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Aliases for TSEN54 Gene

Aliases for TSEN54 Gene

  • TSEN54 TRNA Splicing Endonuclease Subunit 2 3
  • Sen54 3 4 6
  • TRNA-Intron Endonuclease Sen54 3 4
  • SEN54 Homolog 3 4
  • HsSen54 3 4
  • PCH2A 3 6
  • PCH4 3 6
  • TRNA Splicing Endonuclease 54 Homolog (SEN54, S. Cerevisiae) 2
  • TRNA Splicing Endonuclease 54 Homolog (S. Cerevisiae) 2
  • TRNA-Splicing Endonuclease Subunit Sen54 3
  • SEN54L 3
  • PCH5 3

External Ids for TSEN54 Gene

Previous GeneCards Identifiers for TSEN54 Gene

  • GC17P071025
  • GC17P073512
  • GC17P068936

Summaries for TSEN54 Gene

Entrez Gene Summary for TSEN54 Gene

  • This gene encodes a subunit of the tRNA splicing endonuclease complex, which catalyzes the removal of introns from precursor tRNAs. The complex is also implicated in pre-mRNA 3-prime end processing. Mutations in this gene result in pontocerebellar hypoplasia type 2.[provided by RefSeq, Oct 2009]

GeneCards Summary for TSEN54 Gene

TSEN54 (TSEN54 TRNA Splicing Endonuclease Subunit) is a Protein Coding gene. Diseases associated with TSEN54 include pontocerebellar hypoplasia type 2a and pontocerebellar hypoplasia type 4.

UniProtKB/Swiss-Prot for TSEN54 Gene

  • Non-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. 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.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TSEN54 Gene

Genomics for TSEN54 Gene

Regulatory Elements for TSEN54 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for TSEN54 Gene

Start:
75,515,707 bp from pter
End:
75,524,740 bp from pter
Size:
9,034 bases
Orientation:
Plus strand

Genomic View for TSEN54 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for TSEN54 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TSEN54 Gene

Proteins for TSEN54 Gene

  • Protein details for TSEN54 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z6J9-SEN54_HUMAN
    Recommended name:
    tRNA-splicing endonuclease subunit Sen54
    Protein Accession:
    Q7Z6J9
    Secondary Accessions:
    • Q86WV3
    • Q86XE4
    • Q8N9H2

    Protein attributes for TSEN54 Gene

    Size:
    526 amino acids
    Molecular mass:
    58819 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. Also belongs to a complex containing isoform 2 of SEN2
    SequenceCaution:
    • Sequence=AAH53643.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for TSEN54 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TSEN54 Gene

Proteomics data for TSEN54 Gene at MOPED

Post-translational modifications for TSEN54 Gene

  • Ubiquitination at Lys489
  • Modification sites at PhosphoSitePlus

Other Protein References for TSEN54 Gene

Antibody Products

No data available for DME Specific Peptides for TSEN54 Gene

Domains for TSEN54 Gene

Gene Families for TSEN54 Gene

HGNC:
  • TSEN :tRNA splicing endonuclease subunits

Protein Domains for TSEN54 Gene

Suggested Antigen Peptide Sequences for TSEN54 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q7Z6J9

UniProtKB/Swiss-Prot:

SEN54_HUMAN :
  • Q7Z6J9
Family:
  • Belongs to the SEN54 family.
genes like me logo Genes that share domains with TSEN54: view

Function for TSEN54 Gene

Molecular function for TSEN54 Gene

UniProtKB/Swiss-Prot Function: Non-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. 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 Ontology (GO) - Molecular Function for TSEN54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with TSEN54: view

Phenotypes for TSEN54 Gene

GenomeRNAi human phenotypes for TSEN54:
genes like me logo Genes that share phenotypes with TSEN54: view

Animal Model Products

CRISPR Products

miRNA for TSEN54 Gene

miRTarBase miRNAs that target TSEN54

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for TSEN54 Gene

Localization for TSEN54 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TSEN54 Gene

Nucleus. Nucleus, nucleolus. Note=May be transiently localized in the nucleolus. {ECO:0000305}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for TSEN54 Gene COMPARTMENTS Subcellular localization image for TSEN54 gene
Compartment Confidence
nucleus 4
cytosol 2

Gene Ontology (GO) - Cellular Components for TSEN54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus --
GO:0005730 nucleolus IEA --
genes like me logo Genes that share ontologies with TSEN54: view

Pathways for TSEN54 Gene

SuperPathways for TSEN54 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TSEN54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation IDA 17495927
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with TSEN54: view

No data available for Pathways by source for TSEN54 Gene

Transcripts for TSEN54 Gene

Unigene Clusters for TSEN54 Gene

TRNA splicing endonuclease 54 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for TSEN54

