Free for academic non-profit institutions. Other users need a Commercial license

Aliases for TSEN15 Gene

Aliases for TSEN15 Gene

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

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 2F and Pontocerebellar Hypoplasia, Type 2E. Among its related pathways are Gene Expression and tRNA processing. GO annotations related to this gene include tRNA-intron endonuclease activity.

UniProtKB/Swiss-Prot 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

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TSEN15 Gene

Genomics for TSEN15 Gene

Regulatory Elements for TSEN15 Gene

Enhancers for TSEN15 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G183955 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10.3 -94.6 -94559 2.9 PKNOX1 ATF1 WRNIP1 ELK1 CBX5 ZNF143 FOS JUNB TBX21 ZNF592 COLGALT2 TSEN15 GC01P183964 GC01M183940
GH01G184010 0.9 dbSUPER 19.2 -39.4 -39355 4.3 CBX3 CREB3L1 ZBTB40 CHAMP1 ZNF121 CREM ZBTB11 CEBPB TFDP1 ZNF589 COLGALT2 TSEN15 GC01P183964
GH01G184036 1.7 FANTOM5 ENCODE dbSUPER 7.8 -14.5 -14514 2.3 HDGF FOXA2 CREB3L1 ARNT FEZF1 ZNF2 YY1 SLC30A9 CBX5 ZNF302 COLGALT2 TSEN15 RGL1 GC01P183964
GH01G184059 0.8 ENCODE 14.8 +8.9 8949 1.9 CTCF CBX3 NFIB GTF2E2 ZNF175 IRF9 GLI2 SMARCE1 L3MBTL2 NFIA TSEN15 GC01M184052
GH01G183945 1 ENCODE dbSUPER 10.8 -106.0 -105993 1.0 LEF1 TBL1XR1 CHD7 POLR2A NCOR1 ZSCAN5C NR2F6 FOS RNF2 NR2F1 TSEN15 COLGALT2 GC01M183940 GC01M183931
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TSEN15 on UCSC Golden Path with GeneCards custom track

Promoters for TSEN15 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000016946 349 1601 CREB3L1 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 ZNF610

Genomic Location for TSEN15 Gene

Chromosome:
1
Start:
184,051,651 bp from pter
End:
184,095,846 bp from pter
Size:
44,196 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

Protein Domains for TSEN15 Gene

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).

Gene Ontology (GO) - Molecular Function for TSEN15 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000213 tRNA-intron endonuclease 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

Animal Model Products

CRISPR Products

miRNA for TSEN15 Gene

miRTarBase miRNAs that target TSEN15

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
peroxisome 1

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

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

Unigene Clusters for TSEN15 Gene

TRNA splicing endonuclease 15 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA 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
ECgene alternative splicing isoforms for
TSEN15

Expression for TSEN15 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for TSEN15 Gene



Protein tissue co-expression partners for TSEN15 Gene

NURSA nuclear receptor signaling pathways regulating expression of TSEN15 Gene:

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

Primer Products

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 34 35
  • 99.22 (n)
dog
(Canis familiaris)
Mammalia TSEN15 34 35
  • 89.48 (n)
cow
(Bos Taurus)
Mammalia TSEN15 34 35
  • 89.29 (n)
mouse
(Mus musculus)
Mammalia Tsen15 34 16 35
  • 87.9 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TSEN15 35
  • 47 (a)
OneToOne
chicken
(Gallus gallus)
Aves TSEN15 34 35
  • 66.14 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia tsen15 34
  • 59.47 (n)
zebrafish
(Danio rerio)
Actinopterygii tsen15 34 35
  • 51.39 (n)
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)

Paralogs for TSEN15 Gene

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

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 from dbSNP and Humsavar for TSEN15 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs730882223 Pathogenic, Pontocerebellar hypoplasia 2F (PCH2F) [MIM:617026] 184,054,736(+) AAAGC(G/T)GGCAT nc-transcript-variant, reference, missense
VAR_077062 Pontocerebellar hypoplasia 2F (PCH2F) [MIM:617026]
VAR_077063 Pontocerebellar hypoplasia 2F (PCH2F) [MIM:617026]
rs879253779 Pathogenic 184,072,258(+) AGTCT(A/G)TTATA intron-variant, nc-transcript-variant, reference, missense
rs879253780 Pathogenic 184,054,856(+) TCAGC(C/T)ATAAC nc-transcript-variant, reference, missense

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)

Relevant External Links 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

(5) MalaCards diseases for TSEN15 Gene - From: ClinVar, Orphanet, Swiss-Prot, 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.

Relevant External Links for TSEN15

Genetic Association Database (GAD)
TSEN15
Human Genome Epidemiology (HuGE) Navigator
TSEN15
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TSEN15
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 J.L. (J. Mol. Biol. 2007) 2 3 4 22 64
  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 J.D. (Genomics 2001) 2 3 4 64
  3. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. (PMID: 20546612) Zhao J. … Grant S.F. (BMC Med. Genet. 2010) 3 46 64
  4. Many sequence variants affecting diversity of adult human height. (PMID: 18391951) Gudbjartsson D.F. … Stefansson K. (Nat. Genet. 2008) 3 46 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for TSEN15 Gene

Sources for TSEN15 Gene

Content
Loading form....