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Aliases for TSEN34 Gene

Aliases for TSEN34 Gene

  • TRNA Splicing Endonuclease Subunit 34 2 3 5
  • Leukocyte Receptor Cluster (LRC) Member 5 2 3
  • TSEN34 TRNA Splicing Endonuclease Subunit 2 3
  • Leukocyte Receptor Cluster Member 5 3 4
  • TRNA-Intron Endonuclease Sen34 3 4
  • HsSen34 3 4
  • LENG5 3 4
  • SEN34 3 4
  • TRNA Splicing Endonuclease 34 Homolog (SEN34, S. Cerevisiae) 2
  • TRNA Splicing Endonuclease 34 Homolog (S. Cerevisiae) 2
  • TRNA-Splicing Endonuclease Subunit Sen34 3
  • CTD-3093M3.1 3
  • EC 4.6.1.16 4
  • SEN34L 3
  • PCH2C 3

External Ids for TSEN34 Gene

Previous HGNC Symbols for TSEN34 Gene

  • LENG5

Previous GeneCards Identifiers for TSEN34 Gene

  • GC19P059387
  • GC19P054794
  • GC19P054801
  • GC19P051009
  • GC19P054812
  • GC19P054819
  • GC19P054826
  • GC19P054834
  • GC19P054849
  • GC19P054863
  • GC19P054887
  • GC19P054310
  • GC19P054367
  • GC19P054378
  • GC19P054388

Summaries for TSEN34 Gene

Entrez Gene Summary for TSEN34 Gene

  • This gene encodes a catalytic subunit of the tRNA splicing endonuclease, which catalyzes the removal of introns from precursor tRNAs. The endonuclease complex is also associated with a pre-mRNA 3-prime end processing factor. A mutation in this gene results in the neurological disorder pontocerebellar hypoplasia type 2. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Oct 2009]

GeneCards Summary for TSEN34 Gene

TSEN34 (TRNA Splicing Endonuclease Subunit 34) is a Protein Coding gene. Diseases associated with TSEN34 include Pontocerebellar Hypoplasia Type 2C and Pontocerebellar Hypoplasia, Type 2E. Among its related pathways are tRNA processing and Transcription of tRNA. GO annotations related to this gene include nucleic acid binding and tRNA-intron endonuclease activity.

UniProtKB/Swiss-Prot for TSEN34 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. It probably carries the active site for 3-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.

Gene Wiki entry for TSEN34 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TSEN34 Gene

Genomics for TSEN34 Gene

Regulatory Elements for TSEN34 Gene

Enhancers for TSEN34 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
GH19F054199 1 FANTOM5 ENCODE 12.1 +16.2 16194 12.1 CREB3L1 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 LILRB5 PRPF31 RPS9 LILRB3 LILRA6 LILRA2 ZNF765 ZNF525 LILRA4 ENSG00000269288
GH19F054186 0.2 ENCODE 7.1 +0.1 105 6.8 HDGF PKNOX1 ARNT CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF302 PRPF31 ZNF845 LENG1 LENG8-AS1 ZNF525 ENSG00000235681 LILRB3 LILRA6 ENSG00000249189 LILRB5
GH19F054179 0.2 ENCODE 0.4 -9.4 -9379 1.9 ARID4B SIN3A ZNF48 ZNF766 ZNF143 DEK SP3 NFYC MXD4 NCOA1 ENSG00000269873 TMC4 TSEN34
GH19F054178 0.2 ENCODE 0.4 -10.8 -10819 0.2 SUZ12 CREB3L1 ZNF76 DEAF1 ETS1 FOSL1 POLR2A SMARCC2 ZNF143 KLF8 CDC42EP5 ZNF665 PRPF31 ZNF765 ZNF813 ZNF677 TMC4 TSEN34
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around TSEN34 on UCSC Golden Path with GeneCards custom track

Promoters for TSEN34 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001420081 683 4001 HDGF PKNOX1 ARNT CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF302

