LOCUS       NM_175562               2971 bp    mRNA    linear   ROD 06-AUG-2024
DEFINITION  Mus musculus RAB39, member RAS oncogene family (Rab39), mRNA.
ACCESSION   NM_175562
VERSION     NM_175562.3
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 2971)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 2971)
  AUTHORS   Cruz,F.M., Colbert,J.D. and Rock,K.L.
  TITLE     The GTPase Rab39a promotes phagosome maturation into MHC-I
            antigen-presenting compartments
  JOURNAL   EMBO J 39 (2), e102020 (2020)
   PUBMED   31821587
REFERENCE   3  (bases 1 to 2971)
  AUTHORS   Dickinson,M.E., Flenniken,A.M., Ji,X., Teboul,L., Wong,M.D.,
            White,J.K., Meehan,T.F., Weninger,W.J., Westerberg,H., Adissu,H.,
            Baker,C.N., Bower,L., Brown,J.M., Caddle,L.B., Chiani,F., Clary,D.,
            Cleak,J., Daly,M.J., Denegre,J.M., Doe,B., Dolan,M.E., Edie,S.M.,
            Fuchs,H., Gailus-Durner,V., Galli,A., Gambadoro,A., Gallegos,J.,
            Guo,S., Horner,N.R., Hsu,C.W., Johnson,S.J., Kalaga,S., Keith,L.C.,
            Lanoue,L., Lawson,T.N., Lek,M., Mark,M., Marschall,S., Mason,J.,
            McElwee,M.L., Newbigging,S., Nutter,L.M., Peterson,K.A.,
            Ramirez-Solis,R., Rowland,D.J., Ryder,E., Samocha,K.E.,
            Seavitt,J.R., Selloum,M., Szoke-Kovacs,Z., Tamura,M., Trainor,A.G.,
            Tudose,I., Wakana,S., Warren,J., Wendling,O., West,D.B., Wong,L.,
            Yoshiki,A., MacArthur,D.G., Tocchini-Valentini,G.P., Gao,X.,
            Flicek,P., Bradley,A., Skarnes,W.C., Justice,M.J., Parkinson,H.E.,
            Moore,M., Wells,S., Braun,R.E., Svenson,K.L., de Angelis,M.H.,
            Herault,Y., Mohun,T., Mallon,A.M., Henkelman,R.M., Brown,S.D.,
            Adams,D.J., Lloyd,K.C., McKerlie,C., Beaudet,A.L., Bucan,M. and
            Murray,S.A.
  CONSRTM   International Mouse Phenotyping Consortium; Jackson Laboratory;
            Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris
            (ICS); Charles River Laboratories; MRC Harwell; Toronto Centre for
            Phenogenomics; Wellcome Trust Sanger Institute; RIKEN BioResource
            Center
  TITLE     High-throughput discovery of novel developmental phenotypes
  JOURNAL   Nature 537 (7621), 508-514 (2016)
   PUBMED   27626380
  REMARK    Erratum:[Nature. 2017 Nov 16;551(7680):398. doi:
            10.1038/nature24643. PMID: 29144450]
REFERENCE   4  (bases 1 to 2971)
  AUTHORS   Koscielny,G., Yaikhom,G., Iyer,V., Meehan,T.F., Morgan,H.,
            Atienza-Herrero,J., Blake,A., Chen,C.K., Easty,R., Di Fenza,A.,
            Fiegel,T., Grifiths,M., Horne,A., Karp,N.A., Kurbatova,N.,
            Mason,J.C., Matthews,P., Oakley,D.J., Qazi,A., Regnart,J.,
            Retha,A., Santos,L.A., Sneddon,D.J., Warren,J., Westerberg,H.,
            Wilson,R.J., Melvin,D.G., Smedley,D., Brown,S.D., Flicek,P.,
            Skarnes,W.C., Mallon,A.M. and Parkinson,H.
  TITLE     The International Mouse Phenotyping Consortium Web Portal, a
            unified point of access for knockout mice and related phenotyping
            data
  JOURNAL   Nucleic Acids Res 42 (Database issue), D802-D809 (2014)
   PUBMED   24194600
REFERENCE   5  (bases 1 to 2971)
  AUTHORS   Seto,S., Sugaya,K., Tsujimura,K., Nagata,T., Horii,T. and Koide,Y.
