This gene encodes one of the subunits of the tRNA splicing endonuclease. This endonuclease catalyzes the first step in RNA splicing which is the removal of introns. Mutations in this gene have been associated with pontocerebellar hypoplasia type 2. A pseudogene has been identified on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this... See more...

Aliases for TSEN2 Gene

Aliases for TSEN2 Gene

  • TRNA Splicing Endonuclease Subunit 2 2 3 5
  • TSEN2 TRNA Splicing Endonuclease Subunit 2 3
  • TRNA-Splicing Endonuclease Subunit Sen2 3 4
  • TRNA-Intron Endonuclease Sen2 3 4
  • HsSen2 3 4
  • SEN2 3 4
  • TRNA Splicing Endonuclease 2 Homolog (SEN2, S. Cerevisiae) 2
  • TRNA Splicing Endonuclease 2 Homolog (S. Cerevisiae) 2
  • EC 3.1.27.9 52
  • EC 4.6.1.16 4
  • PCH2B 3
  • SEN2L 3

External Ids for TSEN2 Gene

Previous GeneCards Identifiers for TSEN2 Gene

  • GC03P012504
  • GC03P012525

Summaries for TSEN2 Gene

Entrez Gene Summary for TSEN2 Gene

  • This gene encodes one of the subunits of the tRNA splicing endonuclease. This endonuclease catalyzes the first step in RNA splicing which is the removal of introns. Mutations in this gene have been associated with pontocerebellar hypoplasia type 2. A pseudogene has been identified on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2009]

GeneCards Summary for TSEN2 Gene

TSEN2 (TRNA Splicing Endonuclease Subunit 2) is a Protein Coding gene. Diseases associated with TSEN2 include Pontocerebellar Hypoplasia, Type 2B and Pontocerebellar Hypoplasia, Type 2E. Among its related pathways are tRNA processing and Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and tRNA-intron endonuclease activity.

UniProtKB/Swiss-Prot Summary for TSEN2 Gene

  • Constitutes one of the two 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. 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. Isoform 1 probably carries the active site for 5'-splice site cleavage. 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. Isoform 2 is responsible for processing a yet unknown RNA substrate. The complex containing isoform 2 is not able to cleave pre-tRNAs properly, although it retains endonucleolytic activity.

Gene Wiki entry for TSEN2 Gene

Additional gene information for TSEN2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TSEN2 Gene

Genomics for TSEN2 Gene

GeneHancer (GH) Regulatory Elements for TSEN2 Gene

Promoters and enhancers for TSEN2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TSEN2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TSEN2

Top Transcription factor binding sites by QIAGEN in the TSEN2 gene promoter:
  • c-Myc
  • Evi-1
  • LyF-1
  • Max
  • STAT1beta
  • STAT2

Genomic Locations for TSEN2 Gene

Genomic Locations for TSEN2 Gene
chr3:12,484,432-12,539,623
(GRCh38/hg38)
Size:
55,192 bases
Orientation:
Plus strand
chr3:12,525,931-12,581,122
(GRCh37/hg19)
Size:
55,192 bases
Orientation:
Plus strand

Genomic View for TSEN2 Gene

Genes around TSEN2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TSEN2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TSEN2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TSEN2 Gene

Proteins for TSEN2 Gene

  • Protein details for TSEN2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NCE0-SEN2_HUMAN
    Recommended name:
    tRNA-splicing endonuclease subunit Sen2
    Protein Accession:
    Q8NCE0
    Secondary Accessions:
    • B7Z6K1
    • C9IZI7
    • G5E9Q3
    • Q8WTW7
    • Q9BPU7

    Protein attributes for TSEN2 Gene

    Size:
    465 amino acids
    Molecular mass:
    53247 Da
    Quaternary structure:
    • tRNA splicing endonuclease is a heterotetramer composed of isoform 1 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. Isoform 2 belongs to a different complex that contains TSEN54 but low level of TSEN15 and TSEN34/LENG5.

