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] See more...

Aliases for TSEN15 Gene

Aliases for TSEN15 Gene

  • TRNA Splicing Endonuclease Subunit 15 2 3 5
  • TSEN15 TRNA Splicing Endonuclease Subunit 2 3
  • TRNA-Splicing Endonuclease Subunit Sen15 3 4
  • TRNA-Intron Endonuclease Sen15 3 4
  • C1orf19 3 4
  • TRNA Splicing Endonuclease 15 Homolog (S. Cerevisiae) 2
  • TRNA Splicing Endonuclease 15 Homolog 3
  • Chromosome 1 Open Reading Frame 19 2
  • SEN15 Homolog 4
  • HsSEN15 4
  • PCH2F 3
  • Sen15 3
  • SEN15 4

External Ids for TSEN15 Gene

Previous HGNC Symbols for TSEN15 Gene

  • C1orf19

Previous GeneCards Identifiers for TSEN15 Gene

  • GC01P182288
  • GC01P155256

Summaries for TSEN15 Gene

Entrez Gene Summary for TSEN15 Gene

  • 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]

GeneCards Summary for TSEN15 Gene

TSEN15 (TRNA Splicing Endonuclease Subunit 15) is a Protein Coding gene. Diseases associated with TSEN15 include Pontocerebellar Hypoplasia, Type 2F and Primary Microcephaly. Among its related pathways are tRNA processing and Gene Expression. Gene Ontology (GO) annotations related to this gene include tRNA-intron endonuclease activity.

UniProtKB/Swiss-Prot Summary for TSEN15 Gene

  • Non-catalytic subunit of the tRNA-splicing endonuclease complex, a complex responsible for identification and cleavage of the splice sites in pre-tRNA. It cleaves pre-tRNA at the 5' and 3' splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-OH termini (PubMed:15109492, PubMed:27392077). There are no conserved sequences at the splice sites, but the intron is invariably located at the same site in the gene, placing the splice sites an invariant distance from the constant structural features of the tRNA body. The tRNA splicing endonuclease is also involved in mRNA processing via its association with pre-mRNA 3'-end processing factors, establishing a link between pre-tRNA splicing and pre-mRNA 3'-end formation, suggesting that the endonuclease subunits function in multiple RNA-processing events (PubMed:15109492).

Gene Wiki entry for TSEN15 Gene

Additional gene information for TSEN15 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TSEN15 Gene

Genomics for TSEN15 Gene

GeneHancer (GH) Regulatory Elements for TSEN15 Gene

Promoters and enhancers for TSEN15 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J184050 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 508.4 +0.4 370 3.2 EP300 HNRNPK ZBTB40 ZNF217 SIN3A NRF1 TCF12 POLR2G SP1 GTF2E2 TSEN15 COLGALT2 LAMC1-AS1 ENSG00000271387 LAMC2 RF00994-071
GH01J184036 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 7.8 -14.7 -14717 2.7 HNRNPK NRF1 POLR2G GTF2E2 CTCF ZIC2 REST ZBTB10 ZBTB11 ZNF423 COLGALT2 SMG7 TSEN15 RGL1 piR-45035-015
GH01J183955 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 10.3 -95.1 -95107 4 RXRA CTCF SP1 JUND EP300 RELA MEF2C RCOR1 RAD21 CTBP1 COLGALT2 TSEN15 HSALNG0008988 lnc-COLGALT2-6
GH01J183945 Enhancer 1.2 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.8 -106.1 -106051 1.2 ZSCAN5C RUNX1 ATF2 HDAC2 NCOR1 RXRA NANOG TCF12 PBX2 NR2F1 TSEN15 COLGALT2 lnc-COLGALT2-6 HSALNG0008988
GH01J184059 Enhancer 0.8 Ensembl ENCODE 14.8 +10.3 10264 4.6 EP300 ZSCAN5C AFF1 WT1 ZNF316 MAFF EZH2 ZNF335 PRDM6 ZNF3 TSEN15 RF00994-071
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TSEN15 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TSEN15

Top Transcription factor binding sites by QIAGEN in the TSEN15 gene promoter:
  • AP-2rep
  • E4BP4
  • FOXC1
  • FOXI1
  • HFH-1
  • HFH-3
  • Nkx2-5
  • POU6F1 (c2)
  • STAT3

Genomic Locations for TSEN15 Gene

Genomic Locations for TSEN15 Gene
chr1:184,051,651-184,123,978
(GRCh38/hg38)
Size:
72,328 bases
Orientation:
Plus strand
chr1:184,020,811-184,043,346
(GRCh37/hg19)
Size:
22,536 bases
Orientation:
Plus strand

Genomic View for TSEN15 Gene

Genes around TSEN15 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TSEN15 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TSEN15 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TSEN15 Gene

Proteins for TSEN15 Gene

  • Protein details for TSEN15 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WW01-SEN15_HUMAN
    Recommended name:
    tRNA-splicing endonuclease subunit Sen15
    Protein Accession:
    Q8WW01
    Secondary Accessions:
    • B4DKP0
    • Q9BZQ5

