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

Gene ID: 146857, updated on 28-Oct-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, Oct 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 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)

Genotypes

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

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