
ACCESSION   NM_001399656 XM_006230122
VERSION     NM_001399656.1
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 3109)
  AUTHORS   McNally,K.E., Faulkner,R., Steinberg,F., Gallon,M., Ghai,R.,
            Pim,D., Langton,P., Pearson,N., Danson,C.M., Nagele,H.,
            Morris,L.L., Singla,A., Overlee,B.L., Heesom,K.J., Sessions,R.,
            Banks,L., Collins,B.M., Berger,I., Billadeau,D.D., Burstein,E. and
            Cullen,P.J.
  TITLE     Retriever is a multiprotein complex for retromer-independent
            endosomal cargo recycling
  JOURNAL   Nat Cell Biol 19 (10), 1214-1225 (2017)
   PUBMED   28892079
REFERENCE   2  (bases 1 to 3109)
  AUTHORS   Phillips-Krawczak,C.A., Singla,A., Starokadomskyy,P., Deng,Z.,
            Osborne,D.G., Li,H., Dick,C.J., Gomez,T.S., Koenecke,M.,
            Zhang,J.S., Dai,H., Sifuentes-Dominguez,L.F., Geng,L.N.,
            Kaufmann,S.H., Hein,M.Y., Wallis,M., McGaughran,J., Gecz,J.,
            Sluis,Bv., Billadeau,D.D. and Burstein,E.
  TITLE     COMMD1 is linked to the WASH complex and regulates endosomal
            trafficking of the copper transporter ATP7A
  JOURNAL   Mol Biol Cell 26 (1), 91-103 (2015)
   PUBMED   25355947
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000001.1.
            
            On Jan 12, 2022 this sequence version replaced XM_006230122.4.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26643297.3315.1,
                                           SRR26643292.3537.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760383, SAMEA5760386
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-35                JAXUCZ010000001.1  182507576-182507610
            36-135              JAXUCZ010000001.1  182510611-182510710
            136-303             JAXUCZ010000001.1  182513488-182513655
            304-426             JAXUCZ010000001.1  182515760-182515882
            427-451             JAXUCZ010000001.1  182517223-182517247
            452-528             JAXUCZ010000001.1  182520630-182520706
            529-657             JAXUCZ010000001.1  182521478-182521606
            658-742             JAXUCZ010000001.1  182527916-182528000
            743-802             JAXUCZ010000001.1  182533581-182533640
            803-899             JAXUCZ010000001.1  182540317-182540413
            900-947             JAXUCZ010000001.1  182541261-182541308
            948-1041            JAXUCZ010000001.1  182542488-182542581
            1042-1119           JAXUCZ010000001.1  182547071-182547148
            1120-1242           JAXUCZ010000001.1  182547544-182547666
            1243-1289           JAXUCZ010000001.1  182553302-182553348
            1290-1401           JAXUCZ010000001.1  182554781-182554892
            1402-1518           JAXUCZ010000001.1  182555989-182556105
            1519-1572           JAXUCZ010000001.1  182557407-182557460
            1573-1653           JAXUCZ010000001.1  182559715-182559795
            1654-1716           JAXUCZ010000001.1  182561256-182561318
            1717-1802           JAXUCZ010000001.1  182562097-182562182
            1803-1883           JAXUCZ010000001.1  182566619-182566699
            1884-1947           JAXUCZ010000001.1  182569291-182569354
            1948-2046           JAXUCZ010000001.1  182571987-182572085
            2047-2124           JAXUCZ010000001.1  182573793-182573870
            2125-2239           JAXUCZ010000001.1  182575347-182575461
            2240-2379           JAXUCZ010000001.1  182588903-182589042
            2380-2545           JAXUCZ010000001.1  182602812-182602977
            2546-2664           JAXUCZ010000001.1  182606146-182606264
            2665-2811           JAXUCZ010000001.1  182610078-182610224
            2812-3109           JAXUCZ010000001.1  182610724-182611021
FEATURES             Location/Qualifiers
     source          1..3109
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="1"
                     /map="1q35"
     gene            1..3109
                     /gene="Vps35l"
                     /note="VPS35 endosomal protein sorting factor like"