  TITLE     Rab39a interacts with phosphatidylinositol 3-kinase and negatively
            regulates autophagy induced by lipopolysaccharide stimulation in
            macrophages
  JOURNAL   PLoS One 8 (12), e83324 (2013)
   PUBMED   24349490
  REMARK    GeneRIF: These results suggest that Rab39a negatively regulates the
            LPS-induced autophagy in macrophages
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2971)
  AUTHORS   Giannandrea,M., Bianchi,V., Mignogna,M.L., Sirri,A., Carrabino,S.,
            D'Elia,E., Vecellio,M., Russo,S., Cogliati,F., Larizza,L.,
            Ropers,H.H., Tzschach,A., Kalscheuer,V., Oehl-Jaschkowitz,B.,
            Skinner,C., Schwartz,C.E., Gecz,J., Van Esch,H., Raynaud,M.,
            Chelly,J., de Brouwer,A.P., Toniolo,D. and D'Adamo,P.
  TITLE     Mutations in the small GTPase gene RAB39B are responsible for
            X-linked mental retardation associated with autism, epilepsy, and
            macrocephaly
  JOURNAL   Am J Hum Genet 86 (2), 185-195 (2010)
   PUBMED   20159109
REFERENCE   7  (bases 1 to 2971)
  AUTHORS   Itoh,T., Satoh,M., Kanno,E. and Fukuda,M.
  TITLE     Screening for target Rabs of TBC (Tre-2/Bub2/Cdc16)
            domain-containing proteins based on their Rab-binding activity
  JOURNAL   Genes Cells 11 (9), 1023-1037 (2006)
   PUBMED   16923123
REFERENCE   8  (bases 1 to 2971)
  AUTHORS   Fukuda,M.
  TITLE     Distinct Rab binding specificity of Rim1, Rim2, rabphilin, and
            Noc2. Identification of a critical determinant of Rab3A/Rab27A
            recognition by Rim2
  JOURNAL   J Biol Chem 278 (17), 15373-15380 (2003)
   PUBMED   12578829
REFERENCE   9  (bases 1 to 2971)
  AUTHORS   Fukuda,M., Kuroda,T.S. and Mikoshiba,K.
  TITLE     Slac2-a/melanophilin, the missing link between Rab27 and myosin Va:
            implications of a tripartite protein complex for melanosome
            transport
  JOURNAL   J Biol Chem 277 (14), 12432-12436 (2002)
   PUBMED   11856727
REFERENCE   10 (bases 1 to 2971)
  AUTHORS   Kuroda,T.S., Fukuda,M., Ariga,H. and Mikoshiba,K.
  TITLE     The Slp homology domain of synaptotagmin-like proteins 1-4 and
            Slac2 functions as a novel Rab27A binding domain
  JOURNAL   J Biol Chem 277 (11), 9212-9218 (2002)
   PUBMED   11773082
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AC158384.2.
            
            On Mar 21, 2007 this sequence version replaced NM_175562.2.
            
            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.
            
            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 :: AK049038.1, BC049787.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-344               AC158384.2         149072-149415       c
            345-2971            AC158384.2         127293-129919       c
FEATURES             Location/Qualifiers
     source          1..2971
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="9"
                     /map="9 29.12 cM"
     gene            1..2971
                     /gene="Rab39"
                     /gene_synonym="C230094F14Rik; Rab39a"
                     /note="RAB39, member RAS oncogene family"
                     /db_xref="GeneID:270160"
                     /db_xref="MGI:MGI:2442855"
     exon            1..344
                     /gene="Rab39"
                     /gene_synonym="C230094F14Rik; Rab39a"
                     /inference="alignment:Splign:2.1.0"
     exon            345..2971
                     /gene="Rab39"
                     /gene_synonym="C230094F14Rik; Rab39a"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2921..2926
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Rab39"
                     /gene_synonym="C230094F14Rik; Rab39a"
                     /note="hexamer: TATAAA"
     polyA_site      2943
                     /gene="Rab39"
