UniProtKB - Q8NCE0 (SEN2_HUMAN)
tRNA-splicing endonuclease subunit Sen2
TSEN2
Functioni
Constitutes one of the two catalytic subunit of the tRNA-splicing endonuclease complex, a complex responsible for identification and cleavage of the splice sites in pre-tRNA. It cleaves pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3'-cyclic phosphate and 5'-OH termini. There are no conserved sequences at the splice sites, but the intron is invariably located at the same site in the gene, placing the splice sites an invariant distance from the constant structural features of the tRNA body. Isoform 1 probably carries the active site for 5'-splice site cleavage. The tRNA splicing endonuclease is also involved in mRNA processing via its association with pre-mRNA 3'-end processing factors, establishing a link between pre-tRNA splicing and pre-mRNA 3'-end formation, suggesting that the endonuclease subunits function in multiple RNA-processing events. Isoform 2 is responsible for processing a yet unknown RNA substrate. The complex containing isoform 2 is not able to cleave pre-tRNAs properly, although it retains endonucleolytic activity.
1 PublicationCatalytic activityi
- PretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus. EC:4.6.1.16
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 369 | By similarity | 1 | |
Active sitei | 377 | By similarity | 1 | |
Active sitei | 416 | By similarity | 1 |
GO - Molecular functioni
- lyase activity Source: UniProtKB-KW
- nucleic acid binding Source: InterPro
- tRNA-intron endonuclease activity Source: GO_Central
GO - Biological processi
- mRNA processing Source: UniProtKB-KW
- tRNA splicing, via endonucleolytic cleavage and ligation Source: UniProtKB
- tRNA-type intron splice site recognition and cleavage Source: GO_Central
Keywordsi
Molecular function | Lyase |
Biological process | mRNA processing, tRNA processing |
Enzyme and pathway databases
BRENDAi | 4.6.1.16, 2681 |
PathwayCommonsi | Q8NCE0 |
Reactomei | R-HSA-6784531, tRNA processing in the nucleus |
SignaLinki | Q8NCE0 |
Names & Taxonomyi
Protein namesi | Recommended name: tRNA-splicing endonuclease subunit Sen2 (EC:4.6.1.16)Alternative name(s): tRNA-intron endonuclease Sen2 Short name: HsSen2 |
Gene namesi | Name:TSEN2 Synonyms:SEN2 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
HGNCi | HGNC:28422, TSEN2 |
MIMi | 608753, gene |
neXtProti | NX_Q8NCE0 |
VEuPathDBi | HostDB:ENSG00000154743 |
Subcellular locationi
Cytoskeleton
- centrosome Source: HPA
Cytosol
- cytosol Source: HPA
Nucleus
- nucleolus Source: UniProtKB-SubCell
- nucleoplasm Source: HPA
- tRNA-intron endonuclease complex Source: GO_Central
Keywords - Cellular componenti
NucleusPathology & Biotechi
Involvement in diseasei
Pontocerebellar hypoplasia 2B (PCH2B)1 Publication
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_054810 | 309 | Y → C in PCH2B. 1 PublicationCorresponds to variant dbSNP:rs113994149EnsemblClinVar. | 1 |
Keywords - Diseasei
Neurodegeneration, Pontocerebellar hypoplasiaOrganism-specific databases
DisGeNETi | 80746 |
MalaCardsi | TSEN2 |
MIMi | 612389, phenotype |
OpenTargetsi | ENSG00000154743 |
Orphaneti | 2524, Pontocerebellar hypoplasia type 2 |
PharmGKBi | PA142670695 |
Miscellaneous databases
Pharosi | Q8NCE0, Tbio |
Genetic variation databases
BioMutai | TSEN2 |
DMDMi | 50428914 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000109452 | 1 – 465 | tRNA-splicing endonuclease subunit Sen2Add BLAST | 465 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 408 | PhosphoserineBy similarity | 1 | |
Modified residuei | 411 | PhosphoserineBy similarity | 1 | |
Modified residuei | 415 | PhosphoserineBy similarity | 1 |
Keywords - PTMi
PhosphoproteinProteomic databases
EPDi | Q8NCE0 |
jPOSTi | Q8NCE0 |
MassIVEi | Q8NCE0 |
MaxQBi | Q8NCE0 |
PaxDbi | Q8NCE0 |
PeptideAtlasi | Q8NCE0 |
PRIDEi | Q8NCE0 |
ProteomicsDBi | 34009 72878 [Q8NCE0-1] 72879 [Q8NCE0-2] 72880 [Q8NCE0-3] 7810 |
PTM databases
iPTMneti | Q8NCE0 |
PhosphoSitePlusi | Q8NCE0 |
Expressioni
Tissue specificityi
Gene expression databases
Bgeei | ENSG00000154743, Expressed in sural nerve and 193 other tissues |
ExpressionAtlasi | Q8NCE0, baseline and differential |
Genevisiblei | Q8NCE0, HS |
Organism-specific databases
HPAi | ENSG00000154743, Low tissue specificity |
Interactioni
Subunit structurei
tRNA splicing endonuclease is a heterotetramer composed of isoform 1 of TSEN2, TSEN15, TSEN34/LENG5 and TSEN54. tRNA splicing endonuclease complex also contains proteins of the pre-mRNA 3'-end processing machinery such as CLP1, CPSF1, CPSF4 and CSTF2. Isoform 2 belongs to a different complex that contains TSEN54 but low level of TSEN15 and TSEN34/LENG5.
