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TSEN2 tRNA splicing endonuclease subunit 2 [ Homo sapiens (human) ]

Gene ID: 80746, updated on 23-Nov-2023

Summary

Official Symbol
TSEN2provided by HGNC
Official Full Name
tRNA splicing endonuclease subunit 2provided by HGNC
Primary source
HGNC:HGNC:28422
See related
Ensembl:ENSG00000154743 MIM:608753; AllianceGenome:HGNC:28422
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
SEN2; PCH2B; SEN2L
Summary
This gene encodes one of the subunits of the tRNA splicing endonuclease. This endonuclease catalyzes the first step in RNA splicing which is the removal of introns. Mutations in this gene have been associated with pontocerebellar hypoplasia type 2. A pseudogene has been identified on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2009]
Expression
Ubiquitous expression in ovary (RPKM 2.1), thyroid (RPKM 2.1) and 25 other tissues See more
Orthologs
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Genomic context

See TSEN2 in Genome Data Viewer
Location:
3p25.2
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (12480231..12539624)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (12478037..12537426)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (12525979..12581123)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene glutathione S-transferase mu 5 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12328552-12329130 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:12348453-12348660 Neighboring gene peroxisome proliferator activated receptor gamma Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:12386163-12387362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19440 Neighboring gene PPARG eExon liver enhancer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:12486052-12487251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19441 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12558643-12559143 Neighboring gene RNA, 5S ribosomal pseudogene 123 Neighboring gene RNA, U6 small nuclear 377, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14065 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12598813-12599336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19446 Neighboring gene MKRN2 opposite strand Neighboring gene MPRA-validated peak4543 silencer Neighboring gene makorin ring finger protein 2 Neighboring gene Raf-1 proto-oncogene, serine/threonine kinase Neighboring gene small nucleolar RNA U13

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 2B Compare labs

EBI GWAS Catalog

Description
A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC2776, MGC4440

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 protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
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 splicing, via endonucleolytic cleavage and ligation IDA
Inferred from Direct Assay
more info
PubMed 
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 centrosome IDA
Inferred from Direct Assay
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
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 IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
tRNA-splicing endonuclease subunit Sen2
Names
TSEN2 tRNA splicing endonuclease subunit
hsSen2
tRNA-intron endonuclease Sen2
NP_001138864.1
NP_001138865.1
NP_001138866.1
NP_001308206.1
NP_001308207.1
NP_001308208.1
NP_079541.1
XP_011532441.1
XP_016862781.1
XP_016862782.1
XP_016862783.1
XP_016862784.1
XP_016862785.1
XP_024309553.1
XP_047304985.1
XP_047304986.1
XP_047304987.1
XP_047304988.1
XP_047304989.1
XP_047304990.1
XP_054204005.1
XP_054204006.1
XP_054204007.1
XP_054204008.1
XP_054204009.1
XP_054204010.1
XP_054204011.1
XP_054204012.1
XP_054204013.1
XP_054204014.1
XP_054204015.1
XP_054204016.1
XP_054204017.1

NCBI Reference Sequences (RefSeq)

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_011521.2 RefSeqGene

    Range
    5049..54227
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145392.2NP_001138864.1  tRNA-splicing endonuclease subunit Sen2 isoform 1

    See identical proteins and their annotated locations for NP_001138864.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 6 encode the same isoform (1).
    Source sequence(s)
    AC018500, AC090947, BC004178, BM671402
    Consensus CDS
    CCDS2611.1
    UniProtKB/Swiss-Prot
    B7Z6K1, C9IZI7, G5E9Q3, Q8NCE0, Q8WTW7, Q9BPU7
    UniProtKB/TrEMBL
    A8K568
    Related
    ENSP00000385976.3, ENST00000402228.7
    Conserved Domains (2) summary
    pfam01974
    Location:339422
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
    pfam02778
    Location:281329
    tRNA_int_endo_N; tRNA intron endonuclease, N-terminal domain
  2. NM_001145393.3NP_001138865.1  tRNA-splicing endonuclease subunit Sen2 isoform 2

