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Protein

tRNA-splicing endonuclease subunit Sen34

Gene

TSEN34

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. It probably carries the active site for 3'-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.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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei247 – 2471By similarity
Active sitei255 – 2551By similarity
Active sitei286 – 2861By similarity

GO - Molecular functioni

  1. lyase activity Source: UniProtKB-KW
  2. nucleic acid binding Source: InterPro
  3. tRNA-intron endonuclease activity Source: GO_Central

GO - Biological processi

  1. mRNA processing Source: UniProtKB-KW
  2. RNA phosphodiester bond hydrolysis Source: GOC
  3. RNA phosphodiester bond hydrolysis, endonucleolytic Source: GOC
  4. tRNA-type intron splice site recognition and cleavage Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

mRNA processing, tRNA processing

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA-splicing endonuclease subunit Sen34 (EC:4.6.1.16)
Alternative name(s):
Leukocyte receptor cluster member 5
tRNA-intron endonuclease Sen34
Short name:
HsSen34
Gene namesi
Name:TSEN34
Synonyms:LENG5, SEN34
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 19, UP000005640: Unplaced

Organism-specific databases

HGNCiHGNC:15506. TSEN34.

Subcellular locationi

Nucleus 1 Publication. Nucleusnucleolus 1 Publication
Note: May be transiently localized in the nucleolus.

GO - Cellular componenti

  1. nucleolus Source: UniProtKB-SubCell
  2. nucleoplasm Source: HPA
  3. nucleus Source: HPA
  4. tRNA-intron endonuclease complex Source: InterPro
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Pontocerebellar hypoplasia 2C1 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:612390
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti58 – 581R → W in PCH2C. 1 Publication
VAR_054811

Keywords - Diseasei

Disease mutation, Pontocerebellar hypoplasia

Organism-specific databases

MIMi612390. phenotype.
Orphaneti2524. Pontocerebellar hypoplasia type 2.
PharmGKBiPA134871088.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 310310tRNA-splicing endonuclease subunit Sen34PRO_0000109463Add
BLAST

Proteomic databases

MaxQBiQ9BSV6.
PaxDbiQ9BSV6.
PeptideAtlasiQ9BSV6.
PRIDEiQ9BSV6.

PTM databases

PhosphoSiteiQ9BSV6.

Expressioni

Gene expression databases

BgeeiQ9BSV6.
CleanExiHS_TSEN34.
ExpressionAtlasiQ9BSV6. baseline and differential.
GenevestigatoriQ9BSV6.

Organism-specific databases

HPAiHPA041111.

Interactioni

Subunit structurei

tRNA splicing endonuclease is a heterotetramer composed 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 CSTF2.1 Publication

Protein-protein interaction databases

BioGridi122505. 13 interactions.
STRINGi9606.ENSP00000305524.

Structurei

3D structure databases

ProteinModelPortaliQ9BSV6.
SMRiQ9BSV6. Positions 213-306.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the tRNA-intron endonuclease family.Curated

Phylogenomic databases

eggNOGiCOG1676.
GeneTreeiENSGT00390000003912.
HOGENOMiHOG000232197.
HOVERGENiHBG054846.
InParanoidiQ9BSV6.
KOiK15323.
PhylomeDBiQ9BSV6.
TreeFamiTF314631.

Family and domain databases

Gene3Di3.40.1350.10. 1 hit.
InterProiIPR011856. tRNA_endonuc-like_dom.
IPR006677. tRNA_intron_Endonuc_cat-like.
IPR006676. tRNA_splic.
IPR016690. tRNA_splic_SEN34.
[Graphical view]
PfamiPF01974. tRNA_int_endo. 1 hit.
[Graphical view]
PIRSFiPIRSF017250. tRNA_splic_SEN34. 1 hit.
SUPFAMiSSF53032. SSF53032. 1 hit.
TIGRFAMsiTIGR00324. endA. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9BSV6-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MLVVEVANGR SLVWGAEAVQ ALRERLGVGG RTVGALPRGP RQNSRLGLPL
60 70 80 90 100
LLMPEEARLL AEIGAVTLVS APRPDSRHHS LALTSFKRQQ EESFQEQSAL
110 120 130 140 150
AAEARETRRQ ELLEKITEGQ AAKKQKLEQA SGASSSQEAG SSQAAKEDET
160 170 180 190 200
SDGQASGEQE EAGPSSSQAG PSNGVAPLPR SALLVQLATA RPRPVKARPL
210 220 230 240 250
DWRVQSKDWP HAGRPAHELR YSIYRDLWER GFFLSAAGKF GGDFLVYPGD
260 270 280 290 300
PLRFHAHYIA QCWAPEDTIP LQDLVAAGRL GTSVRKTLLL CSPQPDGKVV
310
YTSLQWASLQ
Length:310
Mass (Da):33,652
Last modified:June 1, 2001 - v1
Checksum:i1C1522D030148EC3
GO

