Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

tRNA-splicing endonuclease subunit Sen2

Gene

TSEN2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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 Publication

Catalytic 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.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei369By similarity1
Active sitei377By similarity1
Active sitei416By similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

mRNA processing, tRNA processing

Enzyme and pathway databases

BioCyciZFISH:HS08007-MONOMER.
ReactomeiR-HSA-6784531. tRNA processing in the nucleus.

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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

HGNCiHGNC:28422. TSEN2.

Subcellular locationi

  • Nucleus 1 Publication
  • Nucleusnucleolus 1 Publication

  • Note: May be transiently localized in the nucleolus.

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Pontocerebellar hypoplasia 2B (PCH2B)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder characterized by an abnormally small cerebellum and brainstem, and progressive microcephaly from birth combined with extrapyramidal dyskinesia. Severe chorea occurs and epilepsy is frequent. There are no signs of spinal cord anterior horn cells degeneration.
See also OMIM:612389
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_054810309Y → C in PCH2B. 1 PublicationCorresponds to variant rs113994149dbSNPEnsembl.1

Keywords - Diseasei

Neurodegeneration, Pontocerebellar hypoplasia

Organism-specific databases

DisGeNETi80746.
MalaCardsiTSEN2.
MIMi612389. phenotype.
OpenTargetsiENSG00000154743.
Orphaneti2524. Pontocerebellar hypoplasia type 2.
PharmGKBiPA142670695.

Polymorphism and mutation databases

BioMutaiTSEN2.
DMDMi50428914.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001094521 – 465tRNA-splicing endonuclease subunit Sen2Add BLAST465

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei408PhosphoserineBy similarity1
Modified residuei411PhosphoserineBy similarity1
Modified residuei415PhosphoserineBy similarity1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ8NCE0.
MaxQBiQ8NCE0.
PaxDbiQ8NCE0.
PeptideAtlasiQ8NCE0.
PRIDEiQ8NCE0.

PTM databases

iPTMnetiQ8NCE0.
PhosphoSitePlusiQ8NCE0.

Expressioni

Tissue specificityi

Isoform 1 and isoform 2 are widely expressed at very low level.1 Publication

Gene expression databases

BgeeiENSG00000154743.
CleanExiHS_TSEN2.
ExpressionAtlasiQ8NCE0. baseline and differential.
GenevisibleiQ8NCE0. HS.

Organism-specific databases

HPAiHPA027120.
HPA027125.
HPA027268.

Interactioni

Subunit structurei

tRNA splicing endonuclease is a heterotetramer composed of isoform 1 of SEN2, SEN15, SEN34/LENG5 and SEN54. 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 SEN54 but low level of SEN15 and SEN34/LENG5.

Binary interactionsi

WithEntry#Exp.IntActNotes
TSEN54Q7Z6J97EBI-2559818,EBI-2559824

Protein-protein interaction databases

BioGridi123288. 25 interactors.
IntActiQ8NCE0. 7 interactors.
STRINGi9606.ENSP00000284995.

Structurei

3D structure databases

ProteinModelPortaliQ8NCE0.
SMRiQ8NCE0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the tRNA-intron endonuclease family.Curated

Phylogenomic databases

eggNOGiKOG4685. Eukaryota.
COG1676. LUCA.
GeneTreeiENSGT00390000013266.
HOGENOMiHOG000154285.
HOVERGENiHBG056610.
InParanoidiQ8NCE0.
KOiK15322.
OrthoDBiEOG091G0FMD.
PhylomeDBiQ8NCE0.
TreeFamiTF314679.

Family and domain databases

Gene3Di3.40.1350.10. 1 hit.
InterProiIPR011856. tRNA_endonuc-like_dom.
IPR006677. tRNA_intron_Endonuc_cat-like.
IPR006678. tRNA_intron_Endonuc_N.
IPR006676. tRNA_splic.
IPR016589. tRNA_splic_SEN2.
[Graphical view]
PANTHERiPTHR21227. PTHR21227. 2 hits.
PfamiPF01974. tRNA_int_endo. 1 hit.
PF02778. tRNA_int_endo_N. 1 hit.
[Graphical view]
PIRSFiPIRSF011789. tRNA_splic_SEN2. 1 hit.
SUPFAMiSSF53032. SSF53032. 1 hit.

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8NCE0-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        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
Length:465
Mass (Da):53,247
Last modified:July 19, 2004 - v2
Checksum:iFF523229B05A1345
GO
Isoform 2 (identifier: Q8NCE0-2) [UniParc]FASTAAdd to basket
Also known as: SEN2deltaEx8, DeltaEx8

The sequence of this isoform differs from the canonical sequence as follows:
     304-320: Missing.

Show »
Length:448
Mass (Da):51,265
Checksum:iB616BDFCDA590E32
GO
Isoform 3 (identifier: Q8NCE0-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     278-303: Missing.

Note: No experimental confirmation available.
Show »
Length:439
Mass (Da):49,942
Checksum:i97A9E847199BDE08
GO
Isoform 4 (identifier: Q8NCE0-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     173-231: Missing.

