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

    Gene ID: 80746, updated on 3-Apr-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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
    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

    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
      Related
      ENSP00000505106.1, ENST00000680354.1
    9. XM_047449031.1XP_047304987.1  tRNA-splicing endonuclease subunit Sen2 isoform X4

    10. XM_047449033.1XP_047304989.1  tRNA-splicing endonuclease subunit Sen2 isoform X6

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

      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
    2. XM_054348031.1XP_054204006.1  tRNA-splicing endonuclease subunit Sen2 isoform X1

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

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

    5. XM_054348030.1XP_054204005.1  tRNA-splicing endonuclease subunit Sen2 isoform X1

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

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

    8. XM_054348040.1XP_054204015.1  tRNA-splicing endonuclease subunit Sen2 isoform X6

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

    10. XM_054348035.1XP_054204010.1  tRNA-splicing endonuclease subunit Sen2 isoform X2

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

    12. XM_054348033.1XP_054204008.1  tRNA-splicing endonuclease subunit Sen2 isoform X1

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

    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.