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

Gene ID: 116461, updated on 23-Nov-2021

Summary

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
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

See TSEN15 in Genome Data Viewer
Location:
1q25.3
Exon count:
8
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (184051730..184097485)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (184020864..184066619)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene collagen beta(1-O)galactosyltransferase 2 Neighboring gene NFE2L2 motif-containing MPRA enhancer 281 Neighboring gene Sharpr-MPRA regulatory region 12313 Neighboring gene Sharpr-MPRA regulatory region 13835 Neighboring gene uncharacterized LOC102724830 Neighboring gene RNA, 7SL, cytoplasmic 654, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
GeneReviews: Not available
Many sequence variants affecting diversity of adult human height.
GeneReviews: Not available
Pontocerebellar hypoplasia, type 2f
MedGen: C4310757 OMIM: 617026 GeneReviews: Not available
Compare labs

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables nuclease activity IEA
Inferred from Electronic Annotation
more info
 
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 nucleic acid phosphodiester bond hydrolysis 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

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_001127394.4NP_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/Swiss-Prot
    Q8WW01
    Related
    ENSP00000402002.2, ENST00000423085.7
    Conserved Domains (1) summary
    pfam09631
    Location:65119
    Sen15; Sen15 protein
  2. NM_001300764.2NP_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/Swiss-Prot
    Q8WW01
    Related
    ENSP00000355299.2, ENST00000361641.6
    Conserved Domains (1) summary
    pfam09631
    Location:65165
    Sen15; Sen15 protein
  3. NM_001300766.2NP_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/Swiss-Prot
    Q8WW01
    UniProtKB/TrEMBL
    E9PPN1
    Related
    ENSP00000436996.1, ENST00000533373.6
    Conserved Domains (1) summary
    pfam09631
    Location:65125
    Sen15; Sen15 protein
  4. NM_001363643.2NP_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
    Related
    ENSP00000494932.1, ENST00000643231.1
    Conserved Domains (1) summary
    pfam09631
    Location:65116
    Sen15; Sen15 protein
  5. NM_052965.4NP_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
    Q8WW01
    UniProtKB/TrEMBL
    B1ALV0
    Related
    ENSP00000493902.2, ENST00000645668.2
    Conserved Domains (1) summary
    pfam09631
    Location:65165
    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: Homo sapiens Updated Annotation Release 109.20211119

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

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