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    SBF2 SET binding factor 2 [ Homo sapiens (human) ]

    Gene ID: 81846, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SBF2provided by HGNC
    Official Full Name
    SET binding factor 2provided by HGNC
    Primary source
    HGNC:HGNC:2135
    See related
    Ensembl:ENSG00000133812 MIM:607697; AllianceGenome:HGNC:2135
    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
    CMT4B2; MTMR13; DENND7B
    Summary
    This gene encodes a pseudophosphatase and member of the myotubularin-related protein family. This gene maps within the CMT4B2 candidate region of chromosome 11p15 and mutations in this gene have been associated with Charcot-Marie-Tooth Disease, type 4B2. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 7.7), fat (RPKM 7.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SBF2 in Genome Data Viewer
    Location:
    11p15.4
    Exon count:
    46
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (9778668..10303837, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (9863048..10388341, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (9800215..10315766, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:9733231-9733731 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:9740773-9741273 Neighboring gene RN7SK pseudogene 50 Neighboring gene switching B cell complex subunit SWAP70 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4425 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3138 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:9785216-9785716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:9786625-9787448 Neighboring gene uncharacterized LOC105369149 Neighboring gene long intergenic non-protein coding RNA 2709 Neighboring gene SBF2 antisense RNA 1 Neighboring gene protein GVQW1-like Neighboring gene uncharacterized LOC101928008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4426 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:9884465-9885024 Neighboring gene RNA, U7 small nuclear 28 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:9915190-9915690 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:9915691-9916191 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:9927555-9928139 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:10004023-10005222 Neighboring gene glutamate-ammonia ligase pseudogene 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:10065715-10066914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10098213-10098818 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3140 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4427 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4428 Neighboring gene G protein subunit gamma 10 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4430 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4429 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3143 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3144 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3146 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3147 Neighboring gene Sharpr-MPRA regulatory region 210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4431 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3149 Neighboring gene Sharpr-MPRA regulatory region 6386 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10361038-10361538 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10361539-10362039 Neighboring gene uncharacterized LOC100130460 Neighboring gene VISTA enhancer hs2289 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10375005-10375536 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:10375537-10376067 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:10388109-10388608 Neighboring gene Sharpr-MPRA regulatory region 7754 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:10413861-10414740 Neighboring gene adrenomedullin Neighboring gene RNA, U6atac small nuclear 33, pseudogene

    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 impact of SBF2 on taxane-induced peripheral neuropathy. Cunningham GM, et al. PLoS Genet, 2022 Jan. PMID 34986146, Free PMC Article
    2. Charcot-Marie-Tooth gene, SBF2, associated with taxane-induced peripheral neuropathy in African Americans. Schneider BP, et al. Oncotarget, 2016 Dec 13. PMID 27732968, Free PMC Article
    3. Identification of a novel SBF2 frameshift mutation in charcot-marie-tooth disease type 4B2 using whole-exome sequencing. Chen M, et al. Genomics Proteomics Bioinformatics, 2014 Oct. PMID 25462154, Free PMC Article
    4. Identification of a novel SBF2 missense mutation associated with a rare case of thrombocytopenia using whole-exome sequencing. Abuzenadah AM, et al. J Thromb Thrombolysis, 2013 Nov. PMID 23334996
    5. A new SBF2 mutation in a family with recessive demyelinating Charcot-Marie-Tooth (CMT4B2). Conforti FL, et al. Neurology, 2004 Oct 12. PMID 15477569