Binary interactionsi
Q8NCE0
Protein-protein interaction databases
BioGRIDi | 123288, 85 interactors |
CORUMi | Q8NCE0 |
IntActi | Q8NCE0, 20 interactors |
STRINGi | 9606.ENSP00000284995 |
Miscellaneous databases
RNActi | Q8NCE0, protein |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 157 – 204 | DisorderedSequence analysisAdd BLAST | 48 |
Sequence similaritiesi
Phylogenomic databases
eggNOGi | KOG4685, Eukaryota |
GeneTreei | ENSGT00390000013266 |
HOGENOMi | CLU_046429_1_0_1 |
InParanoidi | Q8NCE0 |
OMAi | TFEETFF |
OrthoDBi | 1219366at2759 |
PhylomeDBi | Q8NCE0 |
TreeFami | TF314679 |
Family and domain databases
Gene3Di | 3.40.1350.10, 1 hit |
InterProi | View protein in InterPro IPR011856, tRNA_endonuc-like_dom_sf IPR036167, tRNA_intron_Endo_cat-like_sf IPR006677, tRNA_intron_Endonuc_cat-like IPR006678, tRNA_intron_Endonuc_N IPR006676, tRNA_splic IPR016589, tRNA_splic_SEN2 |
PANTHERi | PTHR21227, PTHR21227, 1 hit |
Pfami | View protein in Pfam PF01974, tRNA_int_endo, 1 hit PF02778, tRNA_int_endo_N, 1 hit |
PIRSFi | PIRSF011789, tRNA_splic_SEN2, 1 hit |
SUPFAMi | SSF53032, SSF53032, 1 hit |
s (5+)i Sequence
Sequence statusi: Complete.
This entry describes 5 produced by isoformsialternative splicing. AlignAdd to basketThis entry has 5 described isoforms and 19 potential isoforms that are computationally mapped.Show allAlign All
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
10 20 30 40 50
MAEAVFHAPK RKRRVYETYE SPLPIPFGQD HGPLKEFKIF RAEMINNNVI
60 70 80 90 100
VRNAEDIEQL YGKGYFGKGI LSRSRPSFTI SDPKLVAKWK DMKTNMPIIT
110 120 130 140 150
SKRYQHSVEW AAELMRRQGQ DESTVRRILK DYTKPLEHPP VKRNEEAQVH
160 170 180 190 200
DKLNSGMVSN MEGTAGGERP SVVNGDSGKS GGVGDPREPL GCLQEGSGCH
210 220 230 240 250
PTTESFEKSV REDASPLPHV CCCKQDALIL QRGLHHEDGS QHIGLLHPGD
260 270 280 290 300
RGPDHEYVLV EEAECAMSER EAAPNEELVQ RNRLICRRNP YRIFEYLQLS
310 320 330 340 350
LEEAFFLVYA LGCLSIYYEK EPLTIVKLWK AFTVVQPTFR TTYMAYHYFR
360 370 380 390 400
SKGWVPKVGL KYGTDLLLYR KGPPFYHASY SVIIELVDDH FEGSLRRPLS
410 420 430 440 450
WKSLAALSRV SVNVSKELML CYLIKPSTMT DKEMESPECM KRIKVQEVIL
460
SRWVSSRERS DQDDL
Computationally mapped potential isoform sequencesi
There are 19 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basketH7C2Z3 | H7C2Z3_HUMAN | tRNA-splicing endonuclease subunit ... | TSEN2 | 490 | Annotation score: | ||
C9J7Z4 | C9J7Z4_HUMAN | tRNA-intron lyase | TSEN2 | 516 | Annotation score: | ||
A0A7P0T8F8 | A0A7P0T8F8_HUMAN | tRNA-splicing endonuclease subunit ... | TSEN2 | 458 | Annotation score: | ||
A0A7P0T914 | A0A7P0T914_HUMAN | tRNA-splicing endonuclease subunit ... | TSEN2 | 484 | Annotation score: | ||
A0A7P0TA86 | A0A7P0TA86_HUMAN | tRNA-splicing endonuclease subunit ... | TSEN2 | 423 | Annotation score: | ||
A0A7P0Z4J6 | A0A7P0Z4J6_HUMAN | tRNA-splicing endonuclease subunit ... | TSEN2 | 434 | Annotation score: | ||
A0A7P0T841 | A0A7P0T841_HUMAN | tRNA-splicing endonuclease subunit ... | TSEN2 | 473 | Annotation score: | ||
A0A7P0TBE6 | A0A7P0TBE6_HUMAN | tRNA-splicing endonuclease subunit ... | TSEN2 | 460 | Annotation score: | ||
A0A7P0Z492 | A0A7P0Z492_HUMAN | tRNA-splicing endonuclease subunit ... | TSEN2 | 422 | Annotation score: | ||
