LOCUS       NM_021549               2134 bp    mRNA    linear   ROD 06-OCT-2024
DEFINITION  Mus musculus polynucleotide kinase 3'- phosphatase (Pnkp),
            transcript variant 1, mRNA.
ACCESSION   NM_021549
VERSION     NM_021549.3
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 2134)
  AUTHORS   Chakraborty,A., Sreenivasmurthy,S.G., Miller,W., Huai,W.,
            Biswas,T., Mandal,S.M., Bosca,L., Krishnan,B., Ghosh,G. and
            Hazra,T.
  TITLE     Fructose-2,6-bisphosphate restores DNA repair activity of PNKP and
            ameliorates neurodegenerative symptoms in Huntington's disease
  JOURNAL   Proc Natl Acad Sci U S A 121 (39), e2406308121 (2024)
   PUBMED   39298485
  REMARK    GeneRIF: Fructose-2,6-bisphosphate restores DNA repair activity of
            PNKP and ameliorates neurodegenerative symptoms in Huntington's
            disease.
REFERENCE   2  (bases 1 to 2134)
  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   3  (bases 1 to 2134)
  AUTHORS   Shin,W., Alpaugh,W., Hallihan,L.J., Sinha,S., Crowther,E.,
            Martin,G.R., Scheidl-Yee,T., Yang,X., Yoon,G., Goldsmith,T.,
            Berger,N.D., de Almeida,L.G., Dufour,A., Dobrinski,I., Weinfeld,M.,
            Jirik,F.R. and Biernaskie,J.
  TITLE     PNKP is required for maintaining the integrity of progenitor cell
            populations in adult mice
  JOURNAL   Life Sci Alliance 4 (9), e202000790 (2021)
   PUBMED   34226276
  REMARK    GeneRIF: PNKP is required for maintaining the integrity of
            progenitor cell populations in adult mice.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2134)
  AUTHORS   Horton,J.K., Stefanick,D.F., Zhao,M.L., Janoshazi,A.K.,
            Gassman,N.R., Seddon,H.J. and Wilson,S.H.
  TITLE     XRCC1-mediated repair of strand breaks independent of PNKP binding
  JOURNAL   DNA Repair (Amst) 60, 52-63 (2017)
   PUBMED   29100039
  REMARK    GeneRIF: Repair independent of the well documented XRCC1-PNKP
            interaction was studied. XRCC1 can mediate repair of strand breaks
            without PNKP binding.
REFERENCE   5  (bases 1 to 2134)
  AUTHORS   Havali-Shahriari,Z., Weinfeld,M. and Glover,J.N.
  TITLE     Characterization of DNA Substrate Binding to the Phosphatase Domain
            of the DNA Repair Enzyme Polynucleotide Kinase/Phosphatase
  JOURNAL   Biochemistry 56 (12), 1737-1745 (2017)
   PUBMED   28276686
  REMARK    GeneRIF: The work indicates that the phosphatase domain of Pnkp
            binds 3'-phosphorylated single-stranded DNAs in a manner that is
            highly dependent on the presence of the 3'-phosphate.
REFERENCE   6  (bases 1 to 2134)
  AUTHORS   Coquelle,N., Havali-Shahriari,Z., Bernstein,N., Green,R. and
            Glover,J.N.
  TITLE     Structural basis for the phosphatase activity of polynucleotide
            kinase/phosphatase on single- and double-stranded DNA substrates
  JOURNAL   Proc Natl Acad Sci U S A 108 (52), 21022-21027 (2011)
   PUBMED   22171004
REFERENCE   7  (bases 1 to 2134)
  AUTHORS   Garces,F., Pearl,L.H. and Oliver,A.W.
  TITLE     The structural basis for substrate recognition by mammalian
            polynucleotide kinase 3' phosphatase
  JOURNAL   Mol Cell 44 (3), 385-396 (2011)
   PUBMED   22055185
  REMARK    GeneRIF: Structure of dsDNA bound to PNK 5'-kinase domain reveals
            DNA bending facilitating recognition of DNA ends in the context of
            single-strand/double-strand breaks, suggesting close functional
            cooperation in between the kinase/phosphatase active sites.
REFERENCE   8  (bases 1 to 2134)
  AUTHORS   Bernstein,N.K., Hammel,M., Mani,R.S., Weinfeld,M., Pelikan,M.,
            Tainer,J.A. and Glover,J.N.