    See all (50) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The impact of SBF2 on taxane-induced peripheral neuropathy.
      Title: The impact of SBF2 on taxane-induced peripheral neuropathy.
    2. Rare variants in SBF2 predict an increased risk of taxane-induced peripheral neuropathy in African American breast cancer patients receiving paclitaxel.
      Title: Charcot-Marie-Tooth gene, SBF2, associated with taxane-induced peripheral neuropathy in African Americans.
    3. Starvation-induced MTMR13 and RAB21 activity regulates VAMP8 to promote autophagosome-lysosome fusion.
      Title: Starvation-induced MTMR13 and RAB21 activity regulates VAMP8 to promote autophagosome-lysosome fusion.
    4. SBF2 frameshift mutation is associated with charcot-marie-tooth disease type 4B2.
      Title: Identification of a novel SBF2 frameshift mutation in charcot-marie-tooth disease type 4B2 using whole-exome sequencing.
    5. Identification of a novel SBF2 missense mutation associated with a rare case of thrombocytopenia using whole-exome sequencing.
      Title: Identification of a novel SBF2 missense mutation associated with a rare case of thrombocytopenia using whole-exome sequencing.
    6. Germline genetic variation in the SBF2 locus was associated with overall survival in patients with pancreatic adenocarcinoma of European and Asian ancestry.
      Title: Genome-wide association study of survival in patients with pancreatic adenocarcinoma.
    7. REVIEW : MTMR13 and homologous proteins are mutated in several neuromuscular diseases
      Title: Endosomal phosphoinositides and human diseases.
    8. A phylogenetic study revealing co-evolution of myotubularins with PI 3-kinase class III complex
      Title: PtdIns5P regulation through evolution: roles in membrane trafficking?
    9. 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.
    10. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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

    Associated conditions

    Description Tests
    Charcot-Marie-Tooth disease type 4B2
    MedGen: C1858278 OMIM: 604563 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study of smoking behaviours among Bangladeshi adults.
    EBI GWAS Catalog
    Genome-wide association study of survival in patients with pancreatic adenocarcinoma.
    EBI GWAS Catalog

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of SET binding factor 2 (SBF2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ22918, FLJ41627, KIAA1766, DKFZp779B2327

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables guanyl-nucleotide exchange factor activity TAS
    Traceable Author Statement
    more info
    		  
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatase regulator activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol 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 autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in myelination NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in axon IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in vacuolar membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    myotubularin-related protein 13
    Names
    DENN/MADD domain containing 7B
    inactive phosphatidylinositol 3-phosphatase 13

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_008074.1 RefSeqGene

      Range
      5001..520541
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_267

    mRNA and Protein(s)

    1. NM_001386339.1 → NP_001373268.1  myotubularin-related protein 13 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC011092, AC026250, AC080023, AC100763
      Consensus CDS
      CCDS91440.1
      UniProtKB/TrEMBL
      A0A6Q8PH13, A0A8I5KQ02
      Related
      ENSP00000509587.1, ENST00000689128.1
      Conserved Domains (7) summary
      smart00801
      Location:352 → 420
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:1 → 86
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01235
      Location:1774 → 1879
      PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
      cd13339
      Location:882 → 1000
      PH-GRAM_MTMR13; Myotubularian (MTM) related 13 protein Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      cd14589
      Location:1138 → 1517
      PTP-MTMR13; protein tyrosine phosphatase-like pseudophosphatase domain of myotubularin related phosphoinositide phosphatase 13
      pfam02141
      Location:116 → 298
      DENN; DENN (AEX-3) domain
      pfam12335
      Location:531 → 754
      SBF2; Myotubularin protein

    2. NM_001386342.1 → NP_001373271.1  myotubularin-related protein 13 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC011092, AC026250, AC080023, AC100763
      Consensus CDS
      CCDS91439.1
      UniProtKB/TrEMBL
      A0A8I5KWY5, A0A8I5KY55
      Related
      ENSP00000509545.1, ENST00000692716.1
      Conserved Domains (7) summary
      smart00801
      Location:352 → 421
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:1 → 86
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01235
      Location:1699 → 1804
      PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
      cd13339
      Location:839 → 957
      PH-GRAM_MTMR13; Myotubularian (MTM) related 13 protein Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      cd14589
      Location:1095 → 1442
      PTP-MTMR13; protein tyrosine phosphatase-like pseudophosphatase domain of myotubularin related phosphoinositide phosphatase 13
      pfam02141
      Location:116 → 298
      DENN; DENN (AEX-3) domain
      pfam12335
      Location:488 → 711
      SBF2; Myotubularin protein

    3. NM_001424318.1 → NP_001411247.1  myotubularin-related protein 13 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC011092, AC026250, AC080023, AC100763

    4. NM_001425069.1 → NP_001411998.1  myotubularin-related protein 13 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC011092, AC026250, AC080023, AC100763