                     /db_xref="GeneID:361635"
                     /db_xref="RGD:1564485"
     exon            1..35
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     CDS             19..2910
                     /gene="Vps35l"
                     /note="isoform 1 is encoded by transcript variant 1;
                     UPF0505 protein C16orf62 homolog"
                     /codon_start=1
                     /product="VPS35 endosomal protein-sorting factor-like
                     isoform 1"
                     /protein_id="NP_001386585.1"
                     /db_xref="GeneID:361635"
                     /db_xref="RGD:1564485"
                     /translation="MAVFPWHSRNRNYKAELASCRLETVPLECGDYHPLKPITVTESK
                     TKKVSRKGSTSSTSSSSSSSVVDPLSSVLDGTDPLSMFAATSDPAATVTVTESSRKKR
                     DKDDNSFVGPDFEPWANKRGEILARYTTTEKLSINLFMGSEKGRAGAAASAMSEKVRT
                     RLEELDDFEEGSQKELLNLTQQDYVNRIEELNQSLKDAWASDQKVKALKIVIQCSKLL
                     SDTSVIQFYPSKFVLITDILDTFGKLVYERIYSMCVDSRGALPDHFSPENVNDTAKET
                     CLNWFFKIASIRELIPRFYVEASILKCNKFLSKTGISECLPRLTCMIRGIGDPLVSVY
                     ARAYLCRVGMEVAPHLKESLTRNFFDFLLTFKQIHGDTVQNQLVAQGVELLSYLPLYS
                     PAMGWIFQCVSYHAPEALLTEMMERCKKLGNNALLLNSVMSAFRAEFIATRSMDFIGM
                     IKECDESGFPKHLLFRSLGVNLALADPPENDRLQILNEAWKVITKLKSPQDYINCAEV
                     WVEYTCRHFTKREVNTVLADVIKHMTPDRAFEDSYPQLQSIIKKVIAHFHDFSVLFSV
                     EKFLPFLDMFQKESVRVEVCKCIMEAFIKHQQEPTKDPVILNALLHICKTMHDSVNAL
                     TLEDEKRMLAHLINGFIKMVSFGRDFEQQLSFYVESRSMFCNLEPVLVQLIHSVNRLA
                     METRKVMKGNHSRKTAAFVRACVAYCFITIPSLVGIFTRLNLYLHSGQVALANQCLSQ
                     ADAFFKAAISLVPEVPKSISIDGKLRPSEPFLLEFLCNFFSTLLIVPDHPEHGVLFLV
                     RELLNVIQDYTWEDSSDDKIRIYTSVLHLLSAMSQDTYLYHIDKVDSNDSLYGGDSRF
                     LAENSKLCEAAMVQILEHLKTLAKDEALKRQSLLGLSFFNSILAHGDLRNNKLNQLSV
                     NLWHLAQRHGCADTRTMVKTLDYIKKRSKQPDMNHLSELALRLPLQTRT"
     exon            36..135
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            136..303
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            304..426
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            427..451
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            452..528
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            529..657
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            658..742
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            743..802
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            803..899
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            900..947
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            948..1041
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            1042..1119
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            1120..1242
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            1243..1289
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            1290..1401
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            1402..1518
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            1519..1572
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            1573..1653
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            1654..1716
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            1717..1802
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            1803..1883
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            1884..1947
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            1948..2046
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            2047..2124
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            2125..2239
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            2240..2379
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            2380..2545
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            2546..2664
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            2665..2811
