LOCUS       NM_001290283            1773 bp    mRNA    linear   ROD 05-JUN-2024
DEFINITION  Mus musculus phospholipase D family member 6 (Pld6), transcript
            variant 1, mRNA; nuclear gene for mitochondrial product.
ACCESSION   NM_001290283 XM_006532599
VERSION     NM_001290283.1
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 1773)
  AUTHORS   Izumi,N., Shoji,K., Suzuki,Y., Katsuma,S. and Tomari,Y.
  TITLE     Zucchini consensus motifs determine the mechanism of pre-piRNA
            production
  JOURNAL   Nature 578 (7794), 311-316 (2020)
   PUBMED   31996847
  REMARK    GeneRIF: pre-piRNAs are generated by parallel Zucchini-dependent
            and -independent mechanisms; cleavage by Zucchini occurs at
            previously unrecognized consensus motifs on pre-pre-piRNAs,
            requires the RNA helicase Armitage, and is accompanied by
            2'-O-methylation of pre-piRNAs
REFERENCE   2  (bases 1 to 1773)
  AUTHORS   Zhang,P., Qin,Y., Zheng,Y. and Zeng,W.
  TITLE     Phospholipase D Family Member 6 Is a Surface Marker for Enrichment
            of Undifferentiated Spermatogonia in Prepubertal Boars
  JOURNAL   Stem Cells Dev 27 (1), 55-64 (2018)
   PUBMED   29113556
  REMARK    GeneRIF: PLD6 is a surface marker of undifferentiated spermatogonia
            in testes.
REFERENCE   3  (bases 1 to 1773)
  AUTHORS   Chen,Y., Liang,P., Huang,Y., Li,M., Zhang,X., Ding,C., Feng,J.,
            Zhang,Z., Zhang,X., Gao,Y., Zhang,Q., Cao,S., Zheng,H., Liu,D.,
            Songyang,Z. and Huang,J.
  TITLE     Glycerol kinase-like proteins cooperate with Pld6 in regulating
            sperm mitochondrial sheath formation and male fertility
  JOURNAL   Cell Discov 3, 17030 (2017)
   PUBMED   28852571
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1773)
  AUTHORS   Inoue,K., Ichiyanagi,K., Fukuda,K., Glinka,M. and Sasaki,H.
  TITLE     Switching of dominant retrotransposon silencing strategies from
            posttranscriptional to transcriptional mechanisms during male
            germ-cell development in mice
  JOURNAL   PLoS Genet 13 (7), e1006926 (2017)
   PUBMED   28749988
  REMARK    GeneRIF: The Dnmt3l mutation greatly reduced DNA methylation levels
            at most retrotransposons, but its impact on their RNA abundance was
            limited in prospermatogonia. In Pld6 mutant germ cells, although
            only a few retrotransposons exhibited reduced DNA methylation, many
            showed increased expression at the RNA level.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1773)
  AUTHORS   Kabayama,Y., Toh,H., Katanaya,A., Sakurai,T., Chuma,S.,
            Kuramochi-Miyagawa,S., Saga,Y., Nakano,T. and Sasaki,H.
  TITLE     Roles of MIWI, MILI and PLD6 in small RNA regulation in mouse
            growing oocytes
  JOURNAL   Nucleic Acids Res 45 (9), 5387-5398 (2017)
   PUBMED   28115634
  REMARK    GeneRIF: MIWI (or PIWIL1) depletion had a smaller effect. In
            oocytes lacking PLD6 (or ZUCCHINI or MITOPLD), a mitochondrial
            nuclease/phospholipase involved in piRNA biogenesis in male germ
            cells, the piRNA level was decreased to 50% compared to wild-type.
REFERENCE   6  (bases 1 to 1773)
  AUTHORS   Ipsaro,J.J., Haase,A.D., Knott,S.R., Joshua-Tor,L. and Hannon,G.J.
  TITLE     The structural biochemistry of Zucchini implicates it as a nuclease
            in piRNA biogenesis
  JOURNAL   Nature 491 (7423), 279-283 (2012)
   PUBMED   23064227
  REMARK    GeneRIF: crystal structure of mZuc at 1.75 A resolution indicates
            greater architectural similarity to phospholipase-D family
            nucleases than to phospholipases; data suggest that the Zucchini
            proteins act in primary piRNA biogenesis as nucleases, perhaps
            generating the 5' ends of primary piRNAs.
REFERENCE   7  (bases 1 to 1773)
  AUTHORS   Gao,Q. and Frohman,M.A.
  TITLE     Roles for the lipid-signaling enzyme MitoPLD in mitochondrial
            dynamics, piRNA biogenesis, and spermatogenesis
  JOURNAL   BMB Rep 45 (1), 7-13 (2012)
   PUBMED   22281006
  REMARK    GeneRIF: MitoPLD performs a critical function in a pathway that
            creates a specialized form of RNAi required by developing
            spermatocytes to suppress transposon mobilization during meiosis.
