LOCUS       NM_020227               3193 bp    mRNA    linear   PRI 10-FEB-2025
DEFINITION  Homo sapiens PR/SET domain 9 (PRDM9), transcript variant B, mRNA.
ACCESSION   NM_020227
VERSION     NM_020227.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3193)
  AUTHORS   Zhao,M., Rong,R., Zhang,C., Yang,H., Han,X., Fan,Z., Zheng,Y. and
            Zhang,J.
  TITLE     FBLN5 was Regulated by PRDM9, and Promoted Senescence and
            Osteogenic Differentiation of Human Periodontal Ligament Stem Cells
  JOURNAL   Curr Stem Cell Res Ther 19 (3), 417-425 (2024)
   PUBMED   37608663
  REMARK    GeneRIF: FBLN5 was Regulated by PRDM9, and Promoted Senescence and
            Osteogenic Differentiation of Human Periodontal Ligament Stem
            Cells.
REFERENCE   2  (bases 1 to 3193)
  AUTHORS   Ladias,P., Markopoulos,G.S., Kostoulas,C., Bouba,I., Markoula,S.
            and Georgiou,I.
  TITLE     Cancer Associated PRDM9: Implications for Linking Genomic
            Instability and Meiotic Recombination
  JOURNAL   Int J Mol Sci 24 (22), 16522 (2023)
   PUBMED   38003713
  REMARK    GeneRIF: Cancer Associated PRDM9: Implications for Linking Genomic
            Instability and Meiotic Recombination.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3193)
  AUTHORS   Soleymani Moud,S., Kamal Seraji,K., Ramezani,M. and Piravar,Z.
  TITLE     Association of Single Nucleotide Polymorphisms in the PYGO2 and
            PRDM9 Genes with Idiopathic Azoospermia in Iranian Infertile Male
            Patients
  JOURNAL   Iran J Med Sci 48 (1), 77-84 (2023)
   PUBMED   36688188
  REMARK    GeneRIF: Association of Single Nucleotide Polymorphisms in the
            PYGO2 and PRDM9 Genes with Idiopathic Azoospermia in Iranian
            Infertile Male Patients.
REFERENCE   4  (bases 1 to 3193)
  AUTHORS   Pratto,F., Brick,K., Khil,P., Smagulova,F., Petukhova,G.V. and
            Camerini-Otero,R.D.
  TITLE     DNA recombination. Recombination initiation maps of individual
            human genomes
  JOURNAL   Science 346 (6211), 1256442 (2014)
   PUBMED   25395542
  REMARK    Erratum:[Science. 2018 Oct 19;362(6412):eaav6294. doi:
            10.1126/science.aav6294.. PMID: 30337382]
REFERENCE   5  (bases 1 to 3193)
  AUTHORS   Baudat,F., Imai,Y. and de Massy,B.
  TITLE     Meiotic recombination in mammals: localization and regulation
  JOURNAL   Nat Rev Genet 14 (11), 794-806 (2013)
   PUBMED   24136506
  REMARK    Review article
REFERENCE   6  (bases 1 to 3193)
  AUTHORS   Berg,I.L., Neumann,R., Sarbajna,S., Odenthal-Hesse,L., Butler,N.J.
            and Jeffreys,A.J.
  TITLE     Variants of the protein PRDM9 differentially regulate a set of
            human meiotic recombination hotspots highly active in African
            populations
  JOURNAL   Proc Natl Acad Sci U S A 108 (30), 12378-12383 (2011)
   PUBMED   21750151
  REMARK    GeneRIF: Each African-enhanced hotspot is activated by a distinct
            spectrum of PRDM9 variants, despite the fact that all are predicted
            to bind the same motif. This differential activation points to
            complex interactions between the zinc-finger array and hotspots.
REFERENCE   7  (bases 1 to 3193)
  AUTHORS   Berg,I.L., Neumann,R., Lam,K.W., Sarbajna,S., Odenthal-Hesse,L.,
            May,C.A. and Jeffreys,A.J.
  TITLE     PRDM9 variation strongly influences recombination hot-spot activity
            and meiotic instability in humans
  JOURNAL   Nat Genet 42 (10), 859-863 (2010)
   PUBMED   20818382
  REMARK    GeneRIF: PRDM9 variation strongly influences recombination hot-spot
            activity and meiotic instability.
REFERENCE   8  (bases 1 to 3193)
  AUTHORS   Baudat,F., Buard,J., Grey,C., Fledel-Alon,A., Ober,C.,
            Przeworski,M., Coop,G. and de Massy,B.
