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    SPO11 SPO11 initiator of meiotic double strand breaks [ Homo sapiens (human) ]

    Gene ID: 23626, updated on 6-Jun-2024

    Summary

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    Official Symbol
    SPO11provided by HGNC
    Official Full Name
    SPO11 initiator of meiotic double strand breaksprovided by HGNC
    Primary source
    HGNC:HGNC:11250
    See related
    Ensembl:ENSG00000054796 MIM:605114; AllianceGenome:HGNC:11250
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CT35; TOPVIA; SPATA43; TOPOVIA
    Summary
    Meiotic recombination and chromosome segregation require the formation of double-strand breaks (DSBs) in paired chromosome homologs. During meiosis in yeast, a meiotic recombination protein is covalently-linked to the 5' end of DSBs and is essential for the formation of DSBs. The protein encoded by this gene is similar in sequence and conserved features to the yeast meiotic recombination protein. The encoded protein belongs to the TOP6A protein family. Several transcript variants encoding different isoforms have been found for this gene, but the full-length nature of only two of them have been described. [provided by RefSeq, Jul 2008]
    Expression
    Restricted expression toward testis (RPKM 4.0) See more
    Orthologs
    mouse all
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    Genomic context

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    See SPO11 in Genome Data Viewer
    Location:
    20q13.31
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (57329803..57343993)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (59107550..59121740)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (55904859..55919049)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372687 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:55901391-55901894 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:55901895-55902397 Neighboring gene microRNA 4325 Neighboring gene ribosomal protein L39 pseudogene 39 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:55925942-55926510 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18145 Neighboring gene nuclear-encoded mitochondrial tRNA-Leu (TAA) 5-1 Neighboring gene ribonucleic acid export 1 Neighboring gene MT-RNR2 like 3 (pseudogene) Neighboring gene MT-ND1 pseudogene 9

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. The SPO11-C631T gene polymorphism and male infertility risk: a meta-analysis. Ren ZJ, et al. Ren Fail, 2017 Nov. PMID 28050928, Free PMC Article
    2. A new light on the meiotic DSB catalytic complex. Robert T, et al. Semin Cell Dev Biol, 2016 Jun. PMID 26995551
    3. Study of single nucleotide polymorphism (rs28368082) in SPO11 gene and its association with male infertility. Ghalkhani E, et al. J Assist Reprod Genet, 2014 Sep. PMID 25005169, Free PMC Article
    4. An association study of SPO11 gene single nucleotide polymorphisms with idiopathic male infertility in Chinese Han population. Zhang J, et al. J Assist Reprod Genet, 2011 Aug. PMID 21556891, Free PMC Article
    5. Screening the SPO11 and EIF5A2 genes in a population of infertile men. Christensen GL, et al. Fertil Steril, 2005 Sep. PMID 16169419

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Centromeres are dismantled by foundational meiotic proteins Spo11 and Rec8.
      Title: Centromeres are dismantled by foundational meiotic proteins Spo11 and Rec8.
    2. SPO11 gene C631T polymorphism may contribute as a genetic factor susceptible to cause male infertility in Chinese.
      Title: The SPO11-C631T gene polymorphism and male infertility risk: a meta-analysis.
    3. Data suggest that the combined genotypes of glutathionine S-transferase GSTM1 (-/-), GSTT1 (+/+), GSTP1 (AA) and meiotic recombination protein SPO11 (CT) may be associated with idiopathic male infertility in ethnic Han Chinese.
      Title: [Association of SPO11 and GST gene polymorphisms with idiopathic male infertility in ethnic Han Chinese].
    4. Polymorphisms within the SPO11 gene are linked to the susceptibility of azoospermia and oligozoospermia male infertility.
      Title: Study of single nucleotide polymorphism (rs28368082) in SPO11 gene and its association with male infertility.
    5. SPO11 might has an effect on premorbid functioning, which increase susceptibility for idiopathic male reproduction
      Title: An association study of SPO11 gene single nucleotide polymorphisms with idiopathic male infertility in Chinese Han population.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. Data show that there is no association between SPO11 gene mutation and premature ovarian failure.
      Title: Genetic investigation of four meiotic genes in women with premature ovarian failure.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Evaluation of 172 candidate polymorphisms for association with oligozoospermia or azoospermia in a large cohort of men of European descent.
    9. Mutations in the human SPO11 gene are not common causes of infertility in man
      Title: Screening the SPO11 and EIF5A2 genes in a population of infertile men.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC39953

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in double-strand break repair involved in meiotic recombination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in female gamete generation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in male meiosis I IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in meiotic DNA double-strand break formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in meiotic DNA double-strand break processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in meiotic telomere clustering IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in oogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ovarian follicle development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein localization to chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in reciprocal meiotic recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spermatid development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatogenesis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in synaptonemal complex assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome, telomeric region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nuclear chromosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    meiotic recombination protein SPO11
    Names
    SPO11 initiator of meiotic double stranded breaks
    SPO11 meiotic protein covalently bound to DSB homolog
    cancer/testis antigen 35
    spermatogenesis associated 43
    NP_036576.1
    NP_937998.1
    XP_005260436.1
    XP_005260437.1
    XP_005260438.1
    XP_005260439.1
    XP_011527058.1
    XP_011527059.1
    XP_054179275.1
    XP_054179276.1
    XP_054179277.1
    XP_054179278.1
    XP_054179279.1
    XP_054179280.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_012444.3 → NP_036576.1  meiotic recombination protein SPO11 isoform a

