LOCUS       NM_001399770            2556 bp    mRNA    linear   ROD 30-MAR-2024
DEFINITION  Rattus norvegicus VPS33B interacting protein, apical-basolateral
            polarity regulator, spe-39 homolog (Vipas39), transcript variant 1,
            mRNA.
ACCESSION   NM_001399770 XM_006240400
VERSION     NM_001399770.1
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 2556)
  AUTHORS   Banushi,B., Forneris,F., Straatman-Iwanowska,A., Strange,A.,
            Lyne,A.M., Rogerson,C., Burden,J.J., Heywood,W.E., Hanley,J.,
            Doykov,I., Straatman,K.R., Smith,H., Bem,D., Kriston-Vizi,J.,
            Ariceta,G., Risteli,M., Wang,C., Ardill,R.E., Zaniew,M.,
            Latka-Grot,J., Waddington,S.N., Howe,S.J., Ferraro,F., Gjinovci,A.,
            Lawrence,S., Marsh,M., Girolami,M., Bozec,L., Mills,K. and
            Gissen,P.
  TITLE     Regulation of post-Golgi LH3 trafficking is essential for collagen
            homeostasis
  JOURNAL   Nat Commun 7, 12111 (2016)
   PUBMED   27435297
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2556)
  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   3  (bases 1 to 2556)
  AUTHORS   Cullinane,A.R., Straatman-Iwanowska,A., Zaucker,A., Wakabayashi,Y.,
            Bruce,C.K., Luo,G., Rahman,F., Gurakan,F., Utine,E., Ozkan,T.B.,
            Denecke,J., Vukovic,J., Di Rocco,M., Mandel,H., Cangul,H.,
            Matthews,R.P., Thomas,S.G., Rappoport,J.Z., Arias,I.M., Wolburg,H.,
            Knisely,A.S., Kelly,D.A., Muller,F., Maher,E.R. and Gissen,P.
  TITLE     Mutations in VIPAR cause an arthrogryposis, renal dysfunction and
            cholestasis syndrome phenotype with defects in epithelial
            polarization
  JOURNAL   Nat Genet 42 (4), 303-312 (2010)
   PUBMED   20190753
  REMARK    Erratum:[Nat Genet. 2011 Mar;43(3):277]
REFERENCE   4  (bases 1 to 2556)
  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
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000006.1.
            
            On Jan 14, 2022 this sequence version replaced XM_006240400.4.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR22582416.470711.1,
                                           SRR26643291.18652.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA5760383,
                                           SAMEA5760433 [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
            1-141               JAXUCZ010000006.1  112643930-112644070 c
            142-234             JAXUCZ010000006.1  112641239-112641331 c
            235-337             JAXUCZ010000006.1  112639120-112639222 c
            338-478             JAXUCZ010000006.1  112637697-112637837 c
            479-517             JAXUCZ010000006.1  112636124-112636162 c
            518-582             JAXUCZ010000006.1  112634999-112635063 c
            583-639             JAXUCZ010000006.1  112632819-112632875 c
            640-732             JAXUCZ010000006.1  112631597-112631689 c
            733-766             JAXUCZ010000006.1  112631050-112631083 c
            767-869             JAXUCZ010000006.1  112629891-112629993 c
            870-897             JAXUCZ010000006.1  112628647-112628674 c
            898-971             JAXUCZ010000006.1  112627673-112627746 c
            972-1047            JAXUCZ010000006.1  112625783-112625858 c
            1048-1182           JAXUCZ010000006.1  112625092-112625226 c
            1183-1224           JAXUCZ010000006.1  112624022-112624063 c
            1225-1314           JAXUCZ010000006.1  112623649-112623738 c
            1315-1401           JAXUCZ010000006.1  112622436-112622522 c
            1402-1491           JAXUCZ010000006.1  112621879-112621968 c
            1492-1596           JAXUCZ010000006.1  112621380-112621484 c
            1597-2556           JAXUCZ010000006.1  112619228-112620187 c
FEATURES             Location/Qualifiers
     source          1..2556
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="6"
                     /map="6q31"
     gene            1..2556
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /note="VPS33B interacting protein, apical-basolateral
                     polarity regulator, spe-39 homolog"
                     /db_xref="GeneID:681989"
                     /db_xref="RGD:1589291"
     exon            1..141
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     CDS             142..1617
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /note="isoform 1 is encoded by transcript variant 1;
                     protein spe-39 homolog; VPS33B-interacting protein in
                     polarity and apical restriction; spermatogenesis-defective
                     protein 39 homolog; VPS33B-interacting protein in
                     apical-basolateral polarity regulator"
                     /codon_start=1
                     /product="spermatogenesis-defective protein 39 homolog
                     isoform 1"
                     /protein_id="NP_001386699.1"
                     /db_xref="GeneID:681989"
                     /db_xref="RGD:1589291"
                     /translation="MNRTKGDEEEYWNSSKFKAFTFDDEDDELSQLKESKRAVNSLRD
                     FVDDDDDDDLERVSWTGEPVGSISWSIKETAGSSGSTSEGREQMKGRNSFYTQLPKPP
                     STYSLSSFFRGRTRPGSFQSLSDALSDTPAKTYSPELGRPKGEYRDYSNDWSLSDTVR
