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    SLFN12 schlafen family member 12 [ Homo sapiens (human) ]

    Gene ID: 55106, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SLFN12provided by HGNC
    Official Full Name
    schlafen family member 12provided by HGNC
    Primary source
    HGNC:HGNC:25500
    See related
    Ensembl:ENSG00000172123 MIM:614955; AllianceGenome:HGNC:25500
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SLFN3
    Summary
    Enables RNA nuclease activity and ribosome binding activity. Involved in apoptotic signaling pathway and rRNA catabolic process. Part of cytosol and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in spleen (RPKM 3.5), urinary bladder (RPKM 3.0) and 24 other tissues See more
    Orthologs
    all
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    Genomic context

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    See SLFN12 in Genome Data Viewer
    Location:
    17q12
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (35410922..35433174, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (36351811..36381711, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (33737941..33760193, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene UFM1 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:33720941-33721442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:33721443-33721942 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:33735070-33735283 Neighboring gene DTW domain containing 2 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12067 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:33759523-33760722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12069 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:33760881-33761606 Neighboring gene schlafen family member 13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12070 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8437 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr17:33776099-33776600 and GRCh37_chr17:33776601-33777100 Neighboring gene adenylosuccinate synthase 2 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8438

    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. Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells. Kobayashi-Ishihara M, et al. Commun Biol, 2023 May 10. PMID 37165099, Free PMC Article
    2. Schlafen 12 expression modulates prostate cancer cell differentiation. Kovalenko PL, et al. J Surg Res, 2014 Jul. PMID 24768141, Free PMC Article
    3. Schlafen12 Reduces the Aggressiveness of Triple Negative Breast Cancer through Post-Transcriptional Regulation of ZEB1 That Drives Stem Cell Differentiation. Al-Marsoummi S, et al. Cell Physiol Biochem, 2019. PMID 31838790, Free PMC Article
    4. Multiple PDE3A modulators act as molecular glues promoting PDE3A-SLFN12 interaction and induce SLFN12 dephosphorylation and cell death. Yan B, et al. Cell Chem Biol, 2022 Jun 16. PMID 35104454
    5. Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase. Garvie CW, et al. Nat Commun, 2021 Jul 16. PMID 34272366, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells.
      Title: Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells.
    2. Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase.
      Title: Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase.
    3. HSLFN12's partner hSerpinB12 may contribute to heterochromatin formation.
      Title: Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulation.
    4. The SLFN12 protein and an apoptosis activation marker were co-localized in syncytiotrophoblast of human placentas, where levels of estrogen-related hormones are high, and dynamic cell turnover by apoptosis is critical for successful implantation and placenta development.
      Title: Estrogen-Related Hormones Induce Apoptosis by Stabilizing Schlafen-12 Protein Turnover.
    5. SLFN12 overexpression reduced MDA-MB-231 mammosphere formation. SLFN12 overexpression decreased ZEB1 and Slug protein despite increased ZEB1 and Slug mRNA . SLFN12 knockdown increased ZEB1 protein. Co-expressing ZEB1 attenuated the SLFN12 effect on E-cadherin mRNA and proliferation.
      Title: Schlafen12 Reduces the Aggressiveness of Triple Negative Breast Cancer through Post-Transcriptional Regulation of ZEB1 That Drives Stem Cell Differentiation.
    6. Schlafen 12 (SLFN12) is a cytosolic protein that stimulates sucrase-isomaltase (SI) expression.
      Title: Schlafen 12 mediates the effects of butyrate and repetitive mechanical deformation on intestinal epithelial differentiation in human Caco-2 intestinal epithelial cells.
    7. SLFN12 regulates human enterocytic differentiation by a pathway involving SERPB12, the deubiquitylases, and Cdx2.
      Title: Schlafen 12 Interaction with SerpinB12 and Deubiquitylases Drives Human Enterocyte Differentiation.
    8. Vulnerability to antineoplastic phosphodiesterase inhibitors inhibitors has been associated with co-expression of PDE3A and SLFN12 in various tumor types.
      Title: Targeting tumor cells based on Phosphodiesterase 3A expression.
    9. Ad-SLFN12 overexpression increased the ratio of the mature E-cadherin protein to its precursor protein
      Title: Schlafen 12 expression modulates prostate cancer cell differentiation.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • FLJ10260

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA nuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA nuclease activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ribosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in apoptotic signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in rRNA catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in rRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ribonuclease SLFN12

    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_001289009.2 → NP_001275938.1  ribonuclease SLFN12

      See identical proteins and their annotated locations for NP_001275938.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC060766, AK291826, CB045471
      Consensus CDS
      CCDS11295.1
      UniProtKB/Swiss-Prot
      A8K711, Q8IYM2, Q9NP47
      Related
      ENSP00000394903.2, ENST00000452764.3
      Conserved Domains (1) summary
      cl27772
      Location:35 → 341
      B3R; Poxviridae B3 protein

    2. NM_018042.5 → NP_060512.3  ribonuclease SLFN12

      See identical proteins and their annotated locations for NP_060512.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AK001122, BC035605, CB045471
      Consensus CDS
      CCDS11295.1
      UniProtKB/Swiss-Prot
      A8K711, Q8IYM2, Q9NP47
      Related
      ENSP00000302077.5, ENST00000304905.10
      Conserved Domains (1) summary
      cl27772
      Location:35 → 341
      B3R; Poxviridae B3 protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      35410922..35433174 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005257995.6 → XP_005258052.1  ribonuclease SLFN12 isoform X1

      See identical proteins and their annotated locations for XP_005258052.1

      UniProtKB/Swiss-Prot
      A8K711, Q8IYM2, Q9NP47
      Related
      ENSP00000398315.3, ENST00000447040.7
      Conserved Domains (1) summary
      cl27772
      Location:35 → 341
      B3R; Poxviridae B3 protein

    2. XM_024450822.2 → XP_024306590.1  ribonuclease SLFN12 isoform X1

      UniProtKB/Swiss-Prot
      A8K711, Q8IYM2, Q9NP47
      Related
      ENSP00000404175.2, ENST00000445092.6
      Conserved Domains (1) summary
      cl27772
      Location:35 → 341
      B3R; Poxviridae B3 protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      36351811..36381711 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054316600.1 → XP_054172575.1  ribonuclease SLFN12 isoform X1

    2. XM_054316599.1 → XP_054172574.1  ribonuclease SLFN12 isoform X1

    3. XM_054316598.1 → XP_054172573.1  ribonuclease SLFN12 isoform X1

    RNA

    1. XR_008484855.1 RNA Sequence

    2. XR_008484854.1 RNA Sequence

    3. XR_008484852.1 RNA Sequence

    4. XR_008484856.1 RNA Sequence

    5. XR_008484853.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IYM2.2 GenPept UniProtKB/Swiss-Prot:Q8IYM2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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