      See identical proteins and their annotated locations for NP_036576.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AF149310, AF169385, BC033591
      Consensus CDS
      CCDS13456.1
      UniProtKB/Swiss-Prot
      Q5TCI1, Q8N4V0, Q9NQM7, Q9NQM8, Q9Y5K1
      UniProtKB/TrEMBL
      Q5TCH7
      Related
      ENSP00000360310.3, ENST00000371263.8
      Conserved Domains (4) summary
      cd00223
      Location:218 → 380
      TOPRIM_TopoIIB_SPO; TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) ...
      COG1697
      Location:43 → 391
      Spo11; DNA topoisomerase VI, subunit A [Replication, recombination and repair]
      pfam03533
      Location:2 → 44
      SPO11_like; SPO11 homologue
      pfam04406
      Location:107 → 170
      TP6A_N; Type IIB DNA topoisomerase

    2. NM_198265.2 → NP_937998.1  meiotic recombination protein SPO11 isoform b

      See identical proteins and their annotated locations for NP_937998.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) lacks an internal segment compared to isoform a.
      Source sequence(s)
      AF169385, BC033591
      Consensus CDS
      CCDS13457.1
      UniProtKB/TrEMBL
      Q5TCH7
      Related
      ENSP00000316034.4, ENST00000345868.8
      Conserved Domains (2) summary
      pfam03533
      Location:2 → 43
      SPO11_like; SPO11 homolog
      cl27161
      Location:66 → 353
      TP6A_N; Type IIB DNA topoisomerase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      57329803..57343993
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005260379.4 → XP_005260436.1  meiotic recombination protein SPO11 isoform X1

      UniProtKB/TrEMBL
      Q5TCH7
      Conserved Domains (4) summary
      cd00223
      Location:218 → 391
      TOPRIM_TopoIIB_SPO; TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) ...
      COG1697
      Location:43 → 402
      Spo11; DNA topoisomerase VI, subunit A [Replication, recombination and repair]
      pfam03533
      Location:2 → 44
      SPO11_like; SPO11 homologue
      pfam04406
      Location:107 → 170
      TP6A_N; Type IIB DNA topoisomerase

    2. XM_005260380.4 → XP_005260437.1  meiotic recombination protein SPO11 isoform X2

      UniProtKB/TrEMBL
      Q5TCH7
      Conserved Domains (4) summary
      cd00223
      Location:216 → 389
      TOPRIM_TopoIIB_SPO; TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) ...
      PRK04342
      Location:42 → 405
      PRK04342; DNA topoisomerase VI subunit A; Provisional
      pfam03533
      Location:2 → 44
      SPO11_like; SPO11 homologue
      pfam04406
      Location:107 → 170
      TP6A_N; Type IIB DNA topoisomerase

    3. XM_005260381.4 → XP_005260438.1  meiotic recombination protein SPO11 isoform X3

      UniProtKB/TrEMBL
      Q5TCH7
      Conserved Domains (4) summary
      cd00223
      Location:216 → 378
      TOPRIM_TopoIIB_SPO; TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) ...
      COG1697
      Location:43 → 389
      Spo11; DNA topoisomerase VI, subunit A [Replication, recombination and repair]
      pfam03533
      Location:2 → 44
      SPO11_like; SPO11 homologue
      pfam04406
      Location:107 → 170
      TP6A_N; Type IIB DNA topoisomerase

    4. XM_011528756.3 → XP_011527058.1  meiotic recombination protein SPO11 isoform X4

      UniProtKB/TrEMBL
      Q5TCH7
      Conserved Domains (3) summary
      cd00223
      Location:180 → 353
      TOPRIM_TopoIIB_SPO; TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) ...
      pfam03533
      Location:2 → 43
      SPO11_like; SPO11 homologue
      pfam04406
      Location:69 → 132
      TP6A_N; Type IIB DNA topoisomerase

    5. XM_005260382.5 → XP_005260439.1  meiotic recombination protein SPO11 isoform X6

      UniProtKB/TrEMBL
      Q5TCH6
      Related
      ENSP00000413185.1, ENST00000418127.5
      Conserved Domains (3) summary
      cd00223
      Location:218 → 305
      TOPRIM_TopoIIB_SPO; TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) ...
      pfam03533
      Location:2 → 44
      SPO11_like; SPO11 homologue
      pfam04406
      Location:107 → 170
      TP6A_N; Type IIB DNA topoisomerase

    6. XM_011528757.3 → XP_011527059.1  meiotic recombination protein SPO11 isoform X5

      UniProtKB/TrEMBL
      Q5TCH7
      Conserved Domains (2) summary
      cd00223
      Location:128 → 301
      TOPRIM_TopoIIB_SPO; TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) ...
      pfam04406
      Location:17 → 80
      TP6A_N; Type IIB DNA topoisomerase

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      59107550..59121740
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323300.1 → XP_054179275.1  meiotic recombination protein SPO11 isoform X1

      UniProtKB/TrEMBL
      Q5TCH7

    2. XM_054323301.1 → XP_054179276.1  meiotic recombination protein SPO11 isoform X2

      UniProtKB/TrEMBL
      Q5TCH7

    3. XM_054323302.1 → XP_054179277.1  meiotic recombination protein SPO11 isoform X3

      UniProtKB/TrEMBL
      Q5TCH7

    4. XM_054323303.1 → XP_054179278.1  meiotic recombination protein SPO11 isoform X4

      UniProtKB/TrEMBL
      Q5TCH7

    5. XM_054323305.1 → XP_054179280.1  meiotic recombination protein SPO11 isoform X6

      UniProtKB/TrEMBL
      Q5TCH6

    6. XM_054323304.1 → XP_054179279.1  meiotic recombination protein SPO11 isoform X5

      UniProtKB/TrEMBL
      Q5TCH7
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y5K1.1 GenPept UniProtKB/Swiss-Prot:Q9Y5K1

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