LOCUS       NM_028200               2842 bp    mRNA    linear   ROD 30-APR-2024
DEFINITION  Mus musculus VPS9 domain containing 1 (Vps9d1), transcript variant
            2, mRNA.
ACCESSION   NM_028200 XM_902711 XM_925142
VERSION     NM_028200.2
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 2842)
  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 2842)
  AUTHORS   Horiuchi,K., Perez-Cerezales,S., Papasaikas,P., Ramos-Ibeas,P.,
            Lopez-Cardona,A.P., Laguna-Barraza,R., Fonseca Balvis,N.,
            Pericuesta,E., Fernandez-Gonzalez,R., Planells,B., Viera,A.,
            Suja,J.A., Ross,P.J., Alen,F., Orio,L., Rodriguez de Fonseca,F.,
            Pintado,B., Valcarcel,J. and Gutierrez-Adan,A.
  TITLE     Impaired Spermatogenesis, Muscle, and Erythrocyte Function in U12
            Intron Splicing-Defective Zrsr1 Mutant Mice
  JOURNAL   Cell Rep 23 (1), 143-155 (2018)
   PUBMED   29617656
REFERENCE   3  (bases 1 to 2842)
  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   4  (bases 1 to 2842)
  AUTHORS   Yokoyama,S., Ito,Y., Ueno-Kudoh,H., Shimizu,H., Uchibe,K.,
            Albini,S., Mitsuoka,K., Miyaki,S., Kiso,M., Nagai,A., Hikata,T.,
            Osada,T., Fukuda,N., Yamashita,S., Harada,D., Mezzano,V., Kasai,M.,
            Puri,P.L., Hayashizaki,Y., Okado,H., Hashimoto,M. and Asahara,H.
  TITLE     A systems approach reveals that the myogenesis genome network is
            regulated by the transcriptional repressor RP58
  JOURNAL   Dev Cell 17 (6), 836-848 (2009)
   PUBMED   20059953
REFERENCE   5  (bases 1 to 2842)
  AUTHORS   Yaoi,T., Itoh,K., Nakamura,K., Ogi,H., Fujiwara,Y. and Fushiki,S.
  TITLE     Genome-wide analysis of epigenomic alterations in fetal mouse
            forebrain after exposure to low doses of bisphenol A
  JOURNAL   Biochem Biophys Res Commun 376 (3), 563-567 (2008)
   PUBMED   18804091
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AK032561.1, BU053861.1, AK028751.1, AK005046.2 and BQ033590.1.
            
            On Jul 17, 2015 this sequence version replaced NM_028200.1.
            
            Transcript Variant: This variant (2) uses an alternate in-frame
            splice site in the 3' coding region compared to variant 1. It
            encodes isoform 2, which is shorter than isoform 1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AY751521.1, AK028751.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMN00849374,
                                           SAMN00849375 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-47                AK032561.1         4-50
            48-105              BU053861.1         2-59
            106-2133            AK028751.1         2-2029
            2134-2237           AK005046.2         2039-2142
            2238-2824           AK028751.1         2135-2721
            2825-2842           BQ033590.1         1-18                c
FEATURES             Location/Qualifiers
     source          1..2842
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="8"
                     /map="8 72.09 cM"
     gene            1..2842
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /note="VPS9 domain containing 1"
                     /db_xref="GeneID:72325"
                     /db_xref="MGI:MGI:1914143"
     exon            1..235