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
     exon            2812..3109
                     /gene="Vps35l"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gatcatgtga ctgggaagat ggctgtcttt ccctggcact ctcggaacag gaactacaag
       61 gcggagctgg cctcttgcag gttggagaca gtgcctctgg agtgtgggga ctaccacccg
      121 ctgaagccca tcactgtcac cgagtcaaag acaaagaaag tgagccggaa aggaagcact
      181 tcatccacat cctcctcctc ctccagctct gtggtcgatc ctctgagcag tgtccttgat
      241 ggcaccgacc ccctatccat gtttgcagcc acctcggacc cagcagccac agtaacagtc
      301 acagaaagct ccagaaagaa acgtgataag gatgacaact cctttgtggg acctgatttt
      361 gagccctggg ccaacaaacg gggcgaaatc cttgcccggt acacaactac ggagaagctg
      421 tctattaatc tgtttatggg atcagaaaaa ggtagagctg gggctgcggc ttctgccatg
      481 tcagagaagg ttcggactcg tctggaagag ctggatgact ttgaggaggg atcccagaag
      541 gagctgctga acctgaccca gcaggattat gtgaaccgca tagaggagct caaccagtct
      601 ctgaaggatg cctgggcctc ggaccagaaa gttaaggctc tgaagattgt cattcagtgc
      661 tcaaagctgc tgtcagacac cagtgttatt cagttctacc caagcaaatt cgtcctcatc
      721 accgacatcc ttgatacgtt tggaaagctg gtctatgagc gcatctactc catgtgtgtg
      781 gacagccgcg gtgccttgcc agatcatttc tctccagaga acgtgaatga tacagccaag
      841 gagacatgcc tgaactggtt tttcaagatc gcttccatcc gggaactcat tccgagattt
      901 tacgtggaag catccatcct gaagtgtaac aaattcctct ccaaaacggg gatttcagag
      961 tgcctgcccc gactaacctg catgatcaga gggattggag atccactcgt gtccgtgtat
     1021 gcccgggcct acctgtgtcg ggtggggatg gaggtggccc cgcacctcaa ggagagcctc
     1081 acgaggaact tctttgactt cctgcttaca tttaaacaga ttcatggaga cactgtccag
     1141 aaccagctgg tggcccaggg tgtggagctg ctgtcctatc tccctctgta ctcgcctgcc
     1201 atgggctgga tcttccagtg tgtctcctac catgctcctg aggctttgct gacggagatg
     1261 atggaaaggt gtaagaaact agggaacaat gctttgctcc tgaactccgt gatgtcagct
     1321 ttcagggctg agttcattgc caccaggtct atggacttca tcggcatgat taaagagtgt
     1381 gacgagtctg gcttccccaa gcatctcctt ttccgttcac tgggcgtaaa cttggccttg
     1441 gcggatcctc ccgagaacga ccgacttcag attctcaatg aagcttggaa agtcatcact
     1501 aaattgaaga gtcctcagga ctacattaat tgtgccgagg tttgggtgga gtacacctgc
     1561 aggcatttca cgaaacgaga agttaacact gttctggctg atgtcatcaa gcacatgact
     1621 ccagatcgag catttgagga ctcctacccc cagcttcagt caataattaa gaaagtcatc
     1681 gcccacttcc acgatttctc agttcttttc tcagtggaaa agtttctacc atttctggac
     1741 atgttccaga aagagagtgt gcgggtggag gtttgcaagt gcataatgga agcctttatc
     1801 aagcaccagc aggagccaac caaggaccct gtcatcctga atgccctttt gcacatttgt
     1861 aagactatgc acgactctgt gaacgctctc actcttgagg atgagaaaag gatgctggcc
     1921 catttgatca atggctttat aaaaatggtg tcctttggcc gtgattttga acagcagctc
     1981 agcttttacg ttgagtccag gtcgatgttt tgtaacctgg aacctgttct tgtgcagttg
     2041 atccatagtg tgaaccggtt ggcaatggaa acaaggaaag tcatgaaggg aaaccactcc
     2101 agaaagacag ctgcgtttgt ccgggcctgt gttgcctact gcttcatcac catcccctcc
     2161 ctggtgggga tcttcacccg cctcaacctc tacctgcatt ctggtcaggt tgccttggcc
     2221 aaccagtgcc tctcccaagc tgatgctttt ttcaaagccg ccatcagcct tgttccggaa
     2281 gtcccaaagt cgataagcat tgatgggaag ctgcggccat cagaaccctt cctcctggaa
     2341 ttcctgtgca atttcttctc taccctattg atcgtgccgg atcatccaga acacggagtc
     2401 ctatttctgg ttcgagaact tctcaacgtt atccaggact atacctggga ggacagtagt
     2461 gacgacaaaa ttcggatcta cacctctgtc ctgcacctgc tgtctgccat gagccaggac
     2521 acctatcttt accacataga caaagttgac tccaatgaca gcctgtacgg gggagactcc
     2581 aggttcctgg ctgagaacag caagctgtgt gaggcagcga tggttcagat cctggagcat
     2641 ctgaaaaccc tggccaagga tgaggccctg aaacgacaga gcttgctggg cctctctttc
     2701 ttcaatagca tcctagccca cggggacctt cgtaacaaca agctgaacca actctctgtc
     2761 aacttgtggc acttggcaca gaggcatggc tgtgcagaca caaggaccat ggtgaaaact
     2821 ctggactaca tcaagaagcg aagcaaacaa cctgacatga atcatctgtc tgagctggcc
     2881 ctgaggctcc ctctgcaaac caggacttga gaacttgccc tttgaggggg gagcccagtg
     2941 ccacgtcctg gaatgcctgc ttggctgtca tcaactcttc ctagaatcta gaggttttgt
     3001 tatttttact tttatacaga ttggttttaa gcttttgcct tctcttgtct attctgacgg
     3061 aaggggaatt gacacagtat taaaacccag tcttgttctt tagatagca
//