                     RLRQGKVCSLERFRSLQDKLQLLEEAINMHDGNVITAVLIFLKRTLSKEILFRELEVR
                     QVALRHLIHFLKEIGDQKLLLDLFRFLDRTEELALSHYREHLNIQDPEKRKEFLKTCI
                     GLPFSAEDSAHVQDQYTLLERQIIIEANDRHLESSGQTEIFRKHPRKASILNMPLVTT
                     LFYACFYHYTESEGTFSSPVNLKKTFKIPDRQYVLTALAARAKLRAWNDVDALFTTKN
                     WLGYTKKRAPIGFHRVVEILHKNSAPVQILQEYVNLVEDVDTKLNLATKFKCHDVVID
                     TCRDLKDRQQLLAYRSKVDKGSAEEEKIDVILSSSQIRWKN"
     exon            142..234
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            235..337
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            338..478
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            479..517
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            518..582
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            583..639
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            640..732
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            733..766
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            767..869
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            870..897
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            898..971
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            972..1047
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            1048..1182
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            1183..1224
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            1225..1314
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            1315..1401
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            1402..1491
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            1492..1596
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
     exon            1597..2556
                     /gene="Vipas39"
                     /gene_synonym="hSPE-39; Spe39; Vipar"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gcgtgtgttc ctttcacctt cttcagactc tcttcggctg tccccttcgg cccttctcta
       61 tgccacacag cctgtttaga aaggctggtc cggcggcaga gcctggcgct gtcctgagaa
      121 ggagcgcttg gtgcggaaga gatgaaccgg acaaaaggtg atgaggagga atattggaac
      181 agctccaagt tcaaggcgtt cacttttgac gatgaagatg atgagctctc acagttaaag
      241 gaatccaaac gggcagtgaa tagccttcga gacttcgtgg atgacgacga tgacgatgac
      301 ctggagcgag tcagctggac tggagaacct gtgggaagta tctcatggtc catcaaagag
      361 actgctggga gtagcgggtc aacctctgag ggacgtgaac agatgaaggg ccggaacagc
      421 ttctacacac aactacccaa acctccttcc acctactccc tgagcagctt ctttagaggc
      481 agaactagac ctgggagttt ccagtccctt tctgatgctc tgtcagacac acctgccaaa
      541 acttattctc cagagctggg gaggcctaag ggagagtaca gggattacag caatgactgg
      601 agcctcagtg atacagtgcg acgtctccgc cagggcaagg tctgttcact agagcgcttc
      661 cgctccctcc aggataagct gcagctccta gaggaggcca taaacatgca tgatgggaac
      721 gtcatcactg cagttctgat cttcctgaag aggaccctga gcaaagagat ccttttccga
      781 gagctggagg tacgccaggt cgcactgaga catctcatcc acttccttaa agaaataggg
      841 gaccaaaagc tgcttttaga tctcttcagg ttcctagata gaacagaaga gctggcgcta
      901 tcccattatc gagagcattt gaacattcag gaccctgaaa aacgaaaaga atttcttaag
      961 acgtgcattg gtttgccctt ttcagcggaa gactctgcac acgtgcaaga ccagtacaca
     1021 ctgctggagc gccagatcat catcgaggcc aatgaccgac acctggagtc ttcagggcag
     1081 actgagatct tccggaagca cccccgaaaa gcttccatcc tcaacatgcc actagtgacg
     1141 acactcttct acgcctgctt ctatcactac acggagtccg aggggacctt cagcagtcca
     1201 gtcaacctga agaaaacatt caagatccca gacagacagt atgtgctgac agccttggct
     1261 gcgcgggcca agcttagagc ctggaatgat gtcgatgcct tgttcaccac aaagaactgg
     1321 ttgggttaca ccaagaagag agcacccatt ggcttccatc gagttgtgga aattttgcac
     1381 aagaacagtg cccctgtcca gatattgcag gaatatgtca atctggtgga agatgtggac
     1441 acaaagttga acttagccac taagttcaag tgccatgatg ttgtcattga tacttgccga
     1501 gacctgaagg atcgtcaaca gttgcttgca tacaggagca aagtagataa aggatctgct
     1561 gaggaagaga aaatcgatgt catcctcagc agctcgcaaa ttcgatggaa gaactaaggt
     1621 tcttttgcta ccctgaaagc tgcctcgctt ctcactcttt ctgcctctgg aaacagagag
     1681 ctctcttctt aggagagtca ctgcattcta ccacgggagc ctatcgtcca caggcagtgc
     1741 ctgctggttt ggggacagaa accagccttt gagcacatgt atcttgagac tgatctgtcc
     1801 aggggacatc atctacaggc cagtagctaa ggctttgatt ctcaagaagg atgctctgca
     1861 ccggtgctgt ggaaaggtgg gagcccatgg gtaggatgtc tcgtggtcag aggaaagtga
     1921 ccactccaca agtacatctg gactaagccc caggcgtctc aggatggtcg ggacattcct
     1981 ggtcctttca gctattacta cccagaacct gtgttggaca tgctcatttc tgctctaaag
     2041 ggagtcagaa cagaactaaa gtgactcttc atgggcctca ggaaggaata tcagtattgc
     2101 tcaggacctg ctggaaacca gagtcaagtt ctcaaggcac agggccacac atctatgaca
     2161 gtcacttcct aaacattgtg taccttcagc cagcatccat ctgctgttcc tgtcaacgtt
     2221 gtgtagggat gtgtgaggga tgtagggtcc ctctctcacc tgcacactgt ctgggtgtga
     2281 gccatctgtt tccaacatgt cctctgcttc tctgtcagaa acagttttac ctggaattca
     2341 gattcaccag tgctggagcg ctcttttaga caaaaattat ttcaccagaa gcagccacaa
     2401 gtctcacctg ggctactgta gtagtacttc catttagata tctccacagg ccctgttgcc
     2461 ctgctgagga cttgagcaat gttccatttt gccccgtgcc tccctgaact ggattttccc
     2521 aacgtgtaac attcctaata aaactgttgt attctt
//
