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

    Gene ID: 79042, updated on 10-Dec-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (54189441..54194532)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57269829..57274920)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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 (41) 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
    		not available

    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)

    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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    NEW Try the new Transcript table

    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_2024_08

    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
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

    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
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

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

      UniProtKB/Swiss-Prot
      A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

    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
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

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

      UniProtKB/Swiss-Prot
      A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

    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
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

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

      UniProtKB/Swiss-Prot
      A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

    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
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

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

      UniProtKB/Swiss-Prot
      A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

    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
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

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

      UniProtKB/Swiss-Prot
      A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

    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
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

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

      UniProtKB/Swiss-Prot
      A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

    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
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

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

      UniProtKB/Swiss-Prot
      A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

    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
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

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

      UniProtKB/Swiss-Prot
      A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

    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
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

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

      UniProtKB/Swiss-Prot
      A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

    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
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37

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

      UniProtKB/Swiss-Prot
      A6NNB1, B0V3J1, Q9BSV6, Q9BVT1, Q9H6H5
      UniProtKB/TrEMBL
      A0A590UJ73, A0A590UK37
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BSV6.1 GenPept UniProtKB/Swiss-Prot:Q9BSV6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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