LOCUS NM_001310214 3193 bp mRNA linear PRI 12-JUN-2024
DEFINITION Homo sapiens PR/SET domain 9 (PRDM9), transcript variant A, mRNA.
ACCESSION NM_001310214
VERSION NM_001310214.3
KEYWORDS RefSeq.
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 DB636359.1, AK301776.1,
DB518225.2 and AL704903.1.
On Sep 20, 2021 this sequence version replaced NM_001310214.2.
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##
COMPLETENESS: complete on the 3' end.
PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
1-46 DB636359.1 1-46
47-2945 AK301776.1 1-2899
2946-3191 DB518225.2 424-669
3192-3193 AL704903.1 18-19 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"
misc_feature 117..119
/gene="PRDM9"
/gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
/note="upstream in-frame stop codon"
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 A is encoded by transcript variant A;
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 A"
/protein_id="NP_001297143.1"
/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
THQRRHTGEKPYVCRECGRGFSRQSVLLTHQRRHTGEKPYVCRECGRGFSWQSVLLSH
QRTHTGEKPYVCRECGRGFSWQSVLLTHQRTHTGEKPYVCRECGRGFSNKSHLLRHQR
THTGEKPYVCRECGRGFRDKSHLLRHQRTHTGEKPYVCRECGRGFRDKSNLLSHQRTH
TGEKPYVCRECGRGFSNKSHLLRHQRTHTGEKPYVCRECGRGFRNKSHLLRHQRTHTG
EKPYVCRECGRGFSDRSSLCYHQRTHTGEKPYVCREDE"
misc_feature 189..257
/gene="PRDM9"
/gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
/note="propagated from UniProtKB/Swiss-Prot (Q9NQV7.2);
Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
misc_feature 615..710
/gene="PRDM9"
/gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
/note="propagated from UniProtKB/Swiss-Prot (Q9NQV7.2);
Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
misc_feature 1290..1292
/gene="PRDM9"
/gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
/note="N6,N6,N6-trimethyllysine, alternate.
/evidence=ECO:0000250|UniProtKB:Q96EQ9; N6-methyllysine,
alternate. /evidence=ECO:0000250|UniProtKB:Q96EQ9;
propagated from UniProtKB/Swiss-Prot (Q9NQV7.2);
methylation site"
misc_feature 1302..1304
/gene="PRDM9"
/gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
/note="N6-methyllysine.
/evidence=ECO:0000250|UniProtKB:Q96EQ9; propagated from
UniProtKB/Swiss-Prot (Q9NQV7.2); methylation site"
misc_feature 1308..1310
/gene="PRDM9"
/gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
/note="N6-methyllysine.
/evidence=ECO:0000250|UniProtKB:Q96EQ9; propagated from
UniProtKB/Swiss-Prot (Q9NQV7.2); methylation site"
misc_feature 1410..1595
/gene="PRDM9"
/gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
/note="propagated from UniProtKB/Swiss-Prot (Q9NQV7.2);
Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
misc_feature 2376..2648
/gene="PRDM9"
/gene_synonym="KMT8B; MEISETZ; MSBP3; PFM6; ZNF899"
/note="propagated from UniProtKB/Swiss-Prot (Q9NQV7.2);
Region: DNA-binding.
/evidence=ECO:0000269|PubMed:26833727"
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 cacgggagac
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 tcctcctcag 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 tagccacaag 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
//