    See identical proteins and their annotated locations for NP_001138865.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and lacks an alternate in-frame exon in the coding region compared to variant 1. The resulting protein (isoform 2) is shorter than isoform 1.
    Source sequence(s)
    AC018500, AK074794, BM671402, DA614108
    Consensus CDS
    CCDS46757.1
    UniProtKB/TrEMBL
    A0A7P0Z492
    Related
    ENSP00000416510.1, ENST00000415684.6
    Conserved Domains (2) summary
    pfam01974
    Location:313396
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
    cl27367
    Location:277345
    tRNA_int_endo_N; tRNA intron endonuclease, N-terminal domain
  3. NM_001145394.2NP_001138866.1  tRNA-splicing endonuclease subunit Sen2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the coding region compared to variant 1. The resulting protein (isoform 3) is shorter than isoform 1.
    Source sequence(s)
    AC018500, AK225875, BM671402
    Consensus CDS
    CCDS46758.1
    UniProtKB/TrEMBL
    A8K568
    Related
    ENSP00000392029.2, ENST00000454502.6
    Conserved Domains (2) summary
    pfam02778
    Location:224270
    tRNA_int_endo_N; tRNA intron endonuclease, N-terminal domain
    cd22363
    Location:280371
    tRNA-intron_lyase_C; catalytic C-terminal domain of the tRNA-intron lyase
  4. NM_001321277.2NP_001308206.1  tRNA-splicing endonuclease subunit Sen2 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 6 encode the same isoform (1).
    Source sequence(s)
    AC018500, AK225875, BC004178, BM671402, DA614108
    Consensus CDS
    CCDS2611.1
    UniProtKB/Swiss-Prot
    B7Z6K1, C9IZI7, G5E9Q3, Q8NCE0, Q8WTW7, Q9BPU7
    UniProtKB/TrEMBL
    A8K568
    Related
    ENSP00000505274.1, ENST00000679699.1
    Conserved Domains (2) summary
    pfam01974
    Location:339422
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
    pfam02778
    Location:281329
    tRNA_int_endo_N; tRNA intron endonuclease, N-terminal domain
  5. NM_001321278.2NP_001308207.1  tRNA-splicing endonuclease subunit Sen2 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC018500, AF086155, AK225875, BC004178, BE858588, DA614108
    Consensus CDS
    CCDS93216.1
    UniProtKB/TrEMBL
    C9J7Z4, H7C2Z3
    Related
    ENSP00000406238.2, ENST00000446004.6
    Conserved Domains (4) summary
    COG1676
    Location:297425
    SEN2; tRNA splicing endonuclease [Translation, ribosomal structure and biogenesis]
    pfam01974
    Location:339422
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
    pfam02778
    Location:281329
    tRNA_int_endo_N; tRNA intron endonuclease, N-terminal domain
    pfam13900
    Location:450497
    GVQW; Putative domain of unknown function
  6. NM_001321279.2NP_001308208.1  tRNA-splicing endonuclease subunit Sen2 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC018500, AC090947, BC004178, BC019582, BM671402
    Consensus CDS
    CCDS46757.1
    UniProtKB/TrEMBL
    A0A7P0Z492
    Related
    ENSP00000506163.1, ENST00000681676.1
    Conserved Domains (2) summary
    pfam01974
    Location:313396
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
    cl27367
    Location:277345
    tRNA_int_endo_N; tRNA intron endonuclease, N-terminal domain
  7. NM_025265.4NP_079541.1  tRNA-splicing endonuclease subunit Sen2 isoform 1

    See identical proteins and their annotated locations for NP_079541.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1, 2 and 6 encode the same isoform (1).
    Source sequence(s)
    AC018500, AC090947, BC019582, BM671402
    Consensus CDS
    CCDS2611.1
    UniProtKB/Swiss-Prot
    B7Z6K1, C9IZI7, G5E9Q3, Q8NCE0, Q8WTW7, Q9BPU7
    UniProtKB/TrEMBL
    A8K568
    Related
    ENSP00000284995.6, ENST00000284995.11
    Conserved Domains (2) summary
    pfam01974
    Location:339422
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
    pfam02778
    Location:281329
    tRNA_int_endo_N; tRNA intron endonuclease, N-terminal domain

RNA

  1. NR_135607.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC018500, AF086155, AK027821, AK225875, BC004178, DA614108
    Related
    ENST00000680923.1

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    12480231..12539624
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047449029.1XP_047304985.1  tRNA-splicing endonuclease subunit Sen2 isoform X2

