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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
  • TRNA-Splicing Endonuclease Subunit Sen2 3
  • EC 3.1.27.9 56
  • 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. Gene Ontology (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

Additional gene information for TSEN2 Gene

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

Genomics for TSEN2 Gene

GeneHancer (GH) Regulatory Elements for TSEN2 Gene

Promoters and enhancers for TSEN2 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
GH03I012482 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 575.7 -0.3 -296 3.4 PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B TSEN2 VGLL4 TAMM41 RPL32 TIMP4 SYN2 MKRN2 NUP210 GC03P012458 GC03P012338
GH03I012489 Promoter/Enhancer 0.7 EPDnew ENCODE 561.9 +5.8 5804 1.8 TSEN2 TIMP4 RNA5SP123 RNU6-377P SYN2 GC03M012511 GC03P012338
GH03I012362 Enhancer 0.8 dbSUPER 70.1 -120.7 -120668 2.6 ZNF529 ZFP64 ZNF213 ZNF354C ZNF138 ZNF214 ZNF202 ZNF680 SP3 ZBTB11 TAMM41 TSEN2 ENSG00000271716 VGLL4 ENSG00000272263 RPL32 MKRN2 TIMP4 SYN2 PPARG
GH03I012555 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 23.7 +73.0 73046 3.3 FEZF1 DMAP1 IRF4 YY1 ZNF213 ZNF143 SP3 ZNF610 GLIS1 NBN MKRN2 TAMM41 TSEN2 ENSG00000272263 ENSG00000271716 MKRN2OS GC03P012338
GH03I012838 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 12.8 +356.4 356370 3.6 CLOCK DMAP1 YBX1 YY1 ZNF213 E2F8 ZNF143 SP3 SSRP1 NBN GC03M012839 GC03M012841 GC03M012844 SNORA7A RPL32 TAMM41 ENSG00000272263 TSEN2 LINC02022 CAND2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TSEN2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TSEN2 gene promoter:

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)

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

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

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 --
GO:0004519 endonuclease activity IEA --
GO:0005515 protein binding IPI 25416956
GO:0016829 lyase activity IEA --
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

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
cytoskeleton 5
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
  • Cytosol (3)
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 --
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

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: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

Unigene Clusters for TSEN2 Gene

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

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
ECgene alternative splicing isoforms for
TSEN2

Expression for TSEN2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for TSEN2 Gene



Protein tissue co-expression partners for TSEN2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TSEN2 Gene:

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 33 34
  • 99.07 (n)
dog
(Canis familiaris)
Mammalia TSEN2 33 34
  • 82.4 (n)
cow
(Bos Taurus)
Mammalia TSEN2 33 34
  • 77.58 (n)
rat
(Rattus norvegicus)
Mammalia Tsen2 33
  • 75.09 (n)
mouse
(Mus musculus)
Mammalia Tsen2 33 16 34
  • 74.83 (n)
oppossum
(Monodelphis domestica)
Mammalia TSEN2 34
  • 62 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TSEN2 34
  • 60 (a)
OneToOne
chicken
(Gallus gallus)
Aves TSEN2 33 34
  • 63.88 (n)
lizard
(Anolis carolinensis)
Reptilia TSEN2 34
  • 56 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.34894 33
zebrafish
(Danio rerio)
Actinopterygii tsen2 33 34
  • 52.77 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG31812 34
  • 28 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SEN2 34 36
  • 23 (a)
OneToOne
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)

Paralogs for TSEN2 Gene

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 Variation AA Info Type
rs1012375655 uncertain-significance, Pontoneocerebellar hypoplasia 12,484,543(+) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, non_coding_transcript_variant, upstream_transcript_variant
rs111535594 uncertain-significance, Pontocerebellar hypoplasia type 2B 12,531,593(+) T/C coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs113260160 uncertain-significance, Pontoneocerebellar hypoplasia 12,519,088(+) A/G coding_sequence_variant, intron_variant, non_coding_transcript_variant, synonymous_variant
rs113981920 uncertain-significance, conflicting-interpretations-of-pathogenicity, Pontoneocerebellar hypoplasia, not specified 12,531,653(+) A/G coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs113994149 pathogenic, Pontocerebellar hypoplasia type 2B, Pontocerebellar hypoplasia 2B (PCH2B) [MIM:612389] 12,516,627(+) A/G coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant

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

(4) MalaCards diseases for TSEN2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, 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 58
  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 44 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. 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 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for TSEN2 Gene

Sources for TSEN2 Gene

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