  TITLE     Mechanism of DNA substrate recognition by the mammalian DNA repair
            enzyme, Polynucleotide Kinase
  JOURNAL   Nucleic Acids Res 37 (18), 6161-6173 (2009)
   PUBMED   19671525
REFERENCE   9  (bases 1 to 2134)
  AUTHORS   Bernstein,N.K., Williams,R.S., Rakovszky,M.L., Cui,D., Green,R.,
            Karimi-Busheri,F., Mani,R.S., Galicia,S., Koch,C.A., Cass,C.E.,
            Durocher,D., Weinfeld,M. and Glover,J.N.
  TITLE     The molecular architecture of the mammalian DNA repair enzyme,
            polynucleotide kinase
  JOURNAL   Mol Cell 17 (5), 657-670 (2005)
   PUBMED   15749016
  REMARK    GeneRIF: analysis of the molecular architecture of polynucleotide
            kinase
REFERENCE   10 (bases 1 to 2134)
  AUTHORS   Moreira,M.C., Barbot,C., Tachi,N., Kozuka,N., Uchida,E., Gibson,T.,
            Mendonca,P., Costa,M., Barros,J., Yanagisawa,T., Watanabe,M.,
            Ikeda,Y., Aoki,M., Nagata,T., Coutinho,P., Sequeiros,J. and
            Koenig,M.
  TITLE     The gene mutated in ataxia-ocular apraxia 1 encodes the new
            HIT/Zn-finger protein aprataxin
  JOURNAL   Nat Genet 29 (2), 189-193 (2001)
   PUBMED   11586300
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BY118349.1, CX223963.1, AK049992.1, AC158231.2 and BY579541.1.
            
            On Mar 19, 2014 this sequence version replaced NM_021549.2.
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (a). Variants 1 and 2
            both encode the same isoform (a).
            
            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 :: BC057659.1, AK049992.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-13                BY118349.1         1-13
            14-198              CX223963.1         1-185
            199-639             AK049992.1         2-442
            640-640             AC158231.2         131335-131335
            641-2130            AK049992.1         444-1933
            2131-2134           BY579541.1         398-401
FEATURES             Location/Qualifiers
     source          1..2134
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /db_xref="taxon:10090"
                     /chromosome="7"
                     /map="7 28.94 cM"
     gene            1..2134
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /note="polynucleotide kinase 3'- phosphatase"
                     /db_xref="GeneID:59047"
                     /db_xref="MGI:MGI:1891698"
     exon            1..409
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     CDS             259..1827
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /EC_number="2.7.1.78"
                     /EC_number="3.1.3.32"
                     /note="isoform a is encoded by transcript variant 1;
                     bifunctional polynucleotide phosphatase/kinase; DNA
                     5'-kinase/3'-phosphatase"
                     /codon_start=1
                     /product="bifunctional polynucleotide phosphatase/kinase
                     isoform a"
                     /protein_id="NP_067524.2"
                     /db_xref="CCDS:CCDS39945.1"
                     /db_xref="GeneID:59047"
                     /db_xref="MGI:MGI:1891698"
                     /translation="MSQLGSRGRLWLQSPTGGPPPIFLPSDGQALVLGRGPLTQVTDR
                     KCSRNQVELIADPESRTVAVKQLGVNPSTVGVQELKPGLSGSLSLGDVLYLVNGLYPL
                     TLRWEELSTSGSQPDAPPDTPGDPEEGEDTEPQKKRVRKSSLGWESLKKLLVFTASGV
                     KPQGKVAAFDLDGTLITTRSGKVFPTSPSDWRILYPEIPKKLQELAAEGYKLVIFTNQ
                     MGIGRGKLPAEVFKGKVEAVLEKLGVPFQVLVATHAGLNRKPVSGMWDHLQEQANEGI
                     PISVEDSVFVGDAAGRLANWAPGRKKKDFSCADRLFALNVGLPFATPEEFFLKWPAAR
                     FELPAFDPRTISSAGPLYLPESSSLLSPNPEVVVAVGFPGAGKSTFIQEHLVSAGYVH
                     VNRDTLGSWQRCVSSCQAALRQGKRVVIDNTNPDVPSRARYIQCAKDAGVPCRCFNFC
                     ATIEQARHNNRFREMTDPSHAPVSDMVMFSYRKQFEPPTLAEGFLEILEIPFRLQEHL
                     DPALQRLYRQFSEG"
     exon            410..456
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            457..753
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            754..833
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            834..891
