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] See more...

Aliases for TSEN54 Gene

Aliases for TSEN54 Gene

  • TRNA Splicing Endonuclease Subunit 54 2 3 5
  • TSEN54 TRNA Splicing Endonuclease Subunit 2 3
  • TRNA-Splicing Endonuclease Subunit Sen54 3 4
  • TRNA-Intron Endonuclease Sen54 3 4
  • SEN54 Homolog 3 4
  • TRNA Splicing Endonuclease 54 Homolog (SEN54, S. Cerevisiae) 2
  • TRNA Splicing Endonuclease 54 Homolog (S. Cerevisiae) 2
  • HsSen54 3
  • HsSEN54 4
  • SEN54L 3
  • PCH2A 3
  • Sen54 3
  • SEN54 4
  • PCH4 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 (TRNA Splicing Endonuclease Subunit 54) is a Protein Coding gene. Diseases associated with TSEN54 include Pontocerebellar Hypoplasia, Type 4 and Pontocerebellar Hypoplasia, Type 5. Among its related pathways are tRNA processing and Gene Expression.

UniProtKB/Swiss-Prot Summary 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.

Additional gene information for TSEN54 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TSEN54 Gene

Genomics for TSEN54 Gene

GeneHancer (GH) Regulatory Elements for TSEN54 Gene

Promoters and enhancers for TSEN54 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TSEN54 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TSEN54 gene promoter:
  • C/EBPalpha
  • HNF-4alpha1
  • HNF-4alpha2
  • HOXA5
  • HSF1 (long)
  • Ik-1
  • NF-1
  • NF-1/L
  • Pax-6
  • ZIC2

Genomic Locations for TSEN54 Gene

Genomic Locations for TSEN54 Gene
chr17:75,515,707-75,524,739
(GRCh38/hg38)
Size:
9,033 bases
Orientation:
Plus strand
chr17:73,512,141-73,520,820
(GRCh37/hg19)
Size:
8,680 bases
Orientation:
Plus strand

Genomic View for TSEN54 Gene

Genes around TSEN54 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TSEN54 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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 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. 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

Post-translational modifications for TSEN54 Gene

  • Ubiquitination at Lys489
  • Modification sites at PhosphoSitePlus

Other Protein References for TSEN54 Gene

No data available for DME Specific Peptides for TSEN54 Gene

Domains & Families for TSEN54 Gene

Gene Families for TSEN54 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for TSEN54 Gene

Suggested Antigen Peptide Sequences for TSEN54 Gene

GenScript: Design optimal peptide antigens:
  • tRNA-intron endonuclease Sen54 (SEN54_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q7Z6J9

UniProtKB/Swiss-Prot:

SEN54_HUMAN :
  • Belongs to the SEN54 family.
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.

Phenotypes From GWAS Catalog for TSEN54 Gene

Gene Ontology (GO) - Molecular Function for TSEN54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000213 contributes_to tRNA-intron endonuclease activity IBA 21873635
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with TSEN54: view
genes like me logo Genes that share phenotypes with TSEN54: view

Human Phenotype Ontology for TSEN54 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TSEN54

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets 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
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 TSEN54 gene
Compartment Confidence
nucleus 5
cytosol 3
mitochondrion 2

Gene Ontology (GO) - Cellular Components for TSEN54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000214 tRNA-intron endonuclease complex IBA 21873635
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IEA --
genes like me logo Genes that share ontologies with TSEN54: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TSEN54 Gene

Pathways & Interactions for TSEN54 Gene

PathCards logo

SuperPathways for TSEN54 Gene

SuperPathway Contained pathways
1 tRNA processing
2 Transcription of tRNA
-
3 Gene Expression
genes like me logo Genes that share pathways with TSEN54: view

Pathways by source for TSEN54 Gene

3 Reactome pathways for TSEN54 Gene
1 Qiagen pathway for TSEN54 Gene
  • Transcription of tRNA

Gene Ontology (GO) - Biological Process for TSEN54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000379 tRNA-type intron splice site recognition and cleavage IBA 21873635
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation TAS --
GO:0006397 mRNA processing IEA --
GO:0008033 tRNA processing IEA --
GO:0090501 RNA phosphodiester bond hydrolysis IEA --
genes like me logo Genes that share ontologies with TSEN54: view

No data available for SIGNOR curated interactions for TSEN54 Gene

Drugs & Compounds for TSEN54 Gene

No Compound Related Data Available

Transcripts for TSEN54 Gene

mRNA/cDNA for TSEN54 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TSEN54

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE for TSEN54 Gene

Protein differential expression in normal tissues from HIPED for TSEN54 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (28.7), CD8 Tcells (13.0), Testis (7.7), and Lymph node (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TSEN54 Gene