A0A7P0T923 | A0A7P0T923_HUMAN | tRNA-splicing endonuclease subunit ... | TSEN2 | 347 | Annotation score: | ||
There are more potential isoformsShow all |
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 138 | H → Q in BAH13287 (PubMed:14702039).Curated | 1 | |
Sequence conflicti | 208 | K → E in BAH13287 (PubMed:14702039).Curated | 1 |
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_048931 | 41 | R → H. Corresponds to variant dbSNP:rs12495784EnsemblClinVar. | 1 | |
Natural variantiVAR_048932 | 126 | R → H. Corresponds to variant dbSNP:rs33955793EnsemblClinVar. | 1 | |
Natural variantiVAR_054810 | 309 | Y → C in PCH2B. 1 PublicationCorresponds to variant dbSNP:rs113994149EnsemblClinVar. | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_046192 | 173 – 231 | Missing in isoform 4. 1 PublicationAdd BLAST | 59 | |
Alternative sequenceiVSP_046193 | 276 – 301 | Missing in isoform 5. 1 PublicationAdd BLAST | 26 | |
Alternative sequenceiVSP_010985 | 278 – 303 | Missing in isoform 3. 1 PublicationAdd BLAST | 26 | |
Alternative sequenceiVSP_010986 | 304 – 320 | Missing in isoform 2. 1 PublicationAdd BLAST | 17 | |
Alternative sequenceiVSP_046194 | 417 – 465 | ELMLC…DQDDL → VTQHQLCHWSVT in isoform 5. 1 PublicationAdd BLAST | 49 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AK074794 mRNA Translation: BAC11213.1 AK300449 mRNA Translation: BAH13287.1 AK225875 mRNA No translation available. AC018500 Genomic DNA No translation available. AC090947 Genomic DNA No translation available. CH471055 Genomic DNA Translation: EAW64129.1 BC004178 mRNA Translation: AAH04178.1 BC004211 mRNA Translation: AAH04211.1 BC019582 mRNA Translation: AAH19582.1 BC021975 mRNA Translation: AAH21975.2 |
CCDSi | CCDS2611.1 [Q8NCE0-1] CCDS46757.1 [Q8NCE0-3] CCDS46758.1 [Q8NCE0-4] |
RefSeqi | NP_001138864.1, NM_001145392.1 [Q8NCE0-1] NP_001138865.1, NM_001145393.2 [Q8NCE0-3] NP_001138866.1, NM_001145394.1 [Q8NCE0-4] NP_001308206.1, NM_001321277.1 [Q8NCE0-1] NP_001308207.1, NM_001321278.1 NP_001308208.1, NM_001321279.1 [Q8NCE0-3] NP_079541.1, NM_025265.3 [Q8NCE0-1] XP_016862785.1, XM_017007296.1 [Q8NCE0-1] |
Genome annotation databases
Keywords - Coding sequence diversityi
Alternative splicingSimilar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AK074794 mRNA Translation: BAC11213.1 AK300449 mRNA Translation: BAH13287.1 AK225875 mRNA No translation available. AC018500 Genomic DNA No translation available. AC090947 Genomic DNA No translation available. CH471055 Genomic DNA Translation: EAW64129.1 BC004178 mRNA Translation: AAH04178.1 BC004211 mRNA Translation: AAH04211.1 BC019582 mRNA Translation: AAH19582.1 BC021975 mRNA Translation: AAH21975.2 |
CCDSi | CCDS2611.1 [Q8NCE0-1] CCDS46757.1 [Q8NCE0-3] CCDS46758.1 [Q8NCE0-4] |
RefSeqi | NP_001138864.1, NM_001145392.1 [Q8NCE0-1] NP_001138865.1, NM_001145393.2 [Q8NCE0-3] NP_001138866.1, NM_001145394.1 [Q8NCE0-4] NP_001308206.1, NM_001321277.1 [Q8NCE0-1] NP_001308207.1, NM_001321278.1 NP_001308208.1, NM_001321279.1 [Q8NCE0-3] NP_079541.1, NM_025265.3 [Q8NCE0-1] XP_016862785.1, XM_017007296.1 [Q8NCE0-1] |
3D structure databases
AlphaFoldDBi | Q8NCE0 |
SMRi | Q8NCE0 |
ModBasei | Search... |
Protein-protein interaction databases
