LOCUS       NM_001357711            3703 bp    mRNA    linear   ROD 02-MAY-2024
DEFINITION  Mus musculus tudor and KH domain containing protein (Tdrkh),
            transcript variant 2, mRNA.
ACCESSION   NM_001357711 XM_006502138
VERSION     NM_001357711.1
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 3703)
  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 3703)
  AUTHORS   Gainetdinov,I., Colpan,C., Cecchini,K., Arif,A., Jouravleva,K.,
            Albosta,P., Vega-Badillo,J., Lee,Y., Ozata,D.M. and Zamore,P.D.
  TITLE     Terminal modification, sequence, length, and PIWI-protein identity
            determine piRNA stability
  JOURNAL   Mol Cell 81 (23), 4826-4842 (2021)
   PUBMED   34626567
REFERENCE   3  (bases 1 to 3703)
  AUTHORS   Ding,D., Liu,J., Dong,K., Melnick,A.F., Latham,K.E. and Chen,C.
  TITLE     Mitochondrial membrane-based initial separation of MIWI and MILI
            functions during pachytene piRNA biogenesis
  JOURNAL   Nucleic Acids Res 47 (5), 2594-2608 (2019)
   PUBMED   30590800
  REMARK    GeneRIF: we show that mitochondria-anchored TDRKH controls multiple
            steps of pachytene piRNA biogenesis in mice. TDRKH specifically
            recruits MIWI, but not MILI, to engage the piRNA pathway. It is
            required for the production of the entire MIWI-bound piRNA
            population and enables trimming of MILI-bound piRNAs.
REFERENCE   4  (bases 1 to 3703)
  AUTHORS   Zhang,H., Liu,K., Izumi,N., Huang,H., Ding,D., Ni,Z., Sidhu,S.S.,
            Chen,C., Tomari,Y. and Min,J.
  TITLE     Structural basis for arginine methylation-independent recognition
            of PIWIL1 by TDRD2
  JOURNAL   Proc Natl Acad Sci U S A 114 (47), 12483-12488 (2017)
   PUBMED   29118143
  REMARK    GeneRIF: Unlike most other Tudor domains TDRD2 preferentially
            recognizes an unmethylated arginine-rich sequence from PIWIL1.
REFERENCE   5  (bases 1 to 3703)
  AUTHORS   Ding,D., Liu,J., Dong,K., Midic,U., Hess,R.A., Xie,H.,
            Demireva,E.Y. and Chen,C.
  TITLE     PNLDC1 is essential for piRNA 3' end trimming and transposon
            silencing during spermatogenesis in mice
  JOURNAL   Nat Commun 8 (1), 819 (2017)
   PUBMED   29018194
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3703)
  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   7  (bases 1 to 3703)
  AUTHORS   Saxe,J.P., Chen,M., Zhao,H. and Lin,H.
  TITLE     Tdrkh is essential for spermatogenesis and participates in primary
            piRNA biogenesis in the germline
  JOURNAL   EMBO J 32 (13), 1869-1885 (2013)
   PUBMED   23714778
  REMARK    GeneRIF: Loss of Tdrkh is associated with impaired spermatogenesis.
REFERENCE   8  (bases 1 to 3703)
  AUTHORS   Chen,C., Jin,J., James,D.A., Adams-Cioaba,M.A., Park,J.G., Guo,Y.,
            Tenaglia,E., Xu,C., Gish,G., Min,J. and Pawson,T.
  TITLE     Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor
            domain to arginine methylated Miwi
  JOURNAL   Proc Natl Acad Sci U S A 106 (48), 20336-20341 (2009)
   PUBMED   19918066
REFERENCE   9  (bases 1 to 3703)
  AUTHORS   Cote,J. and Richard,S.
  TITLE     Tudor domains bind symmetrical dimethylated arginines
  JOURNAL   J Biol Chem 280 (31), 28476-28483 (2005)
   PUBMED   15955813
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC122808.3 and BC057030.1.
            
            On Nov 4, 2017 this sequence version replaced XM_006502138.3.