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     CDS             137..2086
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /note="isoform 2 is encoded by transcript variant 2; 5-day
                     ovary-specific transcript 1 protein; VSP9 domain
                     containing 1; VPS9 domain-containing protein 1"
                     /codon_start=1
                     /product="VPS9 domain-containing protein 1 isoform 2"
                     /protein_id="NP_082476.1"
                     /db_xref="CCDS:CCDS52698.1"
                     /db_xref="GeneID:72325"
                     /db_xref="MGI:MGI:1914143"
                     /translation="MAAAAGDGGAKPLQSAMKLANKAIELDTGNRPREAYVEYLRSIH
                     YISQVLLEDVENTTEAGETVPPETSKMLKLAEQCLERAQSTATKLGRICLKPAVPAAP
                     PTPLPTSRHRRVCSDEGGKLSPFLPPEIFQKLQVAESQNSKKELTPLEKASLQNQKLR
                     ATYEARMARLDPSQAMQKTSLTLSLQRQMMENLVIAKAREETLQRKMEERRLRLQEAA
                     NRRFCSQVALTPEEREQRALYAAILEYEQDHDWPKHWRAKLKRSPGDLSLVTSLLSHL
                     LSLPDHPISQLLKKLQCAVYSALYPIVSRAATSAAPAPGSCSLPPEANGLLAPGSRRL
                     RSSQSLYCMLSPSEPSAAPRVLDGPPPTPSVPTLHSGPLDREADGSPAGPSSPLVDAL
                     SHLPDKDSSFEDLEQFLAMSEPQTPGAKREPLLECLKSTVKDIHNAIDRLLSLTLLAF
                     ESLNTATSKDRCLACIEEPFFSPLWPLLLALYRSVHRTREAAVSRSMELYRNAPPTAL
                     GIPTKLLPRVPEAQASTYPYCTAAQELGLLVLESCPQKKLECIVRTLRVICICAEDYC
                     RAQEARPEGESQPPAAAIGADDLLPILSFVVLRSGLPQLVSECAALEEFTHEGYLIGE
                     EGYCLTSLQSALSYVELLSRGRLDK"
     exon            236..311
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     exon            312..404
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     exon            405..567
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     exon            568..679
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     exon            680..742
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     exon            743..795
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     exon            796..883
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     exon            884..969
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     exon            970..1454
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     exon            1455..1584
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     exon            1585..1790
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     exon            1791..1887
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     exon            1888..1992
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     exon            1993..2826
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2804..2809
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /note="hexamer: AATAAA"
     polyA_site      2826
                     /gene="Vps9d1"
                     /gene_synonym="1300018I17Rik; 2410004N05Rik; 5DOS1;
                     Vsp9d1"
                     /note="major polyA site"
ORIGIN      
        1 gtgtccgggt ccccttccgg cggtgcgcag ctcctgcgcc tccctcagct ccgcgctccg
       61 cgttccggtc tggaggcgtc cgccccgtcc cgcccctgcc gccgcggcct cccgctcccc
      121 gcccccgccc agcgccatgg ccgctgcggc cggggacggc ggggcgaagc cactgcagag
      181 cgccatgaaa ctggccaaca aggccatcga gctagacacc ggcaaccggc cccgggaagc
