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    SLFN13 schlafen family member 13 [ Homo sapiens (human) ]

    Gene ID: 146857, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SLFN13provided by HGNC
    Official Full Name
    schlafen family member 13provided by HGNC
    Primary source
    HGNC:HGNC:26481
    See related
    Ensembl:ENSG00000154760 MIM:614957; AllianceGenome:HGNC:26481
    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
    SLFN10; hSLFN13
    Summary
    Enables RNA endonuclease activity. Involved in rRNA catabolic process and tRNA decay. Located in cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in bone marrow (RPKM 5.2), spleen (RPKM 4.2) and 24 other tissues See more
    Orthologs
    all
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    Genomic context

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    See SLFN13 in Genome Data Viewer
    Location:
    17q12
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (35435096..35449766, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (36383091..36397836, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (33762115..33775785, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes 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 schlafen family member 12 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 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 Neighboring gene schlafen family member 12 like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12072 Neighboring gene Sharpr-MPRA regulatory region 9708 Neighboring gene E2F transcription factor 3 pseudogene 1

    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. Structure of Schlafen13 reveals a new class of tRNA/rRNA- targeting RNase engaged in translational control. Yang JY, et al. Nat Commun, 2018 Mar 21. PMID 29563550, Free PMC Article
    2. Schlafen, a new family of growth regulatory genes that affect thymocyte development. Schwarz DA, et al. Immunity, 1998 Nov. PMID 9846487
    3. USP7 Cooperates with NOTCH1 to Drive the Oncogenic Transcriptional Program in T-Cell Leukemia. Jin Q, et al. Clin Cancer Res, 2019 Jan 1. PMID 30224337, Free PMC Article
    4. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. Simpson JC, et al. EMBO Rep, 2000 Sep. PMID 11256614, Free PMC Article
    5. The LIFEdb database in 2006. Mehrle A, et al. Nucleic Acids Res, 2006 Jan 1. PMID 16381901, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The cytoplasmically localized SLFN13 inhibits protein synthesis in 293T cells and restricts HIV replication in a nucleolytic activity-dependent manner.
      Title: Structure of Schlafen13 reveals a new class of tRNA/rRNA- targeting RNase engaged in translational control.
    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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    Markers

    Homology

    Clone Names

    • FLJ31952, DKFZp666J196, DKFZp686I026

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA endonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in defense response to virus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in rRNA catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA decay IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    schlafen family member 13
    Names
    schlafen-13

    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_144682.6 → NP_653283.3  schlafen family member 13

      See identical proteins and their annotated locations for NP_653283.3

      Status: VALIDATED

      Source sequence(s)
      AC015911, AC060766, CR749630, DA720331
      Consensus CDS
      CCDS32620.1
      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81
      UniProtKB/TrEMBL
      B7ZVY5
      Related
      ENSP00000285013.6, ENST00000285013.11
      Conserved Domains (3) summary
      cl21455
      Location:595 → 676
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
      cl22977
      Location:848 → 895
      UvrD_C_2; UvrD-like helicase C-terminal domain
      cl27772
      Location:15 → 347
      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
      35435096..35449766 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435464.1 → XP_047291420.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    2. XM_047435468.1 → XP_047291424.1  schlafen family member 13 isoform X2

      UniProtKB/TrEMBL
      B3KV92

    3. XM_047435460.1 → XP_047291416.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    4. XM_047435462.1 → XP_047291418.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    5. XM_024450614.2 → XP_024306382.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81
      UniProtKB/TrEMBL
      B7ZVY5
      Conserved Domains (3) summary
      cl21455
      Location:595 → 676
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
      cl22977
      Location:848 → 895
      UvrD_C_2; UvrD-like helicase C-terminal domain
      cl27772
      Location:15 → 347
      B3R; Poxviridae B3 protein

    6. XM_047435467.1 → XP_047291423.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81
      Related
      ENSP00000467426.1, ENST00000533791.5

    7. XM_011524383.3 → XP_011522685.1  schlafen family member 13 isoform X2

      See identical proteins and their annotated locations for XP_011522685.1

      UniProtKB/TrEMBL
      B3KV92, B3KWY1
      Related
      ENSP00000435442.1, ENST00000534689.5
      Conserved Domains (2) summary
      cl21455
      Location:264 → 345
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
      cl22977
      Location:517 → 564
      UvrD_C_2; UvrD-like helicase C-terminal domain

    8. XM_047435463.1 → XP_047291419.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81
      Related
      ENSP00000434439.1, ENST00000526861.5

    9. XM_017024233.2 → XP_016879722.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81
      UniProtKB/TrEMBL
      B7ZVY5
      Conserved Domains (3) summary
      cl21455
      Location:595 → 676
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
      cl22977
      Location:848 → 895
      UvrD_C_2; UvrD-like helicase C-terminal domain
      cl27772
      Location:15 → 347
      B3R; Poxviridae B3 protein

    10. XM_005257922.3 → XP_005257979.1  schlafen family member 13 isoform X1

      See identical proteins and their annotated locations for XP_005257979.1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81
      UniProtKB/TrEMBL
      B7ZVY5
      Conserved Domains (3) summary
      cl21455
      Location:595 → 676
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
      cl22977
      Location:848 → 895
      UvrD_C_2; UvrD-like helicase C-terminal domain
      cl27772
      Location:15 → 347
      B3R; Poxviridae B3 protein

    11. XM_047435465.1 → XP_047291421.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    12. XM_047435461.1 → XP_047291417.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      36383091..36397836 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315203.1 → XP_054171178.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    2. XM_054315199.1 → XP_054171174.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    3. XM_054315201.1 → XP_054171176.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    4. XM_054315196.1 → XP_054171171.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    5. XM_054315207.1 → XP_054171182.1  schlafen family member 13 isoform X2

      UniProtKB/TrEMBL
      B3KV92

    6. XM_054315198.1 → XP_054171173.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    7. XM_054315204.1 → XP_054171179.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    8. XM_054315206.1 → XP_054171181.1  schlafen family member 13 isoform X2

      UniProtKB/TrEMBL
      B3KV92

    9. XM_054315202.1 → XP_054171177.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    10. XM_054315197.1 → XP_054171172.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    11. XM_054315205.1 → XP_054171180.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81

    12. XM_054315200.1 → XP_054171175.1  schlafen family member 13 isoform X1

      UniProtKB/Swiss-Prot
      E1P645, Q658M1, Q68D06, Q6ZS51, Q96A81
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q68D06.1 GenPept UniProtKB/Swiss-Prot:Q68D06

    Gene LinkOut

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

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