Genomic Location for TSEN34 Gene

Chromosome:
19
Start:
54,189,517 bp from pter
End:
54,194,536 bp from pter
Size:
5,020 bases
Orientation:
Plus strand

Genomic View for TSEN34 Gene

Genes around TSEN34 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TSEN34 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TSEN34 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TSEN34 Gene

Proteins for TSEN34 Gene

  • Protein details for TSEN34 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BSV6-SEN34_HUMAN
    Recommended name:
    tRNA-splicing endonuclease subunit Sen34
    Protein Accession:
    Q9BSV6
    Secondary Accessions:
    • A6NNB1
    • B0V3J1
    • Q9BVT1
    • Q9H6H5

    Protein attributes for TSEN34 Gene

    Size:
    310 amino acids
    Molecular mass:
    33652 Da
    Quaternary structure:
    • tRNA splicing endonuclease is a heterotetramer composed 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.
    Miscellaneous:
    • Belongs to the leukocyte receptor cluster (LRC) present on 19q13.4.
    SequenceCaution:
    • Sequence=BAB15284.1; Type=Erroneous termination; Positions=311; Note=Translated as stop.; Evidence={ECO:0000305};

neXtProt entry for TSEN34 Gene

Post-translational modifications for TSEN34 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for TSEN34 Gene

Domains & Families for TSEN34 Gene

Gene Families for TSEN34 Gene

Graphical View of Domain Structure for InterPro Entry

Q9BSV6

UniProtKB/Swiss-Prot:

SEN34_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 TSEN34: view

Function for TSEN34 Gene

Molecular function for TSEN34 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. It probably carries the active site for 3-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.

Enzyme Numbers (IUBMB) for TSEN34 Gene

Gene Ontology (GO) - Molecular Function for TSEN34 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000213 tRNA-intron endonuclease activity IBA --
GO:0003676 nucleic acid binding IEA --
GO:0004518 nuclease activity IEA --
GO:0004519 endonuclease activity IEA --
GO:0016829 lyase activity IEA --
genes like me logo Genes that share ontologies with TSEN34: view
genes like me logo Genes that share phenotypes with TSEN34: view

Human Phenotype Ontology for TSEN34 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for TSEN34

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for TSEN34 Gene

Localization for TSEN34 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TSEN34 Gene

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

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for TSEN34 Gene COMPARTMENTS Subcellular localization image for TSEN34 gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for TSEN34 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000214 tRNA-intron endonuclease complex IEA --
GO:0005634 nucleus IEA,IDA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IEA --
genes like me logo Genes that share ontologies with TSEN34: view

Pathways & Interactions for TSEN34 Gene

genes like me logo Genes that share pathways with TSEN34: view

Pathways by source for TSEN34 Gene

3 Reactome pathways for TSEN34 Gene
1 Qiagen pathway for TSEN34 Gene

Gene Ontology (GO) - Biological Process for TSEN34 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000379 tRNA-type intron splice site recognition and cleavage IEA,IBA --
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation IEA,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 TSEN34: view

No data available for SIGNOR curated interactions for TSEN34 Gene

Transcripts for TSEN34 Gene

Unigene Clusters for TSEN34 Gene

TRNA splicing endonuclease 34 homolog (S. cerevisiae):
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for TSEN34 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c
SP1: - -
SP2: -
SP3: - - - - -
SP4: - - -
SP5:
SP6:
SP7: - -
SP8:

Relevant External Links for TSEN34 Gene

GeneLoc Exon Structure for
TSEN34
ECgene alternative splicing isoforms for
TSEN34

Expression for TSEN34 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TSEN34 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TSEN34 Gene

This gene is overexpressed in Whole Blood (x8.8).