    Alternative splice isoforms for TSEN2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TSEN2 Gene

Selected DME Specific Peptides for TSEN2 Gene

Q8NCE0:
  • RWVSSRERS
  • KGYFGKGILSRSRP
  • LCYLIKPS
  • TTYMAYHYFRSKGWVPKVGLKYGTDLLLYRKGPPFYHASY

Post-translational modifications for TSEN2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for TSEN2 Gene

Gene Families for TSEN2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for TSEN2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55685, highly similar to tRNA-splicing endonuclease subunit Sen2 (EC 3.1.27.9) (B7Z355_HUMAN)
  • tRNA-intron endonuclease Sen2 (SEN2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8NCE0

UniProtKB/Swiss-Prot:

SEN2_HUMAN :
  • Belongs to the tRNA-intron endonuclease family.
Family:
  • Belongs to the tRNA-intron endonuclease family.
genes like me logo Genes that share domains with TSEN2: view

Function for TSEN2 Gene

Molecular function for TSEN2 Gene

UniProtKB/Swiss-Prot Function:
Constitutes one of the two 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. 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. Isoform 1 probably carries the active site for 5'-splice site cleavage. 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. Isoform 2 is responsible for processing a yet unknown RNA substrate. The complex containing isoform 2 is not able to cleave pre-tRNAs properly, although it retains endonucleolytic activity.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=PretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus.; EC=4.6.1.16;.

Enzyme Numbers (IUBMB) for TSEN2 Gene

Phenotypes From GWAS Catalog for TSEN2 Gene

Gene Ontology (GO) - Molecular Function for TSEN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000213 tRNA-intron endonuclease activity IBA 21873635
GO:0003676 nucleic acid binding IEA --
GO:0004518 nuclease activity IEA --
GO:0004519 endonuclease activity IEA --
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with TSEN2: view
genes like me logo Genes that share phenotypes with TSEN2: view

Human Phenotype Ontology for TSEN2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for TSEN2 Gene

miRTarBase miRNAs that target TSEN2

Clone Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for TSEN2 Gene

Localization for TSEN2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TSEN2 Gene

Nucleus. Nucleus, nucleolus. Note=May be transiently localized in the nucleolus.

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 TSEN2 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 4
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
  • Centrosome (2)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TSEN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000214 tRNA-intron endonuclease complex IBA 21873635
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IEA --
GO:0005813 centrosome IDA --
genes like me logo Genes that share ontologies with TSEN2: view

Pathways & Interactions for TSEN2 Gene

PathCards logo

SuperPathways for TSEN2 Gene

genes like me logo Genes that share pathways with TSEN2: view

Pathways by source for TSEN2 Gene

Gene Ontology (GO) - Biological Process for TSEN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000379 tRNA-type intron splice site recognition and cleavage IBA 21873635
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation TAS --
GO:0006397 mRNA processing IEA --
GO:0008033 tRNA processing IEA --
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
genes like me logo Genes that share ontologies with TSEN2: view

No data available for SIGNOR curated interactions for TSEN2 Gene

Drugs & Compounds for TSEN2 Gene

No Compound Related Data Available

Transcripts for TSEN2 Gene

mRNA/cDNA for TSEN2 Gene

8 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
11 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 TSEN2 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b · 16c ^ 17
SP1: - - - -
SP2: - - -
SP3: - - -
SP4: - - -
SP5:
SP6:
SP7: - - - -
SP8:
SP9:

Relevant External Links for TSEN2 Gene

GeneLoc Exon Structure for
TSEN2

Expression for TSEN2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TSEN2 Gene

Protein differential expression in normal tissues from HIPED for TSEN2 Gene

This gene is overexpressed in Bone (44.5), Platelet (9.9), and Heart (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TSEN2 Gene



Protein tissue co-expression partners for TSEN2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TSEN2

SOURCE GeneReport for Unigene cluster for TSEN2 Gene:

Hs.335550

mRNA Expression by UniProt/SwissProt for TSEN2 Gene:

Q8NCE0-SEN2_HUMAN
Tissue specificity: Isoform 1 and isoform 2 are widely expressed at very low level.