Note: No experimental confirmation available.
Show »
Length:406
Mass (Da):47,124
Checksum:i61FD06EBE21EEEFD
GO
Isoform 5 (identifier: Q8NCE0-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     276-301: Missing.
     417-465: ELMLCYLIKPSTMTDKEMESPECMKRIKVQEVILSRWVSSRERSDQDDL → VTQHQLCHWSVT

Note: No experimental confirmation available.
Show »
Length:402
Mass (Da):45,532
Checksum:i8B231F84B72FA227
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti138H → Q in BAH13287 (PubMed:14702039).Curated1
Sequence conflicti208K → E in BAH13287 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04893141R → H.Corresponds to variant rs12495784dbSNPEnsembl.1
Natural variantiVAR_048932126R → H.Corresponds to variant rs33955793dbSNPEnsembl.1
Natural variantiVAR_054810309Y → C in PCH2B. 1 PublicationCorresponds to variant rs113994149dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_046192173 – 231Missing in isoform 4. 1 PublicationAdd BLAST59
Alternative sequenceiVSP_046193276 – 301Missing in isoform 5. 1 PublicationAdd BLAST26
Alternative sequenceiVSP_010985278 – 303Missing in isoform 3. 1 PublicationAdd BLAST26
Alternative sequenceiVSP_010986304 – 320Missing in isoform 2. 1 PublicationAdd BLAST17
Alternative sequenceiVSP_046194417 – 465ELMLC…DQDDL → VTQHQLCHWSVT in isoform 5. 1 PublicationAdd BLAST49

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.
CCDSiCCDS2611.1. [Q8NCE0-1]
CCDS46757.1. [Q8NCE0-3]
CCDS46758.1. [Q8NCE0-4]
RefSeqiNP_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]
UniGeneiHs.335550.
Hs.670039.

Genome annotation databases

EnsembliENST00000284995; ENSP00000284995; ENSG00000154743. [Q8NCE0-1]
ENST00000402228; ENSP00000385976; ENSG00000154743. [Q8NCE0-1]
ENST00000415684; ENSP00000416510; ENSG00000154743. [Q8NCE0-3]
ENST00000444864; ENSP00000407974; ENSG00000154743. [Q8NCE0-5]
ENST00000454502; ENSP00000392029; ENSG00000154743. [Q8NCE0-4]
GeneIDi80746.
KEGGihsa:80746.
UCSCiuc003bwz.4. human. [Q8NCE0-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

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.
CCDSiCCDS2611.1. [Q8NCE0-1]
CCDS46757.1. [Q8NCE0-3]
CCDS46758.1. [Q8NCE0-4]
RefSeqiNP_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]
UniGeneiHs.335550.
Hs.670039.

3D structure databases

ProteinModelPortaliQ8NCE0.
SMRiQ8NCE0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi123288. 25 interactors.
IntActiQ8NCE0. 7 interactors.
STRINGi9606.ENSP00000284995.

PTM databases

iPTMnetiQ8NCE0.
PhosphoSitePlusiQ8NCE0.

Polymorphism and mutation databases

BioMutaiTSEN2.
DMDMi50428914.

Proteomic databases

EPDiQ8NCE0.
MaxQBiQ8NCE0.
PaxDbiQ8NCE0.
PeptideAtlasiQ8NCE0.
PRIDEiQ8NCE0.

Protocols and materials databases

DNASUi80746.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000284995; ENSP00000284995; ENSG00000154743. [Q8NCE0-1]
ENST00000402228; ENSP00000385976; ENSG00000154743. [Q8NCE0-1]
ENST00000415684; ENSP00000416510; ENSG00000154743. [Q8NCE0-3]
ENST00000444864; ENSP00000407974; ENSG00000154743. [Q8NCE0-5]
ENST00000454502; ENSP00000392029; ENSG00000154743. [Q8NCE0-4]
GeneIDi80746.
KEGGihsa:80746.
UCSCiuc003bwz.4. human. [Q8NCE0-1]

Organism-specific databases

CTDi80746.
DisGeNETi80746.
GeneCardsiTSEN2.
HGNCiHGNC:28422. TSEN2.
HPAiHPA027120.
HPA027125.
HPA027268.
MalaCardsiTSEN2.
MIMi608753. gene.
612389. phenotype.
neXtProtiNX_Q8NCE0.
OpenTargetsiENSG00000154743.
Orphaneti2524. Pontocerebellar hypoplasia type 2.
PharmGKBiPA142670695.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4685. Eukaryota.
COG1676. LUCA.
GeneTreeiENSGT00390000013266.
HOGENOMiHOG000154285.
HOVERGENiHBG056610.
InParanoidiQ8NCE0.
KOiK15322.
OrthoDBiEOG091G0FMD.
PhylomeDBiQ8NCE0.
TreeFamiTF314679.

Enzyme and pathway databases

BioCyciZFISH:HS08007-MONOMER.
ReactomeiR-HSA-6784531. tRNA processing in the nucleus.

Miscellaneous databases

ChiTaRSiTSEN2. human.
GeneWikiiTSEN2.
GenomeRNAii80746.
PROiQ8NCE0.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000154743.
CleanExiHS_TSEN2.
ExpressionAtlasiQ8NCE0. baseline and differential.
GenevisibleiQ8NCE0. HS.

Family and domain databases

Gene3Di3.40.1350.10. 1 hit.
InterProiIPR011856. tRNA_endonuc-like_dom.
IPR006677. tRNA_intron_Endonuc_cat-like.
IPR006678. tRNA_intron_Endonuc_N.
IPR006676. tRNA_splic.
IPR016589. tRNA_splic_SEN2.
[Graphical view]
PANTHERiPTHR21227. PTHR21227. 2 hits.
PfamiPF01974. tRNA_int_endo. 1 hit.
PF02778. tRNA_int_endo_N. 1 hit.
[Graphical view]
PIRSFiPIRSF011789. tRNA_splic_SEN2. 1 hit.
SUPFAMiSSF53032. SSF53032. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiSEN2_HUMAN
AccessioniPrimary (citable) accession number: Q8NCE0
Secondary accession number(s): B7Z6K1
, C9IZI7, G5E9Q3, Q8WTW7, Q9BPU7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: July 19, 2004
Last modified: November 30, 2016
This is version 125 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.