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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
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Genomic context

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See TSEN15 in Genome Data Viewer
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
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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

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