                     /gene_synonym="C230094F14Rik; Rab39a"
                     /note="major polyA site"
ORIGIN      
        1 aggcggcggc cgcagccgca ggaagatgct ggaagcgggc gggcgcgcgc cgcgtaggtg
       61 ctgaagggac agttccttag gcagaacttg ctcctgagcg cacggggcac gtaggcgatg
      121 gagactattt ggatctatca gttccgcctt attgtgatcg gagactccac ggtgggcaag
      181 tcgtgccttc tgcaccgctt cacccagggc cgcttcccag ggctgcactc ccccgcctgc
      241 gaccccacag tcggcgtgga cttcttctcg cgcctgctgg agattgagcc gggcaagagg
      301 atcaagctgc agctctggga cacggcgggg caggagcgct tcagatcaat aactcgatcc
      361 tattaccgca actcagttgg aggattttta gtgtttgaca ttactaaccg acggtctttt
      421 gaacatgtga aagattggct agaagaagca aaaatgcatg tacagccttt tcagattgta
      481 tttctactgg tgggacataa atgtgacctg gcttcgcaac gccaggtttc aagggaagaa
      541 gctgaaagac tgtcaacaga ctgtggaatg aagtacatag agacctcagc caaggacgcg
      601 acaaacgttg aagagtcctt tacaatcctg acaagagaca tatatgagct tatcaaaaaa
      661 ggagagattt gtattcagga tggatgggaa ggggttaaaa gtggtttcgt tccaaatact
      721 gtgcattctt ctgaggaagc agtcaagccc agaaaagagt gcttctgttg acttcaacct
      781 gctgaagaac taccacagac agaccgtgcc actctggata gatgtcaaca ttcacagcag
      841 aatgatgcag ggagtgaacg ccctcaaaca tccagacccg tttcataagc tggtggacac
      901 aacactgtgt ctcaccactt ataccaacag gctgggtagt ctgctaagtt aggaggaaaa
      961 ggagacaact tttctcttga aaccagggtc tacaaaatta catccattct cactttgtta
     1021 gcatagagct gaccttaatg tccagatatg tcagtattta ttatctttct tgacagctga
     1081 aaatagattt tttgtacata tgtaatccct ctgaaaagaa tgtatcagga tttagattct
     1141 cctgggttag ctagtattga atacaaagtg cacttgaagg gccaatgagg tgactcactg
     1201 ggtaaagaag cttgccacca aatctataga cttgagcttc atccctgggg cccgtgtggt
     1261 agaaggaaag aacccacttc ccttgaagtt gtccccagac cacatgcgca ctgtcataca
     1321 catgcacata cagatacaca tgagcaagta caggcccata cactacataa tggtgaagat
     1381 acgtatggtc caacctgaag gctgtgcctg tggctcagtg atagaatgtt cctttagctc
     1441 tgaaaaccca gatccaatcc cctgcatcaa aactagagca ggaaaaaggc agagtaccta
     1501 gaagccgtct tagaaatact gactaggact aaaatataaa ttttctattc aaagaagcag
     1561 agttgccatt cttggaacat aataagtttt atattcccct tgtgttcctg gattttttgc
     1621 tcctggaatc tccacaatta ataagggatg tgaatgttca aaggagatgc tttaggcgaa
     1681 tattgtaagg gaataaaaag gatcacttta tcaaatactt tgatgttata gtacattgtc
     1741 caaatttaac aatgcatata tactgacatt tccaaagaaa aaaatacagt ttaccttgaa
     1801 ctacttttaa aattatcaac atacatagta ttttttccag atttccaaat tatcccattt
     1861 ccagtaaaag tgtggacaag atgttctgaa caagaaaaat ggcgttagaa actcgattta
     1921 gcattcataa ttcattatat aaactcattt gtagaaggga agataaaata gttaagtgaa
     1981 taaaataatg ttcaagttca attctttttt aaaaaacaat attattgttt ttcttcttta
     2041 cagatagttc ttctatatag ctcagatcca cttgcctcag tctcccaagt gctggatatg
     2101 tggcaccatg cccagctcct taatttttag catgggggtc aagaccaggt ctcactctgg
     2161 gaggccttgt ggacctcaaa ctcagtatgt agactcagct agatgtaaac tcaagagatc
     2221 tgcctgcctc tgcctctgtg tgctgggatt caaggtttta acttactgct tgaacatgca
     2281 tggaaaggac attttataag tgttatatat tttataatat gtatacctgt tctatgctat
     2341 aaattgcaaa gtgtatctaa ctacccaatg aagctgactt tttgacattg taaggctctt
     2401 attcttaaac catagtaacc ttatgtgtac aaaaagcaaa atggtttagt gtaaagaata
     2461 ttaagcaaga aaacagagaa catagctcta agcttacctt tgctcatttt tttttctggt
     2521 ttataaaatg agcctaccag actcatttat tgaattctat ggagctattc tgaaaatcaa
     2581 gcaaatggtg ttaaaactat ttgggtgcag aaagcataat acaagtgttt tgctggttct
     2641 ggacatgtcc ttatatttac aatgaagaca gattttcttg agttctttct tgttatttct
     2701 gtgtggagat accagaagac agtgtgtgtt ttcacggacc aggggagctc ttggctggtg
     2761 tttgtcctct gtccttctac cttgaactgc tgctgaatca ctgcttctct aaagcataaa
     2821 caatagagaa gaaaaccctt gggaaactaa ttcaaccaaa aagttgtatc tggaaatatt
     2881 ttgtgcaacg ttgaagtagg tatttaattg tattttaaaa tataaacact tgtacatttt
     2941 ctagatttgt gtatttttaa tagtacccat g
//
