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TSEN34 tRNA splicing endonuclease subunit 34 [ Homo sapiens (human) ]

Gene ID: 79042, updated on 7-Apr-2024

Summary

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Official Symbol
TSEN34provided by HGNC
Official Full Name
tRNA splicing endonuclease subunit 34provided by HGNC
Primary source
HGNC:HGNC:15506
See related
Ensembl:ENSG00000170892 MIM:608754; AllianceGenome:HGNC:15506
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LENG5; PCH2C; SEN34; SEN34L
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 9.1), prostate (RPKM 8.4) and 25 other tissues See more
Orthologs
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Genomic context

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See TSEN34 in Genome Data Viewer
Location:
19q13.42
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (54189441..54194532)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57269829..57274920)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (54694195..54698390)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene CCR4-NOT transcription complex subunit 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:54662792-54663461 Neighboring gene leukocyte receptor cluster member 1 Neighboring gene transmembrane channel like 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54676977-54677793 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54677794-54678609 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54683683-54684198 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54684199-54684714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54684715-54685229 Neighboring gene membrane bound O-acyltransferase domain containing 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54687509-54688008 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:54692762-54693444 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:54693445-54694126 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:54695049-54695250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54696095-54696610 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:54704113-54704783 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54709694-54710202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54710710-54711217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54711218-54711724 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:54711820-54712003 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:54712450-54712625 Neighboring gene ribosomal protein S9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54720754-54721590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54721591-54722426 Neighboring gene uncharacterized LOC124904768 Neighboring gene leukocyte immunoglobulin like receptor B3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Pontocerebellar hypoplasia type 2 and TSEN2: review of the literature and two novel mutations. Bierhals T, et al. Eur J Med Genet, 2013 Jun. PMID 23562994
  2. tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia. Budde BS, et al. Nat Genet, 2008 Sep. PMID 18711368
  3. TSEN54 Pontocerebellar Hypoplasia. Adam MP, et al. , 1993. PMID 20301773
  4. Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3' end formation. Paushkin SV, et al. Cell, 2004 Apr 30. PMID 15109492
  5. Extensive gene duplications and a large inversion characterize the human leukocyte receptor cluster. Wende H, et al. Immunogenetics, 2000 Jul. PMID 10941842

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Pontocerebellar hypoplasia type 2C
MedGen: C2676465 OMIM: 612390 GeneReviews: TSEN54 Pontocerebellar Hypoplasia
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EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables lyase activity IEA
Inferred from Electronic Annotation
more info
  
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables tRNA-intron endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in tRNA-type intron splice site recognition and cleavage IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of tRNA-intron endonuclease complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
tRNA-splicing endonuclease subunit Sen34
Names
CTD-3093M3.1
TSEN34 tRNA splicing endonuclease subunit
leukocyte receptor cluster (LRC) member 5
leukocyte receptor cluster member 5
tRNA-intron endonuclease Sen34
NP_001070914.1
NP_001269261.1
NP_001269262.2
NP_001373669.1
NP_076980.2
XP_011525596.1
XP_047295347.1
XP_054178041.1
XP_054178042.1
XP_054185675.1
XP_054185676.1
XP_054186177.1
XP_054186178.1
XP_054186473.1
XP_054186474.1
XP_054186723.1
XP_054186724.1
XP_054186954.1
XP_054186955.1
XP_054187237.1
XP_054187238.1
XP_054187506.1
XP_054187507.1
XP_054189551.1
XP_054189552.1
XP_054189653.1
XP_054189654.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_015810.2 RefSeqGene

    Range
    6074..9298
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001077446.4 → NP_001070914.1  tRNA-splicing endonuclease subunit Sen34 isoform 1

    See identical proteins and their annotated locations for NP_001070914.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AC245052, AK054944, AK226013, CN256589
    Consensus CDS
    CCDS42609.1
    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
    UniProtKB/TrEMBL
    A0A590UJ73, A0A590UK37
    Related
    ENSP00000379671.2, ENST00000396388.3
    Conserved Domains (1) summary
    cd22363
    Location:218 → 306
    tRNA-intron_lyase_C; catalytic C-terminal domain of the tRNA-intron lyase

  2. NM_001282332.2 → NP_001269261.1  tRNA-splicing endonuclease subunit Sen34 isoform 1

    See identical proteins and their annotated locations for NP_001269261.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same isoform (1)
    Source sequence(s)
    AC245052, AK054944, AK226013, BC004530
    Consensus CDS
    CCDS42609.1
    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
    UniProtKB/TrEMBL
    A0A590UJ73, A0A590UK37
    Related
    ENSP00000379667.1, ENST00000396383.5
    Conserved Domains (1) summary
    cd22363
    Location:218 → 306
    tRNA-intron_lyase_C; catalytic C-terminal domain of the tRNA-intron lyase

  3. NM_001282333.2 → NP_001269262.2  tRNA-splicing endonuclease subunit Sen34 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and 3' coding region, compared to variant 1. The encoded isoform (2) has a longer and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC245052
    Consensus CDS
    CCDS74446.2
    UniProtKB/TrEMBL
    A0A590UJW4, B4DT51
    Related
    ENSP00000499595.1, ENST00000667261.1
    Conserved Domains (2) summary
    PRK09510
    Location:87 → 169
    tolA; cell envelope integrity inner membrane protein TolA; Provisional
    cd22363
    Location:218 → 297
    tRNA-intron_lyase_C; catalytic C-terminal domain of the tRNA-intron lyase

  4. NM_001386740.1 → NP_001373669.1  tRNA-splicing endonuclease subunit Sen34 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC245052
    Consensus CDS
    CCDS42609.1
    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
    UniProtKB/TrEMBL
    A0A590UJ73, A0A590UK37
    Related
    ENSP00000397402.4, ENST00000429671.7
    Conserved Domains (1) summary
    cd22363
    Location:218 → 306
    tRNA-intron_lyase_C; catalytic C-terminal domain of the tRNA-intron lyase

  5. NM_024075.5 → NP_076980.2  tRNA-splicing endonuclease subunit Sen34 isoform 1

    See identical proteins and their annotated locations for NP_076980.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the shorter isoform (1). Variants 1, 2, and 3 encode the same isoform.
    Source sequence(s)
    AC245052, AK054944, AK226013, BE779123
    Consensus CDS
    CCDS42609.1
    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
    UniProtKB/TrEMBL
    A0A590UJ73, A0A590UK37
    Related
    ENSP00000305524.4, ENST00000302937.8
    Conserved Domains (1) summary
    cd22363
    Location:218 → 306
    tRNA-intron_lyase_C; catalytic C-terminal domain of the tRNA-intron lyase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    54189441..54194532
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439391.1 → XP_047295347.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

  2. XM_011527294.4 → XP_011525596.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    See identical proteins and their annotated locations for XP_011525596.1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
    UniProtKB/TrEMBL
    A0A590UJ73, A0A590UK37
    Related
    ENSP00000400743.2, ENST00000455798.6
    Conserved Domains (1) summary
    cd22363
    Location:218 → 306
    tRNA-intron_lyase_C; catalytic C-terminal domain of the tRNA-intron lyase

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003571054.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    164238..169328
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329700.1 → XP_054185675.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

  2. XM_054329701.1 → XP_054185676.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NW_003571055.2 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    164482..169504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330202.1 → XP_054186177.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

  2. XM_054330203.1 → XP_054186178.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NW_003571056.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    164482..169504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330499.1 → XP_054186474.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

  2. XM_054330498.1 → XP_054186473.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NW_003571057.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    164482..169504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330748.1 → XP_054186723.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

  2. XM_054330749.1 → XP_054186724.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NW_003571058.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    164482..169504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330979.1 → XP_054186954.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

  2. XM_054330980.1 → XP_054186955.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NW_003571059.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    164482..169504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331262.1 → XP_054187237.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

  2. XM_054331263.1 → XP_054187238.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NW_003571060.1 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    164405..169495
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331531.1 → XP_054187506.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

  2. XM_054331532.1 → XP_054187507.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

Reference GRCh38.p14 ALT_REF_LOCI_8

Genomic

  1. NW_003571061.2 Reference GRCh38.p14 ALT_REF_LOCI_8

    Range
    164482..169504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333576.1 → XP_054189551.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

  2. XM_054333577.1 → XP_054189552.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

Reference GRCh38.p14 ALT_REF_LOCI_9

Genomic

  1. NT_187693.1 Reference GRCh38.p14 ALT_REF_LOCI_9

    Range
    164482..169504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054333678.1 → XP_054189653.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

  2. XM_054333679.1 → XP_054189654.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    57269829..57274920
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322066.1 → XP_054178041.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5

  2. XM_054322067.1 → XP_054178042.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    UniProtKB/Swiss-Prot
    A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BSV6.1 GenPept UniProtKB/Swiss-Prot:Q9BSV6

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