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

Gene ID: 79042, updated on 7-Jun-2020

Summary

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
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

Genomic context

See TSEN34 in Genome Data Viewer
Location:
19q13.42
Exon count:
7
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (54189970..54194536)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (54694112..54698394)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene transmembrane channel like 4 Neighboring gene uncharacterized LOC112268246 Neighboring gene membrane bound O-acyltransferase domain containing 7 Neighboring gene ribosomal protein S9 Neighboring gene leukocyte immunoglobulin like receptor B3

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

Associated conditions

Description Tests
Pontocerebellar hypoplasia type 2C Compare labs

NHGRI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
lyase activity IEA
Inferred from Electronic Annotation
more info
 
nucleic acid binding IEA
Inferred from Electronic Annotation
more info
 
tRNA-intron endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
RNA phosphodiester bond hydrolysis, endonucleolytic IEA
Inferred from Electronic Annotation
more info
 
mRNA processing IEA
Inferred from Electronic Annotation
more info
 
tRNA splicing, via endonucleolytic cleavage and ligation TAS
Traceable Author Statement
more info
 
tRNA-type intron splice site recognition and cleavage IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nucleolus IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
tRNA-intron endonuclease complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
tRNA-splicing endonuclease subunit Sen34
Names
CTD-3093M3.1
TSEN34 tRNA splicing endonuclease subunit
hsSen34
leukocyte receptor cluster (LRC) member 5
leukocyte receptor cluster member 5
tRNA-intron endonuclease Sen34
NP_001070914.1
NP_001269261.1
NP_001269262.1
NP_076980.2
XP_005278347.1
XP_011525596.1

NCBI Reference Sequences (RefSeq)

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
    5110..9298
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001077446.4NP_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
    Q9BSV6
    UniProtKB/TrEMBL
    A0A024R4N9
    Related
    ENSP00000379671.2, ENST00000396388.3
    Conserved Domains (2) summary
    pfam01974
    Location:217301
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
    cl25545
    Location:87169
    V-ATPase_G_2; Vacuolar (H+)-ATPase G subunit
  2. NM_001282332.1NP_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
    Q9BSV6
    UniProtKB/TrEMBL
    A0A024R4N9
    Related
    ENSP00000379667.1, ENST00000396383.5
    Conserved Domains (2) summary
    pfam01974
    Location:217301
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
    cl25545
    Location:87169
    V-ATPase_G_2; Vacuolar (H+)-ATPase G subunit
  3. NM_001282333.1NP_001269262.1  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, AK300054, BE779123, DR763016
    Consensus CDS
    CCDS74446.1
    UniProtKB/TrEMBL
    B4DT51, E7EQB3
    Related
    ENSP00000397402.3, ENST00000429671.6
    Conserved Domains (2) summary
    COG1676
    Location:223294
    SEN2; tRNA splicing endonuclease [Translation, ribosomal structure and biogenesis]
    pfam01974
    Location:220300
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
  4. NM_024075.5NP_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
    Q9BSV6
    UniProtKB/TrEMBL
    A0A024R4N9
    Related
    ENSP00000305524.4, ENST00000302937.8
    Conserved Domains (2) summary
    pfam01974
    Location:217301
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
    cl25545
    Location:87169
    V-ATPase_G_2; Vacuolar (H+)-ATPase G subunit

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    54189970..54194536
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011527294.3XP_011525596.1  tRNA-splicing endonuclease subunit Sen34 isoform X2

    See identical proteins and their annotated locations for XP_011525596.1

    UniProtKB/Swiss-Prot
    Q9BSV6
    UniProtKB/TrEMBL
    A0A024R4N9
    Conserved Domains (2) summary
    pfam01974
    Location:217301
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
    cl25545
    Location:87169
    V-ATPase_G_2; Vacuolar (H+)-ATPase G subunit
  2. XM_005278290.4XP_005278347.1  tRNA-splicing endonuclease subunit Sen34 isoform X1

    See identical proteins and their annotated locations for XP_005278347.1

    Conserved Domains (2) summary
    COG1676
    Location:223312
    SEN2; tRNA splicing endonuclease [Translation, ribosomal structure and biogenesis]
    pfam01974
    Location:220304
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NW_003571054.1 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    165065..169332
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NW_003571055.2 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    165233..169508
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NW_003571056.2 Reference GRCh38.p13 ALT_REF_LOCI_3

    Range
    165233..169508
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NW_003571057.2 Reference GRCh38.p13 ALT_REF_LOCI_4

    Range
    165233..169508
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NW_003571058.2 Reference GRCh38.p13 ALT_REF_LOCI_5

    Range
    165233..169508
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NW_003571059.2 Reference GRCh38.p13 ALT_REF_LOCI_6

    Range
    165233..169508
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NW_003571060.1 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    165232..169499
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_8

Genomic

  1. NW_003571061.2 Reference GRCh38.p13 ALT_REF_LOCI_8

    Range
    165233..169508
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_9

Genomic

  1. NT_187693.1 Reference GRCh38.p13 ALT_REF_LOCI_9

    Range
    165233..169508
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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