    5. NM_001425070.1 → NP_001411999.1  myotubularin-related protein 13 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC011092, AC026250, AC080023, AC100763

    6. NM_030962.4 → NP_112224.1  myotubularin-related protein 13 isoform 2

      See identical proteins and their annotated locations for NP_112224.1

      Status: REVIEWED

      Source sequence(s)
      AC011092, AC026250, AC080023, AC100763
      Consensus CDS
      CCDS31427.1
      UniProtKB/Swiss-Prot
      Q3MJF0, Q68DQ3, Q6P459, Q6PJD1, Q7Z325, Q7Z621, Q86VE2, Q86WG5, Q96FE2, Q9C097
      UniProtKB/TrEMBL
      A0A8I5KWY5
      Related
      ENSP00000256190.8, ENST00000256190.13
      Conserved Domains (8) summary
      smart00801
      Location:352 → 420
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:1 → 86
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      cd01235
      Location:1742 → 1847
      PH_Sbf1_hMTMR5; Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain
      cd13339
      Location:882 → 1000
      PH-GRAM_MTMR13; Myotubularian (MTM) related 13 protein Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain
      pfam00169
      Location:1747 → 1847
      PH; PH domain
      pfam02141
      Location:116 → 298
      DENN; DENN (AEX-3) domain
      pfam06602
      Location:1116 → 1519
      Myotub-related; Myotubularin-like phosphatase domain
      pfam12335
      Location:531 → 754
      SBF2; Myotubularin protein

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      9778668..10303837 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047427657.1 → XP_047283613.1  myotubularin-related protein 13 isoform X1

    2. XM_011520395.4 → XP_011518697.1  myotubularin-related protein 13 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PH87
      Related
      ENSP00000502578.1, ENST00000676324.2
      Conserved Domains (6) summary
      smart00801
      Location:352 → 420
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:1 → 86
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      pfam02141
      Location:116 → 298
      DENN; DENN (AEX-3) domain
      pfam12335
      Location:531 → 754
      SBF2; Myotubularin protein
      cl17171
      Location:882 → 1000
      PH-like; Pleckstrin homology-like domain
      cl21483
      Location:1116 → 1248
      PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

    3. XM_047427658.1 → XP_047283614.1  myotubularin-related protein 13 isoform X4

    4. XM_011520396.4 → XP_011518698.1  myotubularin-related protein 13 isoform X3

      Related
      ENSP00000509247.1, ENST00000533770.6
      Conserved Domains (5) summary
      smart00801
      Location:352 → 420
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:1 → 86
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      pfam02141
      Location:116 → 298
      DENN; DENN (AEX-3) domain
      pfam12335
      Location:531 → 754
      SBF2; Myotubularin protein
      cl17171
      Location:882 → 1000
      PH-like; Pleckstrin homology-like domain

    5. XM_017018377.3 → XP_016873866.1  myotubularin-related protein 13 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      9863048..10388341 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370087.1 → XP_054226062.1  myotubularin-related protein 13 isoform X10

    2. XM_054370086.1 → XP_054226061.1  myotubularin-related protein 13 isoform X9

    3. XM_054370082.1 → XP_054226057.1  myotubularin-related protein 13 isoform X6

    4. XM_054370083.1 → XP_054226058.1  myotubularin-related protein 13 isoform X7

    5. XM_054370085.1 → XP_054226060.1  myotubularin-related protein 13 isoform X8

    6. XM_054370084.1 → XP_054226059.1  myotubularin-related protein 13 isoform X8

    7. XM_054370088.1 → XP_054226063.1  myotubularin-related protein 13 isoform X1

    8. XM_054370089.1 → XP_054226064.1  myotubularin-related protein 13 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8PH87

    9. XM_054370090.1 → XP_054226065.1  myotubularin-related protein 13 isoform X3

    10. XM_054370091.1 → XP_054226066.1  myotubularin-related protein 13 isoform X4

    11. XM_054370092.1 → XP_054226067.1  myotubularin-related protein 13 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86WG5.1 GenPept UniProtKB/Swiss-Prot:Q86WG5

    Gene LinkOut

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