  TITLE     PRDM9 is a major determinant of meiotic recombination hotspots in
            humans and mice
  JOURNAL   Science 327 (5967), 836-840 (2010)
   PUBMED   20044539
  REMARK    GeneRIF: results provide a molecular basis for the distribution of
            meiotic recombination in mammals in which the binding of PRDM9 to
            specific DNA sequences targets the initiation of recombination at
            specific locations in the genome
            Erratum:[Science. 2010 May 7;328(5979):690]
REFERENCE   9  (bases 1 to 3193)
  AUTHORS   Jiang,G.L. and Huang,S.
  TITLE     The yin-yang of PR-domain family genes in tumorigenesis
  JOURNAL   Histol Histopathol 15 (1), 109-117 (2000)
   PUBMED   10668202
  REMARK    Review article
REFERENCE   10 (bases 1 to 3193)
  AUTHORS   Wahls,W.P., Swenson,G. and Moore,P.D.
  TITLE     Two hypervariable minisatellite DNA binding proteins
  JOURNAL   Nucleic Acids Res 19 (12), 3269-3274 (1991)
   PUBMED   2062643
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC025451.6.
            
            On Nov 22, 2019 this sequence version replaced NM_020227.3.
            
            Summary: The protein encoded by this gene is a zinc finger protein
            with histone methyltransferase activity that catalyzes histone H3
            lysine 4 trimethylation (H3K4me3) during meiotic prophase. This
            protein contains multiple domains, including a Kruppel-associated
            box (KRAB) domain, an SSX repression domain (SSXRD), a PRD1-BF1 and
            RIZ homologous region, a subclass of SET (PR/SET) domain, and a
            tandem array of C2H2 zinc fingers. The zinc finger array recognizes
            a short sequence motif, leading to local H3K4me3, and meiotic
            recombination hotspot activity. The observed allelic variation
            alters the DNA-binding sequence specificity of the protein,
            resulting in distinct meiotic recombination hotspots amongst
            individuals and populations. Multiple alternate alleles of this
            gene have been described. [provided by RefSeq, Jul 2015].
            
            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 :: DQ388610.1, AK301776.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968968, SAMEA2148093
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000296682.4/ ENSP00000296682.4
            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
            1-104               AC025451.6         101121-101224       c
            105-257             AC025451.6         99731-99883         c
            258-381             AC025451.6         99240-99363         c
            382-489             AC025451.6         98806-98913         c
            490-539             AC025451.6         90903-90952         c
            540-696             AC025451.6         87654-87810         c
            697-798             AC025451.6         86428-86529         c
            799-1070            AC025451.6         85948-86219         c
            1071-1138           AC025451.6         85475-85542         c
            1139-1332           AC025451.6         84306-84499         c
            1333-3193           AC025451.6         80740-82600         c
FEATURES             Location/Qualifiers
     source          1..3193
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5p14.2"
     gene            1..3193
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /note="PR/SET domain 9"
                     /db_xref="GeneID:56979"
                     /db_xref="HGNC:HGNC:13994"
                     /db_xref="MIM:609760"
     exon            1..104
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /inference="alignment:Splign:2.1.0"
     exon            105..257
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /inference="alignment:Splign:2.1.0"
     CDS             189..2873
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /EC_number="2.1.1.354"