            
            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.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC057030.1, SRR1660821.74222.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849381, SAMN00849382
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            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
            1-52                AC122808.3         123358-123409       c
            53-1084             BC057030.1         1-1032
            1085-1087           AC122808.3         108740-108742       c
            1088-3144           BC057030.1         1036-3092
            3145-3703           AC122808.3         104003-104561       c
FEATURES             Location/Qualifiers
     source          1..3703
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="3"
                     /map="3 40.62 cM"
     gene            1..3703
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /note="tudor and KH domain containing protein"
                     /db_xref="GeneID:72634"
                     /db_xref="MGI:MGI:1919884"
     exon            1..119
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     exon            120..269
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     CDS             146..1828
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /note="isoform 1 is encoded by transcript variant 2; tudor
                     domain-containing protein 2"
                     /codon_start=1
                     /product="tudor and KH domain-containing protein isoform
                     1"
                     /protein_id="NP_001344640.1"
                     /db_xref="CCDS:CCDS38534.1"
                     /db_xref="GeneID:72634"
                     /db_xref="MGI:MGI:1919884"
                     /translation="MSTERTSWTNLSTIQKIALGLGIPASATVAYILYRRYRESREER
                     LTFVGEDDIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDERVLLIS
                     GFPVQVCKAKAAIHQILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITC
                     DKESEGTLLLSRLIKISGTQKEVAAAKHLILEKVSEDEELRKRIAHSAETRVPRKQPI
                     SVRREEVTEPGGAGEAALWKNTNSSMGPATPLEVPLRKGGGDMVVVGPKEGSWEKPND
                     DSFQNSGAQSSPETSMFEIPSPDFSFHADEYLEVYVSASEHPNHFWIQIIGSRSLQLD
                     KLVSEMTQHYENSLPEDLTVHVGDIVAAPLSTNGSWYRARVLGTLENGNLDLYFVDFG
                     DNGDCALKDLRALRSDFLSLPFQAIECSLARIAPTGEEWEEEALDEFDRLTHCADWKP
                     LVAKISSYVQTGISTWPKIYLYDTSDEKKLDIGLELVRKGYAVELPEDMEENRTVPNM
                     LKDMATETDDSLASILTETKKSPEEMPHTLSCLSLSEAASMSGDDNLEDDLF"
     exon            270..376
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     exon            377..566
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     exon            567..706
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     exon            707..1028
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     exon            1029..1189
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     exon            1190..1362
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     exon            1363..1427
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     exon            1428..1579
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     exon            1580..1681
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     exon            1682..1778
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     exon            1779..1870
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     exon            1871..3703
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2533..2538
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /note="hexamer: AATAAA"
     polyA_site      2552
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /note="major polyA site"
     regulatory      3653..3658
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /note="hexamer: AATAAA"
     regulatory      3666..3671
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
                     /note="hexamer: AATAAA"
     polyA_site      3672
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
     polyA_site      3696
                     /gene="Tdrkh"
                     /gene_synonym="2700091C21Rik; Tdrd2"
ORIGIN      
        1 cggaacaagc ggctgctgaa aagcgacccg ctaggcggct gcgctgaggg agcgacaggg
       61 cggcggcggc gggggtgagg tgcgaggcga agcgcagagc gcgcaactct ggaggagcgg
      121 atgttaagtc agagtacaac agaaaatgtc cactgaacga acttcatgga caaacctgtc
