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Protein

tRNA-splicing endonuclease subunit Sen54

Gene

TSEN54

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

Functioni

Non-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. 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.1 Publication

GO - Biological processi

Keywordsi

Biological processmRNA processing, tRNA processing

Enzyme and pathway databases

BioCyciMetaCyc:HS11953-MONOMER
ReactomeiR-HSA-6784531 tRNA processing in the nucleus

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA-splicing endonuclease subunit Sen54
Alternative name(s):
SEN54 homolog
Short name:
HsSEN54
tRNA-intron endonuclease Sen54
Gene namesi
Name:TSEN54
Synonyms:SEN54
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

EuPathDBiHostDB:ENSG00000182173.12
HGNCiHGNC:27561 TSEN54
MIMi608755 gene
neXtProtiNX_Q7Z6J9

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Pontocerebellar hypoplasia 4 (PCH4)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder characterized by an abnormally small cerebellum and brainstem, severe neonatal encephalopathy, microcephaly, myoclonus and muscular hypertonia. There is a severe inferior olivary and pontine neuronal loss and a diffuse white matter gliosis.
See also OMIM:225753
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05481293S → P in PCH4. 1 PublicationCorresponds to variant dbSNP:rs113994151EnsemblClinVar.1
Pontocerebellar hypoplasia 2A (PCH2A)2 Publications
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:277470
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_073351119Y → D in PCH2A. 1 Publication1
Pontocerebellar hypoplasia 5 (PCH5)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of pontocerebellar hypoplasia, a disorder characterized by structural defects of the pons and cerebellum. Brain MRI shows an abnormally small cerebellum and brainstem, decreased cerebral white matter, and a thin corpus callosum.
See also OMIM:610204

Keywords - Diseasei

Disease mutation, Neurodegeneration, Pontocerebellar hypoplasia

Organism-specific databases

DisGeNETi283989
GeneReviewsiTSEN54
MalaCardsiTSEN54
MIMi225753 phenotype
277470 phenotype
610204 phenotype
OpenTargetsiENSG00000182173
Orphaneti2254 Pontocerebellar hypoplasia type 1
2524 Pontocerebellar hypoplasia type 2
166063 Pontocerebellar hypoplasia type 4
166068 Pontocerebellar hypoplasia type 5
PharmGKBiPA142670692

Polymorphism and mutation databases

BioMutaiTSEN54
DMDMi296452961

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001940291 – 526tRNA-splicing endonuclease subunit Sen54Add BLAST526

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1
Modified residuei178PhosphoserineCombined sources1
Modified residuei180PhosphotyrosineCombined sources1
Modified residuei267PhosphoserineCombined sources1
Modified residuei316Omega-N-methylarginineCombined sources1

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

EPDiQ7Z6J9
MaxQBiQ7Z6J9
PaxDbiQ7Z6J9
PeptideAtlasiQ7Z6J9
PRIDEiQ7Z6J9
ProteomicsDBi69429
69430 [Q7Z6J9-2]

PTM databases

iPTMnetiQ7Z6J9
PhosphoSitePlusiQ7Z6J9

Expressioni

Gene expression databases

BgeeiENSG00000182173 Expressed in 194 organ(s), highest expression level in cerebellar hemisphere
CleanExiHS_TSEN54
ExpressionAtlasiQ7Z6J9 baseline and differential
GenevisibleiQ7Z6J9 HS

Organism-specific databases

HPAiHPA053097

Interactioni

Subunit structurei

tRNA splicing endonuclease is a heterotetramer composed 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. Also belongs to a complex containing isoform 2 of SEN2.

Binary interactionsi

Protein-protein interaction databases

BioGridi129721, 12 interactors
CORUMiQ7Z6J9
IntActiQ7Z6J9, 20 interactors
MINTiQ7Z6J9
STRINGi9606.ENSP00000327487

Structurei

3D structure databases

ProteinModelPortaliQ7Z6J9
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the SEN54 family.Curated

Phylogenomic databases

eggNOGiKOG4772 Eukaryota
ENOG4111KNC LUCA
GeneTreeiENSGT00390000004214
HOGENOMiHOG000049169
HOVERGENiHBG061211
InParanoidiQ7Z6J9
KOiK15326
OMAiHLWDQPV
OrthoDBiEOG091G0I1P
PhylomeDBiQ7Z6J9
TreeFamiTF314691