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for TSEN54

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for TSEN54 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c ^ 9a · 9b ^ 10 ^ 11a · 11b · 11c ^ 12a · 12b ^ 13 ^ 14a · 14b
SP1: - - -
SP2: - - -
SP3: - - -
SP4: - - - - - - - -
SP5: - -
SP6: - - - - - - -
SP7:
SP8: - -
SP9: - - - - -
SP10: -
SP11: -
SP12:

Relevant External Links for TSEN54 Gene

GeneLoc Exon Structure for
TSEN54
ECgene alternative splicing isoforms for
TSEN54

Expression for TSEN54 Gene

mRNA expression in normal human tissues for TSEN54 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for TSEN54 Gene

SOURCE GeneReport for Unigene cluster for TSEN54 Gene Hs.378501

genes like me logo Genes that share expressions with TSEN54: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for TSEN54 Gene

Orthologs for TSEN54 Gene

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

Orthologs for TSEN54 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TSEN54 35
  • 99.24 (n)
  • 99.62 (a)
TSEN54 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia TSEN54 35
  • 86.42 (n)
  • 84.51 (a)
TSEN54 36
  • 84 (a)
OneToOne
dog
(Canis familiaris)
Mammalia TSEN54 35
  • 87.14 (n)
  • 86.5 (a)
TSEN54 36
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Tsen54 35
  • 82.16 (n)
  • 80.57 (a)
Tsen54 16
Tsen54 36
  • 81 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TSEN54 36
  • 67 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TSEN54 36
  • 57 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tsen54 35
  • 82.41 (n)
  • 81.71 (a)
chicken
(Gallus gallus)
Aves TSEN54 35
  • 56.97 (n)
  • 49.09 (a)
TSEN54 36
  • 48 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TSEN54 36
  • 51 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.22688 35
tropical clawed frog
(Silurana tropicalis)
Amphibia tsen54 35
  • 64.6 (n)
  • 60.18 (a)
zebrafish
(Danio rerio)
Actinopterygii tsen54 35
  • 53.69 (n)
  • 47.07 (a)
tsen54 36
  • 26 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG5626 36
  • 25 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SEN54 38
Species with no ortholog for TSEN54:
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TSEN54 Gene

ENSEMBL:
Gene Tree for TSEN54 (if available)
TreeFam:
Gene Tree for TSEN54 (if available)

Paralogs for TSEN54 Gene

No data available for Paralogs for TSEN54 Gene

Variants for TSEN54 Gene

Sequence variations from dbSNP and Humsavar for TSEN54 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type MAF
rs1133933 -- 75,522,451(+) AGGAG(G/T)GAGTG intron-variant, reference, missense, nc-transcript-variant
rs1133934 -- 75,522,769(+) GAACA(C/T)GGTAG intron-variant
rs6501820 Benign 75,522,203(+) CAGCG(C/G)TGCTC synonymous-codon, reference, nc-transcript-variant
rs7220931 -- 75,520,930(+) cagcc(C/T)ggtga intron-variant
rs7225469 -- 75,520,853(+) cggga(C/T)gctga intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TSEN54 Gene

Variant ID Type Subtype PubMed ID
nsv516133 CNV Loss 19592680
nsv908762 CNV Loss 21882294
nsv833542 CNV Loss 17160897
nsv908763 CNV Gain 21882294
dgv3256n71 CNV Loss 21882294
nsv470603 CNV Loss 18288195
dgv3257n71 CNV Loss 21882294
dgv3258n71 CNV Loss 21882294
nsv908775 CNV Loss 21882294
nsv828102 CNV Loss 20364138
nsv833543 CNV Loss 17160897

Relevant External Links for TSEN54 Gene

HapMap Linkage Disequilibrium report
TSEN54
Human Gene Mutation Database (HGMD)
TSEN54

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TSEN54 Gene

Disorders for TSEN54 Gene

(2) OMIM Diseases for TSEN54 Gene (608755)

UniProtKB/Swiss-Prot

SEN54_HUMAN
  • Pontocerebellar hypoplasia 4 (PCH4) [MIM:225753]: A disorder characterized by an abnormally small cerebellum and brainstem, severe neonatal encephalopathy, microcephaly, myoclonus and muscular hypertonia. There is a severe inferior olivary and pontine neuronal loss and a diffuse white matter gliosis. {ECO:0000269 PubMed:18711368}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Pontocerebellar hypoplasia 2A (PCH2A) [MIM:277470]: 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 TSEN54 Gene

Relevant External Links for TSEN54

GeneTests
TSEN54
GeneReviews
TSEN54
genes like me logo Genes that share disorders with TSEN54: view

Publications for TSEN54 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. 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
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  4. tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia. (PMID: 18711368) Budde B.S. … Baas F. (Nat. Genet. 2008) 3 4
  5. TSEN54-Related Pontocerebellar Hypoplasia (PMID: 20301773) Pagon R.A. … Stephens K. ( 1993) 3

Products for TSEN54 Gene

Sources for TSEN54 Gene

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