      181 cactattcag aaaatagccc tgggcctagg aattccagca agtgcaacag ttgcctacat
      241 tctgtatcgt cgatataggg aaagcagaga agagagattg acatttgttg gagaagatga
      301 cattgagata gagatgcgag tcccccagga ggctgtgaag ctcatcattg gtcgacaagg
      361 agccaatatt aaacagttgc ggaaacagac aggcgcgcgg attgatgtgg acacagagga
      421 tgtaggcgat gagcgagtgc tgcttatcag tgggtttcct gttcaggtgt gcaaggccaa
      481 agcagcaatc catcagattc tgacagaaaa caccccagtg tttgagcaac tctcagtccc
      541 tcagagatct gtgggcagaa tcatagggag aggcggtgag acgattcgtt ctatctgtaa
      601 ggcttctgga gccaaaatca cttgcgacaa agaatcagag ggaacgttac tactctcacg
      661 acttataaaa atctcaggaa cacagaagga agtggcagca gctaagcatc tgatactgga
      721 gaaagtttca gaagatgaag aacttcggaa gagaattgcc cattctgcag aaaccagagt
      781 cccacgaaag cagccaatca gtgtgagaag agaggaagtg acagagcctg gtggagctgg
      841 agaagcagct ttatggaaaa ataccaattc tagcatggga ccagctacac ccctggaagt
      901 tcctctccgc aaaggaggtg gtgatatggt tgttgtagga ccaaaagaag gttcctggga
      961 gaaacctaat gatgacagct ttcagaattc tggtgcccag agcagtccag agacgtccat
     1021 gtttgaaatt cccagtcctg acttcagttt ccatgctgat gagtacctag aagtctacgt
     1081 ttctgcttct gaacacccta atcacttctg gatccaaatc attggttccc gcagcctgca
     1141 gttggataaa cttgtcagtg agatgaccca gcactatgag aatagtctgc ctgaagactt
     1201 gactgtgcat gtaggagaca ttgtagcagc acctttatct acaaatggtt cctggtatcg
     1261 agcccgggtt cttggaacct tggaaaatgg aaacttggac ctctactttg ttgactttgg
     1321 agataatgga gattgtgcac taaaggatct cagggctctc aggagtgact ttctaagcct
     1381 cccatttcaa gcaatagaat gcagtctggc acggattgcc cccacaggtg aagagtggga
     1441 agaggaagct ctagatgagt ttgacagact cactcactgt gctgactgga agcccctggt
     1501 ggccaagatt tctagctatg tccagactgg aatctcaact tggccaaaga tctatttgta
     1561 tgataccagt gatgagaaga aacttgatat tgggctagaa ttagttcgta aagggtatgc
     1621 agttgaactt cctgaagaca tggaagaaaa cagaactgtc ccaaatatgt tgaaggacat
     1681 ggccacagaa acagatgatt ctcttgcaag catactcact gaaacaaaaa agagccctga
     1741 agagatgcca cataccctgt cctgcctcag cttgtcagaa gctgcctcta tgtctggtga
     1801 tgataacctt gaagacgact tattctgaaa tctgggcttc agctgctgga tcagccatct
     1861 gctttgctgt gatgtggtgc cgagagagga gtctatgata gagagatcca tgaagtcctt
     1921 tacttcacat ggtgtggctt gctgtgaatc aaatccattt tttgtttcat tggatctacc
     1981 agaaagtaac agacggaggc aaatggagac agatttctcc actccactcc tctggttcct
     2041 cccctatctt tcaatgtttg aatgctgtat aattcccagc ctctccatat caggttcagt
     2101 tccctctgcc agtaatattt tgcattactg ctgggctatg tttttgaggc tgagaaacag
     2161 ccaaggtttg ggcattggaa gtgatgattc tgcagatttc tgactcgact tatcaggtga
     2221 ctgtagttat aggaagtatt tggtggactc agaagactgc agttatcagg agataaggca
     2281 aaatcagcat aactatattt aaaagcctca taaaagggga agagtgtact acctctcacc
     2341 cacagttgcc gaggttattg gagatgggtc ctccagctat ttctttgtga acttcagtta
     2401 aaatacaact agaagggaga agtatcttag gaaatgtgta aacgtgttac aaatatgtgt
     2461 ctgtatacac acaactagag agaaagaatg aatatatata gttctgctta aataatttgg
     2521 ggaatgtttg ctaataaagt tctcaaaaat tatctaaaaa cacatactca gtcacaacgt
     2581 gggagtaggc ctgtgggtaa agtctcttct gagtaagcct tggtagtaat tgccagcacc
     2641 tcacatacgg aagcatcttg agacaaatgt ccttcccata caagtattca cactcttccc
     2701 gtaaagtcac tgcagaagtc cactactccc tcagaaccat aaccagtttt agctatatac
     2761 acaaacctac ttacactgta agagaaggcc tgtactaggg ttctagaagt aggtcttcac
     2821 tataaactta ctttacttct agtgtctttt cattactgac agtagtgcaa gacaccactg
     2881 agacttgtga cagtacttag aattaaatac aaaatgcata gtgatttaac gaactttagg
     2941 aaacaaggca aggtgaactg ggaaatctaa actgaacaca tggatgcctt atataggctt
     3001 ctctaaactc tagtattagt agccatgcct ggtgtcccag acctataccc agcctttgag
     3061 gctagtgaga gagagtgaaa gttaaaggcc atgcctaagc aacttagtaa gatgctatct
     3121 caaaaagagg ctaggggtgt agctgagtgg tatagtgtag cacttgtgtc atttgcagca
     3181 tgccaagtta gcagaaagac atcaaggaag gagcagtttg agcatctctt tactctagag
     3241 aaacctagac aggcccctat taatgttcca ggttctgact gtagtgaacc atttaagtgt
     3301 gttcagccag gcattggagt tactacacaa cagactctgg aggccatttt gtctctagtt
     3361 tcctcggtgc tcttttccct cagttagagg tcataagacc tgtagttaat tgtgtaaaaa
     3421 gcctatttaa accaattgtg tgggactgga aagatgctca aaggttaaga acactgactg
     3481 ctcttgtaga aaacccaggt tcaattctca ccacccacat ggtgactcac aaccatcttt
     3541 taattctagt tctaggggac ctagttctct cttctaactt ctaaccaggt atgcatatgg
     3601 tatacatata tacatgtagg caaaacattc atctacatgt ctaaaatttg agaataaaat
     3661 tttgaaataa aatatggtac atacctattc tcagcacttg aga
//