Protein differential expression in normal tissues from HIPED for TSEN34 Gene

This gene is overexpressed in Lung (38.4), Platelet (11.9), and Ovary (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TSEN34 Gene



Protein tissue co-expression partners for TSEN34 Gene

NURSA nuclear receptor signaling pathways regulating expression of TSEN34 Gene:

TSEN34

SOURCE GeneReport for Unigene cluster for TSEN34 Gene:

Hs.15580
genes like me logo Genes that share expression patterns with TSEN34: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for TSEN34 Gene

Orthologs for TSEN34 Gene

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

Orthologs for TSEN34 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TSEN34 34 35
  • 99.57 (n)
dog
(Canis familiaris)
Mammalia TSEN34 34 35
  • 87.2 (n)
cow
(Bos Taurus)
Mammalia TSEN34 34 35
  • 86.13 (n)
mouse
(Mus musculus)
Mammalia Tsen34 34 16 35
  • 84.52 (n)
rat
(Rattus norvegicus)
Mammalia Tsen34 34
  • 83.44 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TSEN34 35
  • 56 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TSEN34 35
  • 45 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TSEN34 35
  • 46 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tsen34 34
  • 53.1 (n)
zebrafish
(Danio rerio)
Actinopterygii tsen34 34 35
  • 53.48 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG33260 35
  • 23 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea K08D10.12 35
  • 25 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFL012C 34
  • 53.03 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A08932g 34
  • 41.47 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SEN34 34 35 37
  • 40.15 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU08032 34
  • 45.61 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes sen34 34
  • 41.74 (n)
Species where no ortholog for TSEN34 was found in the sources mined by GeneCards:
  • 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)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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)
  • wheat (Triticum aestivum)

Evolution for TSEN34 Gene

ENSEMBL:
Gene Tree for TSEN34 (if available)
TreeFam:
Gene Tree for TSEN34 (if available)

Paralogs for TSEN34 Gene

No data available for Paralogs for TSEN34 Gene

Variants for TSEN34 Gene

Sequence variations from dbSNP and Humsavar for TSEN34 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs113994150 Pontocerebellar hypoplasia 2C (PCH2C) [MIM:612390]
rs17849378 --

Structural Variations from Database of Genomic Variants (DGV) for TSEN34 Gene

Variant ID Type Subtype PubMed ID
esv2718812 CNV deletion 23290073
esv2758771 CNV gain+loss 17122850
nsv1066425 CNV gain 25217958
nsv2546 CNV deletion 18451855
nsv428371 CNV gain+loss 18775914
nsv510774 CNV deletion 20534489
nsv953613 CNV deletion 24416366
nsv9751 CNV gain 18304495

Variation tolerance for TSEN34 Gene

Residual Variation Intolerance Score: 33.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.89; 35.34% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TSEN34 Gene

Human Gene Mutation Database (HGMD)
TSEN34
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TSEN34

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TSEN34 Gene

Disorders for TSEN34 Gene

MalaCards: The human disease database

(6) MalaCards diseases for TSEN34 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
pontocerebellar hypoplasia type 2c
  • pontocerebellar hypoplasia 2c
pontocerebellar hypoplasia, type 2e
  • pontocerebellar hypoplasia type 2a
tsen34-related pontocerebellar hypoplasia
pontocerebellar hypoplasia
  • pch
pontocerebellar hypoplasia, type 6
  • pontocerebellar hypoplasia type 6
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SEN34_HUMAN
  • Pontocerebellar hypoplasia 2C (PCH2C) [MIM:612390]: 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 TSEN34

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TSEN34
genes like me logo Genes that share disorders with TSEN34: view

No data available for Genatlas for TSEN34 Gene

Publications for TSEN34 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 64
  2. Extensive gene duplications and a large inversion characterize the human leukocyte receptor cluster. (PMID: 10941842) Wende H. … Ziegler A. (Immunogenetics 2000) 2 3 4 64
  3. tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia. (PMID: 18711368) Budde B.S. … Baas F. (Nat. Genet. 2008) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. 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 64

Products for TSEN34 Gene

Sources for TSEN34 Gene

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