Sequence cautioni

The sequence BAB15284.1 differs from that shown. Reason: Erroneous termination at position 311. Translated as stop.Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti58 – 581R → W in PCH2C. 1 Publication
VAR_054811
Natural varianti112 – 1121L → V.1 Publication
Corresponds to variant rs17849378 [ dbSNP | Ensembl ].
VAR_061149

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK025929 mRNA. Translation: BAB15284.1. Sequence problems.
CU457734 Genomic DNA. Translation: CAP19124.1.
CU151838 Genomic DNA. Translation: CAQ09596.1.
CH471135 Genomic DNA. Translation: EAW72203.1.
BC004530 mRNA. Translation: AAH04530.1.
BC020805 mRNA. Translation: AAH20805.1.
CCDSiCCDS42609.1.
RefSeqiNP_001070914.1. NM_001077446.3.
NP_001269261.1. NM_001282332.1.
NP_076980.2. NM_024075.4.
UniGeneiHs.15580.

Genome annotation databases

EnsembliENST00000302937; ENSP00000305524; ENSG00000170892.
ENST00000396383; ENSP00000379667; ENSG00000170892.
ENST00000396388; ENSP00000379671; ENSG00000170892.
ENST00000611560; ENSP00000480422; ENSG00000274796.
ENST00000611798; ENSP00000480899; ENSG00000278605.
ENST00000612236; ENSP00000480503; ENSG00000274129.
ENST00000612393; ENSP00000478622; ENSG00000278622.
ENST00000613310; ENSP00000477766; ENSG00000274078.
ENST00000613712; ENSP00000484865; ENSG00000273896.
ENST00000613888; ENSP00000481068; ENSG00000278712.
ENST00000614948; ENSP00000478156; ENSG00000278622.
ENST00000614984; ENSP00000483266; ENSG00000278712.
ENST00000615000; ENSP00000479654; ENSG00000278605.
ENST00000615079; ENSP00000484694; ENSG00000278605.
ENST00000615900; ENSP00000484964; ENSG00000274078.
ENST00000615975; ENSP00000484225; ENSG00000278622.
ENST00000616063; ENSP00000480964; ENSG00000274129.
ENST00000616209; ENSP00000481374; ENSG00000274672.
ENST00000617149; ENSP00000481639; ENSG00000273896.
ENST00000617902; ENSP00000484465; ENSG00000275165.
ENST00000618135; ENSP00000479576; ENSG00000274129.
ENST00000619994; ENSP00000482084; ENSG00000275165.
ENST00000622524; ENSP00000483436; ENSG00000274672.
ENST00000622538; ENSP00000482527; ENSG00000274796.
GeneIDi79042.
KEGGihsa:79042.
UCSCiuc002qdu.3. human.

Polymorphism databases

DMDMi50401668.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK025929 mRNA. Translation: BAB15284.1. Sequence problems.
CU457734 Genomic DNA. Translation: CAP19124.1.
CU151838 Genomic DNA. Translation: CAQ09596.1.
CH471135 Genomic DNA. Translation: EAW72203.1.
BC004530 mRNA. Translation: AAH04530.1.
BC020805 mRNA. Translation: AAH20805.1.
CCDSiCCDS42609.1.
RefSeqiNP_001070914.1. NM_001077446.3.
NP_001269261.1. NM_001282332.1.
NP_076980.2. NM_024075.4.
UniGeneiHs.15580.