    UniProtKB/Swiss-Prot
    B7Z6K1, C9IZI7, G5E9Q3, Q8NCE0, Q8WTW7, Q9BPU7
    UniProtKB/TrEMBL
    A8K568
  2. XM_017007296.3XP_016862785.1  tRNA-splicing endonuclease subunit Sen2 isoform X2

    UniProtKB/Swiss-Prot
    B7Z6K1, C9IZI7, G5E9Q3, Q8NCE0, Q8WTW7, Q9BPU7
    UniProtKB/TrEMBL
    A8K568
    Related
    ENSP00000505799.1, ENST00000680986.1
    Conserved Domains (2) summary
    pfam01974
    Location:339422
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
    pfam02778
    Location:281329
    tRNA_int_endo_N; tRNA intron endonuclease, N-terminal domain
  3. XM_047449032.1XP_047304988.1  tRNA-splicing endonuclease subunit Sen2 isoform X5

    UniProtKB/TrEMBL
    A0A7P0Z492
  4. XM_017007293.2XP_016862782.1  tRNA-splicing endonuclease subunit Sen2 isoform X1

    UniProtKB/TrEMBL
    A0A7P0T914, A8K568
  5. XM_017007294.2XP_016862783.1  tRNA-splicing endonuclease subunit Sen2 isoform X1

    UniProtKB/TrEMBL
    A0A7P0T914, A8K568
  6. XM_024453785.2XP_024309553.1  tRNA-splicing endonuclease subunit Sen2 isoform X5

    UniProtKB/TrEMBL
    A0A7P0Z492
    Conserved Domains (2) summary
    pfam01974
    Location:313396
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
    cl27367
    Location:277345
    tRNA_int_endo_N; tRNA intron endonuclease, N-terminal domain
  7. XM_017007292.2XP_016862781.1  tRNA-splicing endonuclease subunit Sen2 isoform X1

    UniProtKB/TrEMBL
    A0A7P0T914, A8K568
    Related
    ENSP00000505417.1, ENST00000680275.1
  8. XM_047449030.1XP_047304986.1  tRNA-splicing endonuclease subunit Sen2 isoform X3

    UniProtKB/TrEMBL
    A0A7P0T8F8, A0A7P0Z492
    Related
    ENSP00000505106.1, ENST00000680354.1
  9. XM_047449031.1XP_047304987.1  tRNA-splicing endonuclease subunit Sen2 isoform X4

    UniProtKB/TrEMBL
    A0A7P0TBE6
  10. XM_047449033.1XP_047304989.1  tRNA-splicing endonuclease subunit Sen2 isoform X6

    UniProtKB/TrEMBL
    A0A7P0TA86, A0A7P0TBE6
    Related
    ENSP00000505979.1, ENST00000680458.1
  11. XM_047449034.1XP_047304990.1  tRNA-splicing endonuclease subunit Sen2 isoform X7

    UniProtKB/TrEMBL
    A0A7P0Z4J6
    Related
    ENSP00000505351.1, ENST00000680765.1
  12. XM_017007295.3XP_016862784.1  tRNA-splicing endonuclease subunit Sen2 isoform X1

    UniProtKB/TrEMBL
    A0A7P0T914, A8K568
  13. XM_011534139.4XP_011532441.1  tRNA-splicing endonuclease subunit Sen2 isoform X8

    UniProtKB/TrEMBL
    B7Z355
    Conserved Domains (3) summary
    COG1676
    Location:206334
    SEN2; tRNA splicing endonuclease [Translation, ribosomal structure and biogenesis]
    pfam01974
    Location:248331
    tRNA_int_endo; tRNA intron endonuclease, catalytic C-terminal domain
    pfam02778
    Location:190238
    tRNA_int_endo_N; tRNA intron endonuclease, N-terminal domain

RNA

  1. XR_007095741.1 RNA Sequence

  2. XR_007095740.1 RNA Sequence

  3. XR_007095739.1 RNA Sequence

  4. XR_001740289.3 RNA Sequence

    Related
    ENST00000680449.1
  5. XR_001740291.2 RNA Sequence

  6. XR_002959592.2 RNA Sequence

  7. XR_002959593.2 RNA Sequence

  8. XR_007095737.1 RNA Sequence

  9. XR_007095736.1 RNA Sequence

  10. XR_007095742.1 RNA Sequence

  11. XR_007095738.1 RNA Sequence

  12. XR_007095743.1 RNA Sequence

  13. XR_001740290.3 RNA Sequence

  14. XR_007095750.1 RNA Sequence

  15. XR_007095744.1 RNA Sequence

  16. XR_007095747.1 RNA Sequence

  17. XR_007095745.1 RNA Sequence

  18. XR_007095749.1 RNA Sequence

  19. XR_007095746.1 RNA Sequence

  20. XR_007095748.1 RNA Sequence

  21. XR_007095751.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    12478037..12537426
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348034.1XP_054204009.1  tRNA-splicing endonuclease subunit Sen2 isoform X2