Evidence on tissue expression from TISSUES for TSEN2 Gene

  • Intestine(4.2)
  • Skin(4.2)
  • Eye(4)
  • Pancreas(3.2)
  • Nervous system(2.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TSEN2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • face
  • forehead
  • head
  • mouth
  • pharynx
  • skull
Thorax:
  • chest wall
  • heart
Abdomen:
  • abdominal wall
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with TSEN2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for TSEN2 Gene

Orthologs for TSEN2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for TSEN2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TSEN2 31 30
  • 99.07 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TSEN2 31 30
  • 82.4 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TSEN2 31 30
  • 77.58 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tsen2 30
  • 75.09 (n)
mouse
(Mus musculus)
Mammalia Tsen2 17 31 30
  • 74.83 (n)
oppossum
(Monodelphis domestica)
Mammalia TSEN2 31
  • 62 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TSEN2 31
  • 60 (a)
OneToOne
chicken
(Gallus gallus)
Aves TSEN2 31 30
  • 63.88 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TSEN2 31
  • 56 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.34894 30
zebrafish
(Danio rerio)
Actinopterygii tsen2 31 30
  • 52.77 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG31812 31
  • 28 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SEN2 33 31
  • 23 (a)
Species where no ortholog for TSEN2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TSEN2 Gene

ENSEMBL:
Gene Tree for TSEN2 (if available)
TreeFam:
Gene Tree for TSEN2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TSEN2: view image

Paralogs for TSEN2 Gene

No data available for Paralogs for TSEN2 Gene

Variants for TSEN2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TSEN2 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
667568 Benign: not provided 12,491,836(+) A/C INTRON_VARIANT
667569 Benign: not provided 12,529,487(+) T/C INTRON_VARIANT
670254 Benign: not provided 12,531,837(+) A/G INTRON_VARIANT
670802 Benign: not provided 12,532,499(+) T/C INTRON_VARIANT
677138 Likely Benign: not provided 12,516,432(+) A/G INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for TSEN2 Gene

Structural Variations from Database of Genomic Variants (DGV) for TSEN2 Gene

Variant ID Type Subtype PubMed ID
dgv763e201 CNV deletion 23290073
dgv850e199 CNV deletion 23128226
esv2751977 CNV gain 17911159
esv3575548 CNV gain 25503493
nsv1000995 CNV gain 25217958
nsv1112379 CNV deletion 24896259
nsv1147269 CNV deletion 26484159
nsv3703 CNV insertion 18451855
nsv7351 OTHER inversion 18451855

Variation tolerance for TSEN2 Gene

Residual Variation Intolerance Score: 65.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.61; 56.45% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TSEN2 Gene

Human Gene Mutation Database (HGMD)
TSEN2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TSEN2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TSEN2 Gene

Disorders for TSEN2 Gene

MalaCards: The human disease database

(8) MalaCards diseases for TSEN2 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search TSEN2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SEN2_HUMAN
  • Pontocerebellar hypoplasia 2B (PCH2B) [MIM:612389]: A disorder characterized by an abnormally small cerebellum and brainstem, and progressive microcephaly from birth combined with extrapyramidal dyskinesia. Severe chorea occurs and epilepsy is frequent. There are no signs of spinal cord anterior horn cells degeneration. {ECO:0000269 PubMed:18711368}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TSEN2

genes like me logo Genes that share disorders with TSEN2: view

No data available for Genatlas for TSEN2 Gene

Publications for TSEN2 Gene

  1. Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3' end formation. (PMID: 15109492) Paushkin SV … Trotta CR (Cell 2004) 2 3 4 54
  2. A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. (PMID: 22219177) Tao S … Sun J (Carcinogenesis 2012) 3 41 54
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  5. Mapping the Genetic Landscape of Human Cells. (PMID: 30033366) Horlbeck MA … Gilbert LA (Cell 2018) 3 54

Products for TSEN2 Gene

Sources for TSEN2 Gene