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

Gene ID: 55106, updated on 5-Mar-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
Predicted to act upstream of or within negative regulation of cell population proliferation. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in spleen (RPKM 3.5), urinary bladder (RPKM 3.0) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
17q12
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (35410922..35433174, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (36351811..36381711, complement)
105.20220307 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. 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
  3. Schlafen 12 expression modulates prostate cancer cell differentiation. Kovalenko PL, et al. J Surg Res, 2014 Jul. PMID 24768141, 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)

Genotypes

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_2023_10

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
    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
    ENSP00000378063.1, ENST00000394562.5
    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

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