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Aliases for TSEN2 Gene

Aliases for TSEN2 Gene

  • TRNA Splicing Endonuclease Subunit 2 2 3 5
  • TSEN2 TRNA Splicing Endonuclease Subunit 2 3
  • 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 63
  • EC 4.6.1.16 4
  • PCH2B 3
  • SEN2L 3

External Ids for TSEN2 Gene

Previous GeneCards Identifiers for TSEN2 Gene

  • GC03P012504

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 Gene Expression and tRNA processing. 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

Regulatory Elements for TSEN2 Gene

Promoters for TSEN2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around TSEN2 on UCSC Golden Path with GeneCards custom track

Genomic Location for TSEN2 Gene

Chromosome:
3
Start:
12,484,432 bp from pter
End:
12,539,623 bp from pter
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 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 & Families for TSEN2 Gene

Gene Families for TSEN2 Gene

Suggested Antigen Peptide Sequences for TSEN2 Gene

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 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:0003676 nucleic acid binding 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

miRNA for TSEN2 Gene

miRTarBase miRNAs that target TSEN2

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry 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
Jensen Localization Image for TSEN2 Gene COMPARTMENTS Subcellular localization image for TSEN2 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 3

Gene Ontology (GO) - Cellular Components for TSEN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IDA --
genes like me logo Genes that share ontologies with TSEN2: view

Pathways & Interactions 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 --
GO:0010467 gene expression TAS --
GO:0090501 RNA phosphodiester bond hydrolysis IBA --
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

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

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, 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 expression patterns with TSEN2: view

Protein tissue co-expression partners for TSEN2 Gene

- Elite partner

Primer Products

In Situ Assay Products

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 36
  • 73 (a)
OneToOne
TSEN2 35
  • 77.58 (n)
  • 72.71 (a)
dog
(Canis familiaris)
Mammalia TSEN2 35
  • 82.4 (n)
  • 78.66 (a)
TSEN2 36
  • 74 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Tsen2 16
Tsen2 35
  • 74.83 (n)
  • 71.08 (a)
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 36
  • 54 (a)
OneToOne
TSEN2 35
  • 63.88 (n)
  • 55.73 (a)
lizard
(Anolis carolinensis)
Reptilia TSEN2 36
  • 56 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.34894 35
zebrafish
(Danio rerio)
Actinopterygii tsen2 36
  • 63 (a)
OneToOne
tsen2 35
  • 52.77 (n)
  • 47.31 (a)
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
rs12495784 - 12,489,922(+) ATTCC(A/C/G/T)TGCTG nc-transcript-variant, reference, missense
rs33955793 - 12,503,330(+) AGTGC(A/G/T)CAGAA nc-transcript-variant, reference, missense
rs113994149 Pontocerebellar hypoplasia 2B (PCH2B) 12,516,627(+) GGTCT(A/G)TGCTC intron-variant, nc-transcript-variant, reference, missense
rs299631 -- 12,528,551(-) TTAGC(A/G)ACAGC intron-variant
rs299637 -- 12,493,424(-) acaag(C/T)gttgg intron-variant, upstream-variant-2KB

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

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)

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

MalaCards: The human disease database

(16) MalaCards diseases for TSEN2 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
pontocerebellar hypoplasia type 2b
  • pontocerebellar hypoplasia 2b
pontocerebellar hypoplasia, type 2e
  • pontocerebellar hypoplasia type 2a
tsen2-related pontocerebellar hypoplasia
polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis
  • pmgycha
microcephaly, short stature, and impaired glucose metabolism
  • microcephaly, short stature, and impaired glucose metabolism 1
- 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.

Relevant External Links for TSEN2

Genetic Association Database (GAD)
TSEN2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 S.V. … Trotta C.R. (Cell 2004) 2 3 4 67
  2. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  3. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3
  4. A high-throughput approach for measuring temporal changes in the interactome. (PMID: 22863883) Kristensen A.R. … Foster L.J. (Nat. Methods 2012) 3
  5. A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. (PMID: 22219177) Tao S. … Sun J. (Carcinogenesis 2012) 3

Products for TSEN2 Gene

Sources for TSEN2 Gene

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