Family and domain databases

InterProiView protein in InterPro
IPR024337 tRNA_splic_suSen54
IPR024336 tRNA_splic_suSen54_N
PANTHERiPTHR21027 PTHR21027, 1 hit
PfamiView protein in Pfam
PF12928 tRNA_int_end_N2, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 2 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q7Z6J9-1) [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
MEPEPEPAAV EVPAGRVLSA RELFAARSRS QKLPQRSHGP KDFLPDGSAA
60 70 80 90 100
QAERLRRCRE ELWQLLAEQR VERLGSLVAA EWRPEEGFVE LKSPAGKFWQ
110 120 130 140 150
TMGFSEQGRQ RLHPEEALYL LECGSIHLFH QDLPLSIQEA YQLLLTDHTV
160 170 180 190 200
TFLQYQVFSH LKRLGYVVRR FQPSSVLSPY ERQLNLDASV QHLEDGDGKR
210 220 230 240 250
KRSSSSPRSI NKKAKALDNS LQPKSLAASS PPPCSQPSQC PEEKPQESSP
260 270 280 290 300
MKGPGGPFQL LGSLGPSPGP AREGVGCSWE SGRAENGVTG AGKRRWNFEQ
310 320 330 340 350
ISFPNMASDS RHTLLRAPAP ELLPANVAGR ETDAESWCQK LNQRKEKLSR
360 370 380 390 400
REREHHAEAA QFQEDVNADP EVQRCSSWRE YKELLQRRQV QRSQRRAPHL
410 420 430 440 450
WGQPVTPLLS PGQASSPAVV LQHISVLQTT HLPDGGARLL EKSGGLEIIF
460 470 480 490 500
DVYQADAVAT FRKNNPGKPY ARMCISGFDE PVPDLCSLKR LSYQSGDVPL
510 520
IFALVDHGDI SFYSFRDFTL PQDVGH
Length:526
Mass (Da):58,819
Last modified:May 18, 2010 - v3
Checksum:i857D95C8F7C39461
GO
Isoform 2 (identifier: Q7Z6J9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     157-177: VFSHLKRLGYVVRRFQPSSVL → PPEEVGLCGSTIPTKLCPVPV
     178-526: Missing.

Note: No experimental confirmation available.
Show »
Length:177
Mass (Da):19,981
Checksum:i68B620EF98884157
GO

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
J9JIH8J9JIH8_HUMAN
tRNA-splicing endonuclease subunit ...
TSEN54
259Annotation score:
J3KRC5J3KRC5_HUMAN
tRNA-splicing endonuclease subunit ...
TSEN54
142Annotation score:
E7EN92E7EN92_HUMAN
tRNA-splicing endonuclease subunit ...
TSEN54
72Annotation score:
J3QLM6J3QLM6_HUMAN
tRNA-splicing endonuclease subunit ...
TSEN54
178Annotation score:
J3QRQ5J3QRQ5_HUMAN
tRNA-splicing endonuclease subunit ...
TSEN54
167Annotation score:

Sequence cautioni

The sequence AAH53643 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0194594E → DCombined sources2 PublicationsCorresponds to variant dbSNP:rs7216673EnsemblClinVar.1
Natural variantiVAR_01946138H → Q. Corresponds to variant dbSNP:rs8079373EnsemblClinVar.1
Natural variantiVAR_07335085E → V Found in familial late-onset hereditary ataxia; unknown pathological significance. 1 Publication1
Natural variantiVAR_05481293S → P in PCH4. 1 PublicationCorresponds to variant dbSNP:rs113994151EnsemblClinVar.1
Natural variantiVAR_073351119Y → D in PCH2A. 1 Publication1
Natural variantiVAR_057721137I → L. Corresponds to variant dbSNP:rs11559205EnsemblClinVar.1
Natural variantiVAR_054813307A → S in PCH2A and PCH4. 2 PublicationsCorresponds to variant dbSNP:rs113994152EnsemblClinVar.1
Natural variantiVAR_019462347K → N1 PublicationCorresponds to variant dbSNP:rs9911502EnsemblClinVar.1
Natural variantiVAR_019463437A → V1 PublicationCorresponds to variant dbSNP:rs8064529EnsemblClinVar.1
Natural variantiVAR_057722525G → R. Corresponds to variant dbSNP:rs11870627EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_010988157 – 177VFSHL…PSSVL → PPEEVGLCGSTIPTKLCPVP V in isoform 2. 1 PublicationAdd BLAST21
Alternative sequenceiVSP_010989178 – 526Missing in isoform 2. 1 PublicationAdd BLAST349