            Review article
REFERENCE   8  (bases 1 to 1773)
  AUTHORS   Watanabe,T., Tomizawa,S., Mitsuya,K., Totoki,Y., Yamamoto,Y.,
            Kuramochi-Miyagawa,S., Iida,N., Hoki,Y., Murphy,P.J., Toyoda,A.,
            Gotoh,K., Hiura,H., Arima,T., Fujiyama,A., Sado,T., Shibata,T.,
            Nakano,T., Lin,H., Ichiyanagi,K., Soloway,P.D. and Sasaki,H.
  TITLE     Role for piRNAs and noncoding RNA in de novo DNA methylation of the
            imprinted mouse Rasgrf1 locus
  JOURNAL   Science 332 (6031), 848-852 (2011)
   PUBMED   21566194
REFERENCE   9  (bases 1 to 1773)
  AUTHORS   Huang,H., Gao,Q., Peng,X., Choi,S.Y., Sarma,K., Ren,H., Morris,A.J.
            and Frohman,M.A.
  TITLE     piRNA-associated germline nuage formation and spermatogenesis
            require MitoPLD profusogenic mitochondrial-surface lipid signaling
  JOURNAL   Dev Cell 20 (3), 376-387 (2011)
   PUBMED   21397848
  REMARK    GeneRIF: Data suggest that mitochondrial-surface phosphatidic acid
            generated by MitoPLD/Zuc recruits or activates nuage components
            critical for piRNA production.
REFERENCE   10 (bases 1 to 1773)
  AUTHORS   Watanabe,T., Chuma,S., Yamamoto,Y., Kuramochi-Miyagawa,S.,
            Totoki,Y., Toyoda,A., Hoki,Y., Fujiyama,A., Shibata,T., Sado,T.,
            Noce,T., Nakano,T., Nakatsuji,N., Lin,H. and Sasaki,H.
  TITLE     MITOPLD is a mitochondrial protein essential for nuage formation
            and piRNA biogenesis in the mouse germline
  JOURNAL   Dev Cell 20 (3), 364-375 (2011)
   PUBMED   21397847
  REMARK    GeneRIF: Results indicate a conserved role for MITOPLD/Zuc in the
            piRNA pathway and link mitochondrial membrane metabolism/signaling
            to small RNA biogenesis.
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BC119245.1, AL596204.8 and AW554531.2.
            
            On Mar 5, 2014 this sequence version replaced XM_006532599.1.
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longer isoform (a).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript 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 :: BC145052.1, SRR7652917.172404.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            gene product(s) localized to mito. :: inferred from homology
            RefSeq Select criteria             :: based on conservation,
                                                  expression, longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-436               BC119245.1         1-436
            437-440             AL596204.8         26213-26216
            441-1485            AL596204.8         28209-29253
            1486-1773           AW554531.2         1-288               c
FEATURES             Location/Qualifiers
     source          1..1773
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /db_xref="taxon:10090"
                     /chromosome="11"
                     /map="11 37.79 cM"
     gene            1..1773
                     /gene="Pld6"
                     /gene_synonym="4933433K01Rik; Gm10; mitoPLD; mZuc; Zuc"
                     /note="phospholipase D family member 6"
                     /db_xref="GeneID:194908"
                     /db_xref="MGI:MGI:2687283"
     exon            1..440
                     /gene="Pld6"
                     /gene_synonym="4933433K01Rik; Gm10; mitoPLD; mZuc; Zuc"
                     /inference="alignment:Splign:2.1.0"
     CDS             23..688
                     /gene="Pld6"
                     /gene_synonym="4933433K01Rik; Gm10; mitoPLD; mZuc; Zuc"
                     /EC_number="3.1.4.4"
                     /note="isoform a is encoded by transcript variant 1;
                     phospholipase D6; mitochondrial cardiolipin hydrolase;
                     novel Phospholipase D Active site motif-containing
                     protein; protein zucchini homolog; choline phosphatase 6;
                     phosphatidylcholine-hydrolyzing phospholipase D6;