Protein tissue co-expression partners for TSEN54 Gene

NURSA nuclear receptor signaling pathways regulating expression of TSEN54 Gene:

TSEN54

SOURCE GeneReport for Unigene cluster for TSEN54 Gene:

Hs.378501

Evidence on tissue expression from TISSUES for TSEN54 Gene

  • Nervous system(4.5)
  • Blood(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TSEN54 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • pharynx
  • skull
  • tongue
Thorax:
  • chest wall
  • clavicle
  • heart
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • abdominal wall
Pelvis:
  • pelvis
  • placenta
  • uterus
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with TSEN54: view

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 33 32
  • 99.24 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TSEN54 33 32
  • 87.14 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TSEN54 33 32
  • 86.42 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tsen54 32
  • 82.41 (n)
mouse
(Mus musculus)
Mammalia Tsen54 17 33 32
  • 82.16 (n)
oppossum
(Monodelphis domestica)
Mammalia TSEN54 33
  • 67 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TSEN54 33
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves TSEN54 33 32
  • 56.97 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TSEN54 33
  • 51 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tsen54 32
  • 64.6 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.22688 32
zebrafish
(Danio rerio)
Actinopterygii tsen54 33 32
  • 53.69 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG5626 33
  • 25 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SEN54 35
Species where no ortholog for TSEN54 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TSEN54 Gene

ENSEMBL:
Gene Tree for TSEN54 (if available)
TreeFam:
Gene Tree for TSEN54 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TSEN54: view image

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 Variation AA Info Type
rs1012275384 pathogenic, Pontocerebellar hypoplasia type 2A, Pontocerebellar hypoplasia type 4 75,522,019(+) CCC/CC coding_sequence_variant, frameshift
rs111972085 uncertain-significance, Pontoneocerebellar hypoplasia 75,524,581(+) T/C/G 3_prime_UTR_variant
rs113994151 pathogenic, likely-pathogenic, Pontocerebellar hypoplasia type 4, Pontocerebellar hypoplasia type 2A, Pontocerebellar hypoplasia 4 (PCH4) [MIM:225753] 75,517,064(+) T/C coding_sequence_variant, missense_variant
rs113994152 pathogenic, pathogenic-likely-pathogenic, likely-pathogenic, Pontocerebellar hypoplasia type 2A, Pontocerebellar hypoplasia type 4, Olivopontocerebellar hypoplasia, Pontocerebellar hypoplasia type 5, not provided, Global developmental delay, Microcephaly, Congenital cerebellar hypoplasia, Non-syndromic pontocerebellar hypoplasia, Inborn genetic diseases, Amblyopia, Hypertonia, Pontocerebellar hypoplasia 2A (PCH2A) [MIM:277470], Pontocerebellar hypoplasia 4 (PCH4) [MIM:225753] 75,522,000(+) G/T coding_sequence_variant, missense_variant
rs113994153 pathogenic, Pontocerebellar hypoplasia type 4 75,521,817(+) C/T coding_sequence_variant, stop_gained

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

Variant ID Type Subtype PubMed ID
nsv470603 CNV loss 18288195
nsv516133 CNV loss 19592680
nsv576027 CNV gain 21841781
nsv828102 CNV loss 20364138
nsv833542 CNV loss 17160897
nsv833543 CNV loss 17160897
nsv952368 CNV deletion 24416366

Variation tolerance for TSEN54 Gene

Residual Variation Intolerance Score: 97.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 18.04; 98.43% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TSEN54 Gene

Human Gene Mutation Database (HGMD)
TSEN54
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TSEN54

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

Disorders for TSEN54 Gene

MalaCards: The human disease database

(15) MalaCards diseases for TSEN54 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

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, ECO:0000269 PubMed:21824568}. 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, ECO:0000269 PubMed:23307886}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Pontocerebellar hypoplasia 5 (PCH5) [MIM:610204]: A form of pontocerebellar hypoplasia, a disorder characterized by structural defects of the pons and cerebellum. Brain MRI shows an abnormally small cerebellum and brainstem, decreased cerebral white matter, and a thin corpus callosum. {ECO:0000269 PubMed:21368912}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TSEN54

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

No data available for Genatlas for TSEN54 Gene

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 SV … Trotta CR (Cell 2004) 2 3 4 56
  2. A familial late‑onset hereditary ataxia mimicking pontocerebellar hypoplasia caused by a novel TSEN54 mutation. (PMID: 24938831) Qian Y … Chen L (Molecular medicine reports 2014) 3 4 56
  3. tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia. (PMID: 18711368) Budde BS … Baas F (Nature genetics 2008) 3 4 56
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56
  5. 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 56

Products for TSEN54 Gene

Sources for TSEN54 Gene