3D structure databases

ProteinModelPortaliQ9BSV6.
SMRiQ9BSV6. Positions 213-306.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122505. 13 interactions.
STRINGi9606.ENSP00000305524.

PTM databases

PhosphoSiteiQ9BSV6.

Polymorphism databases

DMDMi50401668.

Proteomic databases

MaxQBiQ9BSV6.
PaxDbiQ9BSV6.
PeptideAtlasiQ9BSV6.
PRIDEiQ9BSV6.

Protocols and materials databases

DNASUi79042.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000302937; ENSP00000305524; ENSG00000170892.
ENST00000396383; ENSP00000379667; ENSG00000170892.
ENST00000396388; ENSP00000379671; ENSG00000170892.
ENST00000611560; ENSP00000480422; ENSG00000274796.
ENST00000611798; ENSP00000480899; ENSG00000278605.
ENST00000612236; ENSP00000480503; ENSG00000274129.
ENST00000612393; ENSP00000478622; ENSG00000278622.
ENST00000613310; ENSP00000477766; ENSG00000274078.
ENST00000613712; ENSP00000484865; ENSG00000273896.
ENST00000613888; ENSP00000481068; ENSG00000278712.
ENST00000614948; ENSP00000478156; ENSG00000278622.
ENST00000614984; ENSP00000483266; ENSG00000278712.
ENST00000615000; ENSP00000479654; ENSG00000278605.
ENST00000615079; ENSP00000484694; ENSG00000278605.
ENST00000615900; ENSP00000484964; ENSG00000274078.
ENST00000615975; ENSP00000484225; ENSG00000278622.
ENST00000616063; ENSP00000480964; ENSG00000274129.
ENST00000616209; ENSP00000481374; ENSG00000274672.
ENST00000617149; ENSP00000481639; ENSG00000273896.
ENST00000617902; ENSP00000484465; ENSG00000275165.
ENST00000618135; ENSP00000479576; ENSG00000274129.
ENST00000619994; ENSP00000482084; ENSG00000275165.
ENST00000622524; ENSP00000483436; ENSG00000274672.
ENST00000622538; ENSP00000482527; ENSG00000274796.
GeneIDi79042.
KEGGihsa:79042.
UCSCiuc002qdu.3. human.

Organism-specific databases

CTDi79042.
GeneCardsiGC19P054887.
HGNCiHGNC:15506. TSEN34.
HPAiHPA041111.
MIMi608754. gene.
612390. phenotype.
neXtProtiNX_Q9BSV6.
Orphaneti2524. Pontocerebellar hypoplasia type 2.
PharmGKBiPA134871088.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG1676.
GeneTreeiENSGT00390000003912.
HOGENOMiHOG000232197.
HOVERGENiHBG054846.
InParanoidiQ9BSV6.
KOiK15323.
PhylomeDBiQ9BSV6.
TreeFamiTF314631.

Miscellaneous databases

GeneWikiiTSEN34.
GenomeRNAii79042.
NextBioi67781.
PROiQ9BSV6.
SOURCEiSearch...

Gene expression databases

BgeeiQ9BSV6.
CleanExiHS_TSEN34.
ExpressionAtlasiQ9BSV6. baseline and differential.
GenevestigatoriQ9BSV6.

Family and domain databases

Gene3Di3.40.1350.10. 1 hit.
InterProiIPR011856. tRNA_endonuc-like_dom.
IPR006677. tRNA_intron_Endonuc_cat-like.
IPR006676. tRNA_splic.
IPR016690. tRNA_splic_SEN34.
[Graphical view]
PfamiPF01974. tRNA_int_endo. 1 hit.
[Graphical view]
PIRSFiPIRSF017250. tRNA_splic_SEN34. 1 hit.
SUPFAMiSSF53032. SSF53032. 1 hit.
TIGRFAMsiTIGR00324. endA. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Identification of a human endonuclease complex reveals a link between tRNA splicing and pre-mRNA 3' end formation."
    Paushkin S.V., Patel M., Furia B.S., Peltz S.W., Trotta C.R.
    Cell 117:311-321(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION, COMPONENT OF A COMPLEX WITH SEN2; