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Aliases for TSEN2 Gene

Aliases for TSEN2 Gene

  • TSEN2 TRNA Splicing Endonuclease Subunit 2 3
  • SEN2 3 4 6
  • TRNA-Intron Endonuclease Sen2 3 4
  • HsSen2 3 4
  • PCH2B 3 6
  • TRNA Splicing Endonuclease 2 Homolog (SEN2, S. Cerevisiae) 2
  • TRNA Splicing Endonuclease 2 Homolog (S. Cerevisiae) 2
  • TRNA-Splicing Endonuclease Subunit Sen2 3
  • EC 3.1.27.9 63
  • EC 4.6.1.16 4
  • SEN2L 3

External Ids for TSEN2 Gene

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 (TSEN2 TRNA Splicing Endonuclease Subunit) is a Protein Coding gene. Diseases associated with TSEN2 include tsen2-related pontocerebellar hypoplasia and pontocerebellar hypoplasia, type 2e. GO annotations related to this gene include nucleic acid binding and tRNA-intron endonuclease activity.

UniProtKB/Swiss-Prot 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TSEN2 Gene

Genomics for TSEN2 Gene

Genomic Location for TSEN2 Gene

Start:
12,484,432 bp from pter
End:
12,539,630 bp from pter
Size:
55,199 bases
Orientation:
Plus strand

Genomic View for TSEN2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for TSEN2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TSEN2 Gene

Regulatory Elements 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 SEN2, SEN15, SEN34/LENG5 and SEN54. 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 SEN54 but low level of SEN15 and SEN34/LENG5

    Alternative splice isoforms for TSEN2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TSEN2 Gene

Proteomics data for TSEN2 Gene at MOPED

Selected DME Specific Peptides for TSEN2 Gene

Post-translational modifications for TSEN2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains for TSEN2 Gene

Gene Families for TSEN2 Gene

HGNC:
  • TSEN :tRNA splicing endonuclease subunits

Suggested Antigen Peptide Sequences for TSEN2 Gene

Graphical View of Domain Structure for InterPro Entry

Q8NCE0

UniProtKB/Swiss-Prot:

SEN2_HUMAN
Family:
  • Belongs to the tRNA-intron endonuclease family.:
    • Q8NCE0
genes like me logo Genes that share domains with TSEN2: view

Function for TSEN2 Gene

Molecular function for TSEN2 Gene

UniProtKB/Swiss-Prot CatalyticActivity: 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
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.

Enzyme Numbers (IUBMB) 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 --
GO:0003676 nucleic acid binding IEA --
GO:0005515 protein binding IPI 25416956
GO:0016829 lyase activity IEA --
genes like me logo Genes that share ontologies with TSEN2: view

Phenotypes for TSEN2 Gene

GenomeRNAi human phenotypes for TSEN2:
genes like me logo Genes that share phenotypes with TSEN2: view

miRNA for TSEN2 Gene

miRTarBase miRNAs that target TSEN2

No data available for Animal Models , Transcription Factor Targeting 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
Jensen Localization Image for TSEN2 Gene COMPARTMENTS Subcellular localization image for TSEN2 gene
Compartment Confidence
nucleus 5
cytoskeleton 4
cytosol 3
peroxisome 1

Gene Ontology (GO) - Cellular Components for TSEN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000214 tRNA-intron endonuclease complex IBA --
GO:0005634 nucleus --
GO:0005654 nucleoplasm IDA --
GO:0005730 nucleolus IEA --
GO:0005737 cytoplasm IDA --
genes like me logo Genes that share ontologies with TSEN2: view

Pathways for TSEN2 Gene

SuperPathways for TSEN2 Gene

No Data Available

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 --
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation IDA 17495927
GO:0006397 mRNA processing IEA --
GO:0090501 RNA phosphodiester bond hydrolysis IBA --
GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic IEA --
genes like me logo Genes that share ontologies with TSEN2: view

No data available for Pathways by source for TSEN2 Gene

Transcripts for TSEN2 Gene

Unigene Clusters for TSEN2 Gene

TRNA splicing endonuclease 2 homolog (S. cerevisiae):
Representative Sequences:

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
ECgene alternative splicing isoforms for
TSEN2

Expression for TSEN2 Gene

mRNA expression in normal human tissues for TSEN2 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for TSEN2 Gene

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.
genes like me logo Genes that share expressions 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 35
  • 99.07 (n)
  • 99.14 (a)
TSEN2 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia TSEN2 35
  • 77.58 (n)
  • 72.71 (a)
TSEN2 36
  • 73 (a)
OneToOne
dog
(Canis familiaris)
Mammalia TSEN2 35
  • 82.4 (n)
  • 78.66 (a)
TSEN2 36
  • 74 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Tsen2 35
  • 74.83 (n)
  • 71.08 (a)
Tsen2 16
Tsen2 36
  • 69 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TSEN2 36
  • 62 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TSEN2 36
  • 60 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tsen2 35
  • 75.09 (n)
  • 70.81 (a)
chicken
(Gallus gallus)
Aves TSEN2 35
  • 63.88 (n)
  • 55.73 (a)
TSEN2 36
  • 54 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TSEN2 36
  • 56 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.34894 35
zebrafish
(Danio rerio)
Actinopterygii tsen2 35
  • 52.77 (n)
  • 47.31 (a)
tsen2 36
  • 63 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG31812 36
  • 28 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SEN2 36
  • 23 (a)
OneToOne
SEN2 38
Species with no ortholog for TSEN2:
  • 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)

Paralogs for TSEN2 Gene

Pseudogenes.org Pseudogenes for TSEN2 Gene

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

No data available for Paralogs for TSEN2 Gene

Variants for TSEN2 Gene

Sequence variations from dbSNP and Humsavar for TSEN2 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type MAF
rs116002 -- 12,536,605(+) AGTTC(A/G)TAATT intron-variant
rs167257 -- 12,532,499(+) TTATA(C/T)TGTTA intron-variant
rs299628 -- 12,535,896(+) gcgac(C/G)ttgga intron-variant
rs299629 -- 12,535,347(+) AGTCT(A/G)TCTAA intron-variant
rs299630 -- 12,526,926(-) AAATG(A/C)CATTA intron-variant

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

Variant ID Type Subtype PubMed ID
dgv810e201 CNV Deletion 23290073
dgv850e199 CNV Deletion 23128226
nsv7351 OTHER Inversion 18451855
esv2751977 CNV Gain 17911159
nsv3703 CNV Insertion 18451855
nsv876541 CNV Gain 21882294

Relevant External Links for TSEN2 Gene

HapMap Linkage Disequilibrium report
TSEN2
Human Gene Mutation Database (HGMD)
TSEN2

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

Disorders for TSEN2 Gene

(1) OMIM Diseases for TSEN2 Gene (608753)

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.

(1) University of Copenhagen DISEASES for TSEN2 Gene

Relevant External Links for TSEN2

GeneTests
TSEN2
GeneReviews
TSEN2
Genetic Association Database (GAD)
TSEN2
genes like me logo Genes that share disorders with TSEN2: view

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 S.V. … Trotta C.R. (Cell 2004) 2 3 4
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  3. A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. (PMID: 22219177) Tao S. … Sun J. (Carcinogenesis 2012) 3 48
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PMID: 16344560) Kimura K. … Sugano S. (Genome Res. 2006) 3

Products for TSEN2 Gene

Sources for TSEN2 Gene

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