BioGRIDi | 123288, 85 interactors |
CORUMi | Q8NCE0 |
IntActi | Q8NCE0, 20 interactors |
STRINGi | 9606.ENSP00000284995 |
PTM databases
iPTMneti | Q8NCE0 |
PhosphoSitePlusi | Q8NCE0 |
Genetic variation databases
BioMutai | TSEN2 |
DMDMi | 50428914 |
Proteomic databases
EPDi | Q8NCE0 |
jPOSTi | Q8NCE0 |
MassIVEi | Q8NCE0 |
MaxQBi | Q8NCE0 |
PaxDbi | Q8NCE0 |
PeptideAtlasi | Q8NCE0 |
PRIDEi | Q8NCE0 |
ProteomicsDBi | 34009 72878 [Q8NCE0-1] 72879 [Q8NCE0-2] 72880 [Q8NCE0-3] 7810 |
Protocols and materials databases
Antibodypediai | 26210, 200 antibodies from 25 providers |
DNASUi | 80746 |
Genome annotation databases
Organism-specific databases
CTDi | 80746 |
DisGeNETi | 80746 |
GeneCardsi | TSEN2 |
HGNCi | HGNC:28422, TSEN2 |
HPAi | ENSG00000154743, Low tissue specificity |
MalaCardsi | TSEN2 |
MIMi | 608753, gene 612389, phenotype |
neXtProti | NX_Q8NCE0 |
OpenTargetsi | ENSG00000154743 |
Orphaneti | 2524, Pontocerebellar hypoplasia type 2 |
PharmGKBi | PA142670695 |
VEuPathDBi | HostDB:ENSG00000154743 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG4685, Eukaryota |
GeneTreei | ENSGT00390000013266 |
HOGENOMi | CLU_046429_1_0_1 |
InParanoidi | Q8NCE0 |
OMAi | TFEETFF |
OrthoDBi | 1219366at2759 |
PhylomeDBi | Q8NCE0 |
TreeFami | TF314679 |
Enzyme and pathway databases
BRENDAi | 4.6.1.16, 2681 |
PathwayCommonsi | Q8NCE0 |
Reactomei | R-HSA-6784531, tRNA processing in the nucleus |
SignaLinki | Q8NCE0 |
Miscellaneous databases
BioGRID-ORCSi | 80746, 534 hits in 1084 CRISPR screens |
ChiTaRSi | TSEN2, human |
GeneWikii | TSEN2 |
GenomeRNAii | 80746 |
Pharosi | Q8NCE0, Tbio |
PROi | PR:Q8NCE0 |
RNActi | Q8NCE0, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000154743, Expressed in sural nerve and 193 other tissues |
ExpressionAtlasi | Q8NCE0, baseline and differential |
Genevisiblei | Q8NCE0, HS |
Family and domain databases
Gene3Di | 3.40.1350.10, 1 hit |
InterProi | View protein in InterPro IPR011856, tRNA_endonuc-like_dom_sf IPR036167, tRNA_intron_Endo_cat-like_sf IPR006677, tRNA_intron_Endonuc_cat-like IPR006678, tRNA_intron_Endonuc_N IPR006676, tRNA_splic IPR016589, tRNA_splic_SEN2 |
PANTHERi | PTHR21227, PTHR21227, 1 hit |
Pfami | View protein in Pfam PF01974, tRNA_int_endo, 1 hit PF02778, tRNA_int_endo_N, 1 hit |
PIRSFi | PIRSF011789, tRNA_splic_SEN2, 1 hit |
SUPFAMi | SSF53032, SSF53032, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | SEN2_HUMAN | |
Accessioni | Q8NCE0Primary (citable) accession number: Q8NCE0 Secondary accession number(s): B7Z6K1 Q9BPU7 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | July 19, 2004 |
Last sequence update: | July 19, 2004 | |
Last modified: | May 25, 2022 | |
This is version 159 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. |
Miscellaneousi
Keywords - Technical termi
Reference proteomeDocuments
- Human chromosome 3
Human chromosome 3: entries, gene names and cross-references to MIM - Human entries with genetic variants
List of human entries with genetic variants - Human variants curated from literature reports
Index of human variants curated from literature reports - MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - SIMILARITY comments
Index of protein domains and families