                     mitochondrial phospholipase"
                     /codon_start=1
                     /product="mitochondrial cardiolipin hydrolase isoform a"
                     /protein_id="NP_001277212.1"
                     /db_xref="CCDS:CCDS70199.1"
                     /db_xref="GeneID:194908"
                     /db_xref="MGI:MGI:2687283"
                     /translation="MGRSSWRLVFAAGAGLALALEALPWLMRWLLAGRRPRREVLFFP
                     SQVTCTEALLQAPGLPPGPSGCPCSLPHSESSLSRLLRALLAARSSLELCLFAFSSPQ
                     LGRAVQLLHQRGVRVRVITDCDYMALNGSQIGLLRKAGIQVRHDQDLGYMHHKFAIVD
                     KKVLITGSLNWTTQAIQNNRENVLIMEDTEYVRLFLEEFERIWEEFDPTKYSFFPQKH
                     RGH"
     exon            441..1773
                     /gene="Pld6"
                     /gene_synonym="4933433K01Rik; Gm10; mitoPLD; mZuc; Zuc"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1465..1470
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Pld6"
                     /gene_synonym="4933433K01Rik; Gm10; mitoPLD; mZuc; Zuc"
                     /note="hexamer: ATTAAA"
     polyA_site      1486
                     /gene="Pld6"
                     /gene_synonym="4933433K01Rik; Gm10; mitoPLD; mZuc; Zuc"
                     /note="major polyA site"
     regulatory      1749..1754
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Pld6"
                     /gene_synonym="4933433K01Rik; Gm10; mitoPLD; mZuc; Zuc"
                     /note="hexamer: AATAAA"
     polyA_site      1769
                     /gene="Pld6"
                     /gene_synonym="4933433K01Rik; Gm10; mitoPLD; mZuc; Zuc"
                     /note="major polyA site"
ORIGIN      
        1 gctgacctta gaggtggcgg ccatggggcg ctcgagttgg cggttggtgt tcgcggctgg
       61 tgcgggtctc gcgctggccc tagaggcact gccgtggctg atgcgttggc tgctggctgg
      121 gcggcggcca aggcgcgagg tgctcttctt cccctcacag gtgacctgca ccgaggcttt
      181 actgcaggcc ccagggttgc ctcccgggcc ctcgggctgc ccgtgtagcc tcccccacag
      241 cgagagttca ctgagccgcc tgctgcgcgc gctgttggcc gcccgctcca gcttggagct
      301 ctgcctcttc gccttctcca gcccgcagct ggggcgtgca gtgcagctgc tgcatcagcg
      361 tggggtgcgc gtgcgggtca tcactgactg cgactacatg gccctcaacg gctctcagat
      421 cggcctgctg cgcaaggcag ggatacaggt acggcacgac caggacctag gctacatgca
      481 ccacaagttt gccatcgttg acaagaaggt gctcatcacc ggctccctca actggaccac
      541 acaggccatc cagaacaacc gggagaacgt cctgattatg gaggacaccg agtatgtgcg
      601 gctgttcctg gaggagtttg agcgcatctg ggaagaattt gaccccacca agtacagctt
      661 tttcccccaa aagcatcgag ggcactgacc ctgctttgtt tgctcctctt ccagcttgtg
      721 cttgtgatgt cccctcctgc tttgcatgag cctttcctgg ctggctgggg agcagctgcc
      781 agtcttcctg tgcatgcagc cccagcagaa gttaggaagg tgacagtgtt ggacagtact
      841 gtaggctccc tagtacttgc ctagataggc agcatcctct cctgggcatc actagacagg
      901 cctcagagtg cattggccct tgtctccaag gcagtgttta gtcgctggtg ggcactaccc
      961 attggccacg cctgcagctt gcccaggctt tgctttgctt gtccgtgccc ctcacacgta
     1021 gagccagact gtggacttgg gaggggcctc gcctctagcc ctgtggtgga ctctgcgttt
     1081 actcagtagt ggatcagaag ctgacgacaa agggaaccct ggaggtaagc aggctgccca
     1141 ggctgttacc tcagctctgc tgggcactga caggagtcgg aggaacagct tctcgcgcac
     1201 atctgtgaca tgagttgcat tttgtcattg ttcatgcttg tgtgcacgac aaactccatg
     1261 cggctcctga cgtgtctgtc ctttaactta acagcagaca ctgtgcaatg catgttttct
     1321 cacttaaaaa catttttttg gggggtgggg gtggaaggag gtggggaggg tctcactctg
     1381 tagccctggc taacctggaa ctcactatgt agtctaggct agtcttcagt tcagagatct
     1441 gccgggtttg cttcaagcac tgggattaaa ggcgtgcacc accagaccct gctgttttcg
     1501 cacttttttt ttcttttttt ttttttttaa ggaaaggaaa gaggaaggga gagtgggggg
     1561 agcatgttgg agtaacaagt cctgatatcc ccttcttggg ccacccttag cctctcttcc
     1621 tcaggtcctc aatcccatgt tttcacactt tttaacgttc cttttactta gtgttagaca
     1681 agtaaacttg atgttgattt tccaaaagat tgaacagaaa cggagaccct taacttgtgg
     1741 catatttcaa taaatatttt caagtatgag ctg
//