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            892..999
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            1000..1071
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            1072..1120
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            1121..1191
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            1192..1284
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            1285..1381
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            1382..1443
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            1444..1553
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            1554..1641
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            1642..1703
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     exon            1704..2134
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1834..1839
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /note="hexamer: AATAAA"
     polyA_site      1855
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /note="major polyA site"
     regulatory      2098..2103
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /note="hexamer: AATAAT"
     regulatory      2110..2115
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
                     /note="hexamer: AAGAAA"
     polyA_site      2115
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
     polyA_site      2132
                     /gene="Pnkp"
                     /gene_synonym="1810009G08Rik; PNK"
ORIGIN      
        1 gagccaaatt ttcgaacagt ctttcccata gcatagatga gctttggaat gaattcagaa
       61 gtgactctac ctatatgcaa tcctcactgc gcattggaac cgttgtggta gcttgggaaa
      121 cgtcgaaccc gcccatgggc aaggggcgga atttccggtg tggctcgcat tgggaaagca
      181 gaacttccgg tggcgggtgg gttgccggct gctgagcaag ctccactgtg attctgttcc
      241 ccttcacagc atccgaggat gtcacagctt ggatcccggg gccgcctgtg gctgcagagc
      301 cccaccggtg ggccgccccc tatattcctg ccgtcggatg gccaagccct ggtcctcggt
      361 cggggacccc tgacccaagt gacggaccgg aagtgctccc gaaaccaagt ggagctgatt
      421 gcagaccctg aaagccggac agtggcagtg aaacagctgg gtgttaaccc gtcaactgtt
      481 ggggtccagg agttgaagcc aggactgtct ggctctctaa gcttggggga tgtcctttat
      541 ctggttaatg gcctatatcc cctgaccctg cgttgggaag agctcagcac atcaggatcc
      601 cagccagatg ctccaccaga cactcctggg gatccggagg agggagagga tactgagcct
      661 cagaaaaagc gagttcggaa atcctctctt ggctgggaga gcttaaagaa gttactggtg
      721 ttcacagcgt ctggggtgaa gccccagggc aaggtggctg cctttgacct agatgggacc
      781 ctcatcacca cccgctctgg aaaggtcttc cccactagcc ctagtgactg gaggattctg
      841 tacccagaga ttccaaagaa gctccaggag ctggctgctg aaggctacaa gttggtaatc
      901 ttcaccaacc aaatgggcat cgggcgaggc aagctgccag cagaggtgtt caagggcaag
      961 gtggaagctg tattggagaa gttaggggtc ccatttcagg tgctggtggc aacacatgca
     1021 ggtctaaacc gaaagccagt gagtggcatg tgggaccatc tgcaggagca ggccaacgag
     1081 ggcatcccca tctcggtaga ggacagtgtc ttcgtgggag atgcagcagg gcgcctagcc
     1141 aactgggcac cggggaggaa aaaaaaggat ttctcttgtg cagaccgcct gttcgccctt
     1201 aacgtcggcc tgccctttgc cactccggaa gagtttttcc ttaagtggcc ggctgcccgc
     1261 tttgagcttc cagctttcga cccgaggact atctccagtg ctgggcccct ctaccttcca
     1321 gagtccagct ctctcctgag ccccaaccca gaggtggtgg tcgcagtagg attccctggg
     1381 gccggcaagt ccactttcat ccaggagcac ctagtgtcag ctggctacgt ccatgtgaac
     1441 agggacacgc tgggctcgtg gcagcgctgt gtgagctcat gccaggcggc actgaggcag
     1501 gggaagcgag tcgtgattga caacaccaac ccagatgtcc caagtcgggc caggtacatc
     1561 caatgtgcca aagatgcagg tgtgccctgc cgctgtttca acttctgtgc tacaatagag
     1621 caggcacgcc acaacaacag gtttcgtgag atgaccgacc cttcgcatgc acctgtgtcg
     1681 gacatggtca tgtttagcta caggaagcag tttgagccgc ccacactggc tgaaggcttc
     1741 ctggagatcc ttgagattcc attccggtta caggagcatc tggacccggc actgcagcga
     1801 ctgtaccgcc agttttccga gggctgagcc ctcaataaac actggtgcca ctctgtgcac
     1861 agccatcttg ctggggttgt gggaggcaaa acaggtgcca cggcatcctg cattgagctt
     1921 gggcttccaa gtgggctctt gtgtatctgg catacttggc ctgggggctt gagcagccac
     1981 agccattttg tggtgtgact caccagccag caccaggttt cagaacccag ttgtgggaca
     2041 ctggacccga gactggagtc tggggatgtt aaatttgacc aggtacagga agattataat
     2101 aatgtgtcaa agaaaggctg tcatgtgggt aact
//