    UniProtKB/Swiss-Prot
    B7Z6K1, C9IZI7, G5E9Q3, Q8NCE0, Q8WTW7, Q9BPU7
    UniProtKB/TrEMBL
    A8K568
  2. XM_054348031.1XP_054204006.1  tRNA-splicing endonuclease subunit Sen2 isoform X1

    UniProtKB/TrEMBL
    A0A7P0T914, A8K568
  3. XM_054348032.1XP_054204007.1  tRNA-splicing endonuclease subunit Sen2 isoform X1

    UniProtKB/TrEMBL
    A0A7P0T914, A8K568
  4. XM_054348038.1XP_054204013.1  tRNA-splicing endonuclease subunit Sen2 isoform X5

    UniProtKB/TrEMBL
    A0A7P0Z492
  5. XM_054348030.1XP_054204005.1  tRNA-splicing endonuclease subunit Sen2 isoform X1

    UniProtKB/TrEMBL
    A0A7P0T914, A8K568
  6. XM_054348036.1XP_054204011.1  tRNA-splicing endonuclease subunit Sen2 isoform X3

    UniProtKB/TrEMBL
    A0A7P0T8F8, A0A7P0Z492
  7. XM_054348037.1XP_054204012.1  tRNA-splicing endonuclease subunit Sen2 isoform X4

    UniProtKB/TrEMBL
    A0A7P0TBE6
  8. XM_054348040.1XP_054204015.1  tRNA-splicing endonuclease subunit Sen2 isoform X6

    UniProtKB/TrEMBL
    A0A7P0TA86, A0A7P0TBE6
  9. XM_054348041.1XP_054204016.1  tRNA-splicing endonuclease subunit Sen2 isoform X7

    UniProtKB/TrEMBL
    A0A7P0Z4J6
  10. XM_054348035.1XP_054204010.1  tRNA-splicing endonuclease subunit Sen2 isoform X2

    UniProtKB/Swiss-Prot
    B7Z6K1, C9IZI7, G5E9Q3, Q8NCE0, Q8WTW7, Q9BPU7
    UniProtKB/TrEMBL
    A8K568
  11. XM_054348039.1XP_054204014.1  tRNA-splicing endonuclease subunit Sen2 isoform X5

    UniProtKB/TrEMBL
    A0A7P0Z492
  12. XM_054348033.1XP_054204008.1  tRNA-splicing endonuclease subunit Sen2 isoform X1

    UniProtKB/TrEMBL
    A0A7P0T914, A8K568
  13. XM_054348042.1XP_054204017.1  tRNA-splicing endonuclease subunit Sen2 isoform X8

    UniProtKB/TrEMBL
    B7Z355

RNA

  1. XR_008486816.1 RNA Sequence

  2. XR_008486814.1 RNA Sequence

  3. XR_008486822.1 RNA Sequence

  4. XR_008486811.1 RNA Sequence

  5. XR_008486815.1 RNA Sequence

  6. XR_008486812.1 RNA Sequence

  7. XR_008486810.1 RNA Sequence

  8. XR_008486819.1 RNA Sequence

  9. XR_008486813.1 RNA Sequence

  10. XR_008486821.1 RNA Sequence

  11. XR_008486820.1 RNA Sequence

  12. XR_008486829.1 RNA Sequence

  13. XR_008486823.1 RNA Sequence

  14. XR_008486826.1 RNA Sequence

  15. XR_008486824.1 RNA Sequence

  16. XR_008486828.1 RNA Sequence

  17. XR_008486825.1 RNA Sequence

  18. XR_008486827.1 RNA Sequence

  19. XR_008486830.1 RNA Sequence

  20. XR_008486818.1 RNA Sequence

  21. XR_008486817.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001145395.1: Suppressed sequence

    Description
    NM_001145395.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.