                     /EC_number="2.1.1.355"
                     /EC_number="2.1.1.361"
                     /EC_number="2.1.1.362"
                     /EC_number="2.1.1.359"
                     /note="isoform PRDM9 B is encoded by transcript variant B;
                     minisatellite binding protein 3 (115kD); PR domain
                     containing 9; histone-lysine N-methyltransferase PRDM9; PR
                     domain zinc finger protein 9; PR domain 9; histone methyl
                     transferase; protein-lysine N-methyltransferase PRDM9;
                     [histone H4]-lysine20 N-methyltransferase PRDM9; [histone
                     H3]-lysine4 N-trimethyltransferase PRDM9; [histone
                     H3]-lysine9 N-trimethyltransferase PRDM9; [histone
                     H3]-lysine36 N-trimethyltransferase PRDM9; [histone
                     H4]-N-methyl-L-lysine20 N-methyltransferase PRDM9"
                     /codon_start=1
                     /product="histone-lysine N-methyltransferase PRDM9 isoform
                     PRDM9 B"
                     /protein_id="NP_064612.2"
                     /db_xref="CCDS:CCDS43307.1"
                     /db_xref="GeneID:56979"
                     /db_xref="HGNC:HGNC:13994"
                     /db_xref="MIM:609760"
                     /translation="MSPEKSQEESPEEDTERTERKPMVKDAFKDISIYFTKEEWAEMG
                     DWEKTRYRNVKRNYNALITIGLRATRPAFMCHRRQAIKLQVDDTEDSDEEWTPRQQVK
                     PPWMALRVEQRKHQKGMPKASFSNESSLKELSRTANLLNASGSEQAQKPVSPSGEAST
                     SGQHSRLKLELRKKETERKMYSLRERKGHAYKEVSEPQDDDYLYCEMCQNFFIDSCAA
                     HGPPTFVKDSAVDKGHPNRSALSLPPGLRIGPSGIPQAGLGVWNEASDLPLGLHFGPY
                     EGRITEDEEAANNGYSWLITKGRNCYEYVDGKDKSWANWMRYVNCARDDEEQNLVAFQ
                     YHRQIFYRTCRVIRPGCELLVWYGDEYGQELGIKWGSKWKKELMAGREPKPEIHPCPS
                     CCLAFSSQKFLSQHVERNHSSQNFPGPSARKLLQPENPCPGDQNQEQQYPDPHSRNDK
                     TKGQEIKERSKLLNKRTWQREISRAFSSPPKGQMGSCRVGKRIMEEESRTGQKVNPGN
                     TGKLFVGVGISRIAKVKYGECGQGFSVKSDVITHQRTHTGEKLYVCRECGRGFSWKSH
                     LLIHQRIHTGEKPYVCRECGRGFSWQSVLLTHQRTHTGEKPYVCRECGRGFSRQSVLL
                     THQRRHTGEKPYVCRECGRGFSRQSVLLTHQRRHTGEKPYVCRECGRGFSWQSVLLTH
                     QRTHTGEKPYVCRECGRGFSWQSVLLTHQRTHTGEKPYVCRECGRGFSNKSHLLRHQR
                     THTGEKPYVCRECGRGFRDKSHLLRHQRTHTGEKPYVCRECGRGFRDKSNLLSHQRTH
                     TGEKPYVCRECGRGFSNKSHLLRHQRTHTGEKPYVCRECGRGFRNKSHLLRHQRTHTG
                     EKPYVCRECGRGFSDRSSLCYHQRTHTGEKPYVCREDE"
     exon            258..381
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /inference="alignment:Splign:2.1.0"
     exon            382..489
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /inference="alignment:Splign:2.1.0"
     exon            490..539
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /inference="alignment:Splign:2.1.0"
     exon            540..696
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /inference="alignment:Splign:2.1.0"
     exon            697..798
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /inference="alignment:Splign:2.1.0"
     exon            799..1070
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /inference="alignment:Splign:2.1.0"
     exon            1071..1138
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /inference="alignment:Splign:2.1.0"
     exon            1139..1332
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /inference="alignment:Splign:2.1.0"
     exon            1333..3193
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3165..3170
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /note="hexamer: AATAAA"
     polyA_site      3193
                     /gene="PRDM9"
                     /gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
                     /note="major polyA site"
ORIGIN      
        1 gagggactct gagagaacgc ccggccaggg tgaacgccgc ggcaggagag cacgggagat