    Protein attributes for TSEN15 Gene

    Size:
    171 amino acids
    Molecular mass:
    18641 Da
    Quaternary structure:
    • Homodimer (PubMed:17166513). tRNA splicing endonuclease is a heterotetramer composed of TSEN2, TSEN15, TSEN34/LENG5 and TSEN54. tRNA splicing endonuclease complex also contains proteins of the Pre-mRNA 3' end processing machinery, such as CLP1, CPSF1, CPSF4 and CSTF2.
    SequenceCaution:
    • Sequence=AAG60614.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TSEN15 Gene

    Alternative splice isoforms for TSEN15 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TSEN15 Gene

Post-translational modifications for TSEN15 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for TSEN15 Gene

Domains & Families for TSEN15 Gene

Gene Families for TSEN15 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for TSEN15 Gene

Suggested Antigen Peptide Sequences for TSEN15 Gene

GenScript: Design optimal peptide antigens:
  • tRNA splicing endonuclease 15 homolog (S. cerevisiae) (B1ALU9_HUMAN)
  • tRNA splicing endonuclease 15 homolog (S. cerevisiae) (B1ALV0_HUMAN)
  • tRNA splicing endonuclease 15 homolog (S. cerevisiae) (B1ALV1_HUMAN)
  • cDNA FLJ50793, highly similar to tRNA-splicing endonuclease subunit Sen15 (B4DKP0_HUMAN)
  • tRNA-intron endonuclease Sen15 (SEN15_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8WW01

UniProtKB/Swiss-Prot:

SEN15_HUMAN :
  • Belongs to the SEN15 family.
Family:
  • Belongs to the SEN15 family.
genes like me logo Genes that share domains with TSEN15: view

Function for TSEN15 Gene

Molecular function for TSEN15 Gene

UniProtKB/Swiss-Prot Function:
Non-catalytic subunit of the tRNA-splicing endonuclease complex, a complex responsible for identification and cleavage of the splice sites in pre-tRNA. It cleaves pre-tRNA at the 5' and 3' splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-OH termini (PubMed:15109492, PubMed:27392077). There are no conserved sequences at the splice sites, but the intron is invariably located at the same site in the gene, placing the splice sites an invariant distance from the constant structural features of the tRNA body. The tRNA splicing endonuclease is also involved in mRNA processing via its association with pre-mRNA 3'-end processing factors, establishing a link between pre-tRNA splicing and pre-mRNA 3'-end formation, suggesting that the endonuclease subunits function in multiple RNA-processing events (PubMed:15109492).

Phenotypes From GWAS Catalog for TSEN15 Gene

Gene Ontology (GO) - Molecular Function for TSEN15 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000213 tRNA-intron endonuclease activity IEA --
GO:0003676 nucleic acid binding IEA --
GO:0004518 nuclease activity IEA --
GO:0004519 endonuclease activity IEA --
genes like me logo Genes that share ontologies with TSEN15: view
genes like me logo Genes that share phenotypes with TSEN15: view

Human Phenotype Ontology for TSEN15 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for TSEN15 Gene

miRTarBase miRNAs that target TSEN15

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for TSEN15 Gene

Localization for TSEN15 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TSEN15 Gene

Nucleus. Nucleus, nucleolus. Note=May be transiently localized in the nucleolus. {ECO:0000305}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TSEN15 gene
Compartment Confidence
nucleus 5
cytosol 3
cytoskeleton 1
mitochondrion 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TSEN15 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IEA --
genes like me logo Genes that share ontologies with TSEN15: view

Pathways & Interactions for TSEN15 Gene

PathCards logo

SuperPathways for TSEN15 Gene

genes like me logo Genes that share pathways with TSEN15: view

Pathways by source for TSEN15 Gene

3 Reactome pathways for TSEN15 Gene

Gene Ontology (GO) - Biological Process for TSEN15 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation TAS,IEA --
GO:0006397 mRNA processing IEA --
GO:0008033 tRNA processing IEA --
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
GO:0090501 RNA phosphodiester bond hydrolysis IEA --
genes like me logo Genes that share ontologies with TSEN15: view

No data available for SIGNOR curated interactions for TSEN15 Gene

Drugs & Compounds for TSEN15 Gene

No Compound Related Data Available

Transcripts for TSEN15 Gene

mRNA/cDNA for TSEN15 Gene

5 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
20 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TSEN15 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c · 6d · 6e ^ 7a · 7b · 7c · 7d · 7e · 7f
SP1: - - - -
SP2: - - - - -
SP3: - - - - - - -
SP4: - - - -
SP5: - -
SP6: - - - -
SP7: - - - - - - - -
SP8: -
SP9: - - -

Relevant External Links for TSEN15 Gene

GeneLoc Exon Structure for
TSEN15

Expression for TSEN15 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TSEN15 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TSEN15 Gene

This gene is overexpressed in Fetal Brain (11.4), Pancreas (9.8), NK cells (7.3), and Ovary (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TSEN15 Gene



Protein tissue co-expression partners for TSEN15 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TSEN15

SOURCE GeneReport for Unigene cluster for TSEN15 Gene:

Hs.548197

mRNA Expression by UniProt/SwissProt for TSEN15 Gene:

Q8WW01-SEN15_HUMAN
Tissue specificity: Widely expressed. Highly expressed in testis and uterus.