      241 gtacgtggaa tacctgcgca gcatccacta catctcccag gtattgctcg aagacgtgga
      301 aaacactaca gaagctgggg aaactgtgcc ccctgagacc tcaaagatgc taaagctggc
      361 tgaacagtgt ctggagcggg cccagtcaac agctaccaag cttgggagaa tatgcctgaa
      421 gccagccgta cctgcggctc ctcccacacc cttgccaacc agcagacacc gccgagtgtg
      481 ttcagatgaa ggggggaagc tgtctccttt cctgccccct gagatcttcc agaagctgca
      541 ggtggcagaa tcacaaaact ctaagaagga gctgacacca ctggagaagg cctccctaca
      601 aaaccagaag ctgagggcca catatgaggc ccggatggcc cgtctggacc ccagccaggc
      661 catgcagaag acatcgctga ccctgtctct acagcggcag atgatggaga atctggtgat
      721 cgccaaagca agagaagaga cactgcagcg gaagatggag gagcgccgcc tgcgccttca
      781 ggaggctgcc aacaggaggt tctgcagtca agttgctctg accccagagg agcgggagca
      841 gcgagccctc tatgctgcca tcttggagta tgagcaagac catgactggc caaaacactg
      901 gagagccaag ctcaagcgga gtccaggaga cctgtcgcta gtgaccagcc tgctctccca
      961 cttgctcagc cttcctgatc acccaatctc ccagctcctg aagaagctgc agtgtgcggt
     1021 atacagtgcg ctgtatccga ttgtgagccg ggctgccacc agtgccgcgc ctgccccagg
     1081 cagctgctcc ctgcccccag aagccaacgg cctcctggcc cctgggagcc gtcgacttcg
     1141 gtcctcccag agcctctact gcatgctttc cccctccgag cccagtgcag ccccacgagt
     1201 gctggatgga cctcctccca cgccctctgt ccccacactc cactcaggcc ccttggacag
     1261 agaggcagac ggcagcccag cagggccctc ctcaccccta gtagatgctt tatcccacct
     1321 gccagacaag gacagctcct ttgaggatct ggaacagttt ttggctatgt ctgagcctca
     1381 gaccccagga gcaaagaggg aacccttgtt ggagtgtctg aagagcacag tcaaggacat
     1441 tcacaatgcc attgatagac tgctctcgct gacccttttg gccttcgaaa gcctgaacac
     1501 agccacctcc aaagaccgct gcctggcctg catcgaggag cccttcttct ccccactgtg
     1561 gcccctgctg ctggccctct acaggagtgt gcaccgtacc cgggaggccg ctgtaagcag
     1621 gagcatggag ctgtacagga acgcaccccc tacagcccta ggcatcccca ccaagctcct
     1681 cccacgagtt cctgaggctc aagcctccac ctacccctac tgcactgcag cccaggagct
     1741 ggggctgctg gtcttggaga gctgccctca gaagaagctc gagtgcatcg tgcggacgct
     1801 gcgggtcatc tgcatctgtg cagaagacta ctgccgtgcc caagaggcca ggcctgaggg
     1861 tgaatcccag ccccctgccg ctgccatcgg tgctgatgac ttgctgccca tcctgtcctt
     1921 cgtggtgctg agaagcggcc tcccccagct ggtgtcagag tgtgcggccc tggaagagtt
     1981 cactcatgag gggtacttga ttggagaaga agggtattgt ctgacatcac tgcagagcgc
     2041 cctgagctat gtggaacttc tgtcccgggg acggctggac aagtagtggt ggctggacct
     2101 cacagaccaa aggagccacg ggacctccac gctgcactgc atatctggtg tggggacact
     2161 gaaggccagc ttgctgtggt agcactctat agcacttgct caccttcttt accatgcatc
     2221 tgtcctggag gcctaggaca gtgcctcttt aacagggcat ggctggctga gtcaggcctg
     2281 ccccagaccc cataggagaa atctagctgc cgttccctgg ggagcctgca gcactgattg
     2341 atggctctga cctcttctca tggacactag gcagccccca ctggggtatc agcacagaaa
     2401 tgggtattgg gaaccttgcc gggccaatct agttttacat gcctccagtc tcctgagaca
     2461 gcccaagttt gtgtgagcca gtttcttgtt agtcacaagt gggctttacc ctgcccccag
     2521 agaactgggt gtaggtagtg tgaggctgta ctgtttattt accaggtagc aactgccctg
     2581 tttgcttttg ctggcccggg tgtcactgcc caggcctggg ttatgagcct ttctcctacc
     2641 aaggtccagg acatcctgcc ctgggcttat cttggttggg gacagtgaaa tatgttcagg
     2701 acactggcta acaaatacag ttgtacagac tcttcaatgt cagagtctag aggtcagccc
     2761 ctagactgtt atatgtctcc aagtggctac caactcagcc taaaataaag aagtcactct
     2821 accgaaaaaa aaaaaaaaaa aa
//