       61 tgtgaagagc atggggagcc tttgtcgtgc agcgtgaaac ccttgagcct ttggcctagg
      121 agctgggaga ctcagggccc ttctcacact cagaattgga gcagggcctt ctagacagtc
      181 ccagcaccat gagccctgaa aagtcccaag aggagagccc agaagaagac acagagagaa
      241 cagagcggaa gcccatggtc aaagatgcct tcaaagacat ttccatatac ttcaccaagg
      301 aagaatgggc agagatggga gactgggaga aaactcgcta taggaatgtg aaaaggaact
      361 ataatgcact gattactata ggtctcagag ccactcgacc agctttcatg tgtcaccgaa
      421 ggcaggccat caaactccag gtggatgaca cagaagattc tgatgaagaa tggaccccta
      481 ggcagcaagt caaacctcct tggatggcct taagagtgga acagcgtaaa caccagaagg
      541 gaatgcccaa ggcgtcattc agtaatgaat ctagtttgaa agaattgtca agaacagcaa
      601 atttactgaa tgcaagtggc tcagagcagg ctcagaaacc agtgtcccct tctggagaag
      661 caagtacctc tggacagcac tcaagactaa aactggaact caggaagaag gagactgaaa
      721 gaaagatgta tagcctgcga gaaagaaagg gtcatgcata caaagaggtc agcgagccgc
      781 aggatgatga ttacctctat tgtgagatgt gtcagaactt cttcattgac agctgtgctg
      841 cccatgggcc ccctacattt gtaaaggaca gtgcagtgga caaggggcac cccaaccgtt
      901 cagccctcag tctgccccca gggctgagaa ttgggccatc aggcatccct caggctgggc
      961 ttggagtatg gaatgaggca tctgatctgc cgctgggtct gcactttggc ccttatgagg
     1021 gccgaattac agaagacgaa gaggcagcca acaatggata ctcctggctg atcaccaagg
     1081 ggagaaactg ctatgagtat gtggatggaa aagataaatc ctgggccaac tggatgaggt
     1141 atgtgaactg tgcccgggat gatgaagagc agaacctggt ggccttccag taccacaggc
     1201 agatcttcta tagaacctgc cgagtcatta ggccaggctg tgaactgctg gtctggtatg
     1261 gggatgaata cggccaggaa ctgggcatca agtggggcag caagtggaag aaagagctca
     1321 tggcagggag agaaccaaag ccagagatcc atccatgtcc ctcatgctgt ctggcctttt
     1381 caagtcagaa atttctcagt caacatgtag aacgcaatca ctcctctcag aacttcccag
     1441 gaccatctgc aagaaaactc ctccaaccag agaatccctg cccaggggat cagaatcagg
     1501 agcagcaata tccagatcca cacagccgta atgacaaaac caaaggtcaa gagatcaaag
     1561 aaaggtccaa actcttgaat aaaaggacat ggcagaggga gatttcaagg gccttttcta
     1621 gcccacccaa aggacaaatg gggagctgta gagtgggaaa aagaataatg gaagaagagt
     1681 ccagaacagg ccagaaagtg aatccaggga acacaggcaa attatttgtg ggggtaggaa
     1741 tctcaagaat tgcaaaagtc aagtatggag agtgtggaca aggtttcagt gttaaatcag
     1801 atgttattac acaccaaagg acacatacag gggagaagct ctacgtctgc agggagtgtg
     1861 ggcggggctt tagctggaag tcacacctcc tcattcacca gaggatacac acaggggaga
     1921 agccctatgt ctgcagggag tgtgggcggg gctttagctg gcagtcagtc ctcctcactc
     1981 accagaggac acacacaggg gagaagccct atgtctgcag ggagtgtggg cggggcttta
     2041 gccggcagtc agtcctcctc actcaccaga ggagacacac aggggagaag ccctatgtct
     2101 gcagggagtg tgggcggggc tttagccggc agtcagtcct cctcactcac cagaggagac
     2161 acacagggga gaagccctat gtctgcaggg agtgtgggcg gggctttagc tggcagtcag
     2221 tcctcctcac tcaccagagg acacacacag gggagaagcc ctatgtctgc agggagtgtg
     2281 ggcggggctt tagctggcag tcagtcctcc tcactcacca gaggacacac acaggggaga
     2341 agccctatgt ctgcagggag tgtgggcggg gctttagcaa taagtcacac ctcctcagac
     2401 accagaggac acacacaggg gagaagccct atgtctgcag ggagtgtggg cggggctttc
     2461 gcgataagtc acacctcctc agacaccaga ggacacacac aggggagaag ccctatgtct
     2521 gcagggagtg tgggcggggc tttagagata agtcaaacct cctcagtcac cagaggacac
     2581 acacagggga gaagccctat gtctgcaggg agtgtgggcg gggctttagc aataagtcac
     2641 acctcctcag acaccagagg acacacacag gggagaagcc ctatgtctgc agggagtgtg
     2701 ggcggggctt tcgcaataag tcacacctcc tcagacacca gaggacacac acaggggaga
     2761 agccctacgt ctgcagggag tgtgggcggg gctttagcga taggtcaagc ctctgctatc
     2821 accagaggac acacacaggg gagaagccct acgtctgcag ggaggatgag taagtcatta
     2881 gtaataaaac ctcatctcaa tagccacaaa aagacaaatg tggtcaccac acacttgcac
     2941 accccagctg tgaggtggct tcagcggaag tctgctgacc ccttatattc cccgagagta
     3001 taaagagatc ggaaataact gattaaacaa atccgccact ttcatgacta gagatgagga
     3061 agaacaaggg atagttctgt aagtgttcgg gggacatcag catgtgtggt tctttcccgc
     3121 actgatcccc tccatttttt gtttgttttt ttgcctcctg ttctaataaa ttttgtctcc
     3181 atacaaatct gaa
//