Evidence on tissue expression from TISSUES for TSEN15 Gene

  • Intestine(4.2)
  • Nervous system(2.4)
genes like me logo Genes that share expression patterns with TSEN15: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TSEN15 Gene

Orthologs for TSEN15 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TSEN15 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TSEN15 31 30
  • 99.22 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TSEN15 31 30
  • 89.48 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TSEN15 31 30
  • 89.29 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Tsen15 17 31 30
  • 87.9 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TSEN15 31
  • 47 (a)
OneToOne
chicken
(Gallus gallus)
Aves TSEN15 31 30
  • 66.14 (n)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tsen15 30
  • 59.47 (n)
zebrafish
(Danio rerio)
Actinopterygii tsen15 31 30
  • 51.39 (n)
OneToOne
Species where no ortholog for TSEN15 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TSEN15 Gene

ENSEMBL:
Gene Tree for TSEN15 (if available)
TreeFam:
Gene Tree for TSEN15 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TSEN15: view image

Paralogs for TSEN15 Gene

(1) SIMAP similar genes for TSEN15 Gene using alignment to 4 proteins:

  • SEN15_HUMAN
  • E9PPN1_HUMAN
  • F2Z3M0_HUMAN
  • H0YCV5_HUMAN

Pseudogenes.org Pseudogenes for TSEN15 Gene

genes like me logo Genes that share paralogs with TSEN15: view

No data available for Paralogs for TSEN15 Gene

Variants for TSEN15 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TSEN15 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs1557877253 Uncertain Significance: not provided 184,054,751(+) T/C MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs730882223 Pathogenic/Likely Pathogenic: Seizures; Global developmental delay; Primary microcephaly; Pontocerebellar hypoplasia, type 2f. Pontocerebellar hypoplasia 2F (PCH2F) [MIM:617026] 184,054,736(+) T/Gp.Trp76Gly MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs879253779 Pathogenic: Pontocerebellar hypoplasia, type 2f. Pontocerebellar hypoplasia 2F (PCH2F) [MIM:617026] 184,072,258(+) A/Gp.Tyr152Cys MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT
rs879253780 Pathogenic: Pontocerebellar hypoplasia, type 2f. Pontocerebellar hypoplasia 2F (PCH2F) [MIM:617026] 184,054,856(+) C/Tp.His116Tyr MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs1046934 - p.Gln59His

Additional dbSNP identifiers (rs#s) for TSEN15 Gene

Variation tolerance for TSEN15 Gene

Residual Variation Intolerance Score: 55.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.91; 94.88% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TSEN15 Gene

Human Gene Mutation Database (HGMD)
TSEN15
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TSEN15

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for TSEN15 Gene

Disorders for TSEN15 Gene

MalaCards: The human disease database

(10) MalaCards diseases for TSEN15 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SEN15_HUMAN
  • Pontocerebellar hypoplasia 2F (PCH2F) [MIM:617026]: A neurodevelopmental disorder characterized by progressive microcephaly, cognitive and motor delay, poor or absent speech, seizures, and spasticity. PCH2F inheritance is autosomal recessive. {ECO:0000269 PubMed:25558065, ECO:0000269 PubMed:27392077}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TSEN15

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TSEN15: view

No data available for Genatlas for TSEN15 Gene

Publications for TSEN15 Gene

  1. Three-dimensional structure determined for a subunit of human tRNA splicing endonuclease (Sen15) reveals a novel dimeric fold. (PMID: 17166513) Song J … Markley JL (Journal of molecular biology 2007) 2 3 4 23 54
  2. Cloning and characterization of 13 novel transcripts and the human RGS8 gene from the 1q25 region encompassing the hereditary prostate cancer (HPC1) locus. (PMID: 11318611) Sood R … Carpten JD (Genomics 2001) 2 3 4 54
  3. Autosomal-Recessive Mutations in the tRNA Splicing Endonuclease Subunit TSEN15 Cause Pontocerebellar Hypoplasia and Progressive Microcephaly. (PMID: 27392077) Breuss MW … Gleeson JG (American journal of human genetics 2016) 3 4 54
  4. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. (PMID: 20546612) Zhao J … Grant SF (BMC medical genetics 2010) 3 41 54
  5. Many sequence variants affecting diversity of adult human height. (PMID: 18391951) Gudbjartsson DF … Stefansson K (Nature genetics 2008) 3 41 54

Products for TSEN15 Gene

Sources for TSEN15 Gene