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    TSEN15 tRNA splicing endonuclease subunit 15 [ Homo sapiens (human) ]

    Gene ID: 116461, updated on 3-Apr-2024

    Summary

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    Official Symbol
    TSEN15provided by HGNC
    Official Full Name
    tRNA splicing endonuclease subunit 15provided by HGNC
    Primary source
    HGNC:HGNC:16791
    See related
    Ensembl:ENSG00000198860 MIM:608756; AllianceGenome:HGNC:16791
    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
    PCH2F; sen15; C1orf19
    Summary
    This gene encodes a subunit of the tRNA splicing endonuclease, which catalyzes the removal of introns from tRNA precursors. Alternative splicing results in multiple transcript variants. There is a pseudogene of this gene on chromosome 17. [provided by RefSeq, Jul 2014]
    Expression
    Ubiquitous expression in thyroid (RPKM 5.4), brain (RPKM 4.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1q25.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (184051730..184097485)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (183414898..183460648)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (184020864..184066619)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ral guanine nucleotide dissociation stimulator like 1 Neighboring gene T-box transcription factor T pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:183692952-183693452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2228 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:183887920-183888109 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:183913934-183914776 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:183914777-183915619 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:183924966-183925130 Neighboring gene collagen beta(1-O)galactosyltransferase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2229 Neighboring gene NFE2L2 motif-containing MPRA enhancer 281 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:183993995-183994734 Neighboring gene Sharpr-MPRA regulatory region 12313 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1636 Neighboring gene Sharpr-MPRA regulatory region 13835 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:184037463-184038001 Neighboring gene uncharacterized LOC102724830 Neighboring gene uncharacterized LOC124904466

    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. Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia. Sekulovski S, et al. Nat Commun, 2021 Sep 28. PMID 34584079, Free PMC Article
    2. Autosomal-Recessive Mutations in the tRNA Splicing Endonuclease Subunit TSEN15 Cause Pontocerebellar Hypoplasia and Progressive Microcephaly. Breuss MW, et al. Am J Hum Genet, 2016 Jul 7. PMID 27392077, Free PMC Article
    3. Genetic variants related to height and risk of atrial fibrillation: the cardiovascular health study. Rosenberg MA, et al. Am J Epidemiol, 2014 Jul 15. PMID 24944287, Free PMC Article
    4. Three-dimensional structure determined for a subunit of human tRNA splicing endonuclease (Sen15) reveals a novel dimeric fold. Song J, et al. J Mol Biol, 2007 Feb 9. PMID 17166513, Free PMC Article
    5. Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3' end formation. Paushkin SV, et al. Cell, 2004 Apr 30. PMID 15109492

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia.
      Title: Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia.
    2. results demonstrate that mutations in any known subunit of the TSEN complex can cause pontocerebellar hypoplasia and progressive microcephaly, emphasizing the importance of its function during brain development
      Title: Autosomal-Recessive Mutations in the tRNA Splicing Endonuclease Subunit TSEN15 Cause Pontocerebellar Hypoplasia and Progressive Microcephaly.
    3. A candidate SNP associated with the tRNA-splicing protein gene TSEN15 was independently associated with the risk of atrial fibrillation.
      Title: Genetic variants related to height and risk of atrial fibrillation: the cardiovascular health study.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature.
    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

    Associated conditions

    Description Tests
    Pontocerebellar hypoplasia, type 2F
    MedGen: C4310757 OMIM: 617026 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables nucleic acid 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 mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tRNA splicing, via endonucleolytic cleavage and ligation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    tRNA-splicing endonuclease subunit Sen15
    Names
    TSEN15 tRNA splicing endonuclease subunit
    tRNA splicing endonuclease 15 homolog
    tRNA-intron endonuclease Sen15

    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.

    Genomic

    1. NG_050569.1 RefSeqGene

      Range
      5080..27562
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001127394.4 → NP_001120866.1  tRNA-splicing endonuclease subunit Sen15 isoform 2

      See identical proteins and their annotated locations for NP_001120866.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AF288394, BC022030, BM887891
      Consensus CDS
      CCDS44286.1
      UniProtKB/TrEMBL
      F2Z3M0
      Related
      ENSP00000402002.2, ENST00000423085.7
      Conserved Domains (1) summary
      pfam09631
      Location:65 → 119
      Sen15; Sen15 protein

    2. NM_001300764.2 → NP_001287693.1  tRNA-splicing endonuclease subunit Sen15 isoform 3

      See identical proteins and their annotated locations for NP_001287693.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is longer than isoform 1.
      Source sequence(s)
      BC022030, BM146150, BP326115
      Consensus CDS
      CCDS86038.1
      UniProtKB/TrEMBL
      A0A2R8Y6A4, A0A2U3TZM3
      Related
      ENSP00000355299.2, ENST00000361641.6
      Conserved Domains (1) summary
      pfam09631
      Location:65 → 165
      Sen15; Sen15 protein

    3. NM_001300766.2 → NP_001287695.1  tRNA-splicing endonuclease subunit Sen15 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      BC022030, BI821111
      Consensus CDS
      CCDS72993.1
      UniProtKB/TrEMBL
      E9PPN1, F2Z3M0
      Related
      ENSP00000436996.1, ENST00000533373.6
      Conserved Domains (1) summary
      pfam09631
      Location:65 → 125
      Sen15; Sen15 protein

    4. NM_001363643.2 → NP_001350572.1  tRNA-splicing endonuclease subunit Sen15 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (5) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AL157943, AL158011
      Consensus CDS
      CCDS91127.1
      UniProtKB/TrEMBL
      A0A2R8YDU8
      Related
      ENSP00000494932.1, ENST00000643231.1
      Conserved Domains (1) summary
      pfam09631
      Location:65 → 116
      Sen15; Sen15 protein

    5. NM_052965.4 → NP_443197.1  tRNA-splicing endonuclease subunit Sen15 isoform 1

      See identical proteins and their annotated locations for NP_443197.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AF288394, BC022030
      Consensus CDS
      CCDS1361.1
      UniProtKB/Swiss-Prot
      B4DKP0, Q8WW01, Q9BZQ5
      UniProtKB/TrEMBL
      A0A2R8Y6A4, B1ALV0
      Related
      ENSP00000493902.2, ENST00000645668.2
      Conserved Domains (1) summary
      pfam09631
      Location:65 → 165
      Sen15; Sen15 protein

    RNA

    1. NR_023349.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF288394, AK307241, BC022030
      Related
      ENST00000462677.3

    2. NR_125335.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC022030, BU195337
      Related
      ENST00000644145.1

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      184051730..184097485
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      183414898..183460648
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WW01.1 GenPept UniProtKB/Swiss-Prot:Q8WW01

    Gene LinkOut

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