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK094466 mRNA Translation: BAC04362.1
BC047793 mRNA Translation: AAH47793.1
AC100787 Genomic DNA No translation available.
BC053643 mRNA Translation: AAH53643.1 Different initiation.
CCDSiCCDS11724.1 [Q7Z6J9-1]
RefSeqiNP_997229.2, NM_207346.2 [Q7Z6J9-1]
UniGeneiHs.378501

Genome annotation databases

EnsembliENST00000333213; ENSP00000327487; ENSG00000182173 [Q7Z6J9-1]
GeneIDi283989
KEGGihsa:283989
UCSCiuc002jof.2 human [Q7Z6J9-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK094466 mRNA Translation: BAC04362.1
BC047793 mRNA Translation: AAH47793.1
AC100787 Genomic DNA No translation available.
BC053643 mRNA Translation: AAH53643.1 Different initiation.
CCDSiCCDS11724.1 [Q7Z6J9-1]
RefSeqiNP_997229.2, NM_207346.2 [Q7Z6J9-1]
UniGeneiHs.378501

3D structure databases

ProteinModelPortaliQ7Z6J9
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi129721, 12 interactors
CORUMiQ7Z6J9
IntActiQ7Z6J9, 20 interactors
MINTiQ7Z6J9
STRINGi9606.ENSP00000327487

PTM databases

iPTMnetiQ7Z6J9
PhosphoSitePlusiQ7Z6J9

Polymorphism and mutation databases

BioMutaiTSEN54
DMDMi296452961

Proteomic databases

EPDiQ7Z6J9
MaxQBiQ7Z6J9
PaxDbiQ7Z6J9
PeptideAtlasiQ7Z6J9
PRIDEiQ7Z6J9
ProteomicsDBi69429
69430 [Q7Z6J9-2]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000333213; ENSP00000327487; ENSG00000182173 [Q7Z6J9-1]
GeneIDi283989
KEGGihsa:283989
UCSCiuc002jof.2 human [Q7Z6J9-1]

Organism-specific databases

CTDi283989
DisGeNETi283989
EuPathDBiHostDB:ENSG00000182173.12
GeneCardsiTSEN54
GeneReviewsiTSEN54
H-InvDBiHIX0022516
HGNCiHGNC:27561 TSEN54
HPAiHPA053097
MalaCardsiTSEN54
MIMi225753 phenotype
277470 phenotype
608755 gene
610204 phenotype
neXtProtiNX_Q7Z6J9
OpenTargetsiENSG00000182173
Orphaneti2254 Pontocerebellar hypoplasia type 1
2524 Pontocerebellar hypoplasia type 2
166063 Pontocerebellar hypoplasia type 4
166068 Pontocerebellar hypoplasia type 5
PharmGKBiPA142670692
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4772 Eukaryota
ENOG4111KNC LUCA
GeneTreeiENSGT00390000004214
HOGENOMiHOG000049169
HOVERGENiHBG061211
InParanoidiQ7Z6J9
KOiK15326
OMAiHLWDQPV
OrthoDBiEOG091G0I1P
PhylomeDBiQ7Z6J9
TreeFamiTF314691

Enzyme and pathway databases

BioCyciMetaCyc:HS11953-MONOMER
ReactomeiR-HSA-6784531 tRNA processing in the nucleus

Miscellaneous databases

ChiTaRSiTSEN54 human
GenomeRNAii283989
PROiPR:Q7Z6J9
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000182173 Expressed in 194 organ(s), highest expression level in cerebellar hemisphere
CleanExiHS_TSEN54
ExpressionAtlasiQ7Z6J9 baseline and differential
GenevisibleiQ7Z6J9 HS

Family and domain databases

InterProiView protein in InterPro
IPR024337 tRNA_splic_suSen54
IPR024336 tRNA_splic_suSen54_N
PANTHERiPTHR21027 PTHR21027, 1 hit
PfamiView protein in Pfam
PF12928 tRNA_int_end_N2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSEN54_HUMAN
AccessioniPrimary (citable) accession number: Q7Z6J9
Secondary accession number(s): Q86WV3, Q86XE4, Q8N9H2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: May 18, 2010
Last modified: November 7, 2018
This is version 125 of the entry and version 3 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  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. Human chromosome 17
    Human chromosome 17: entries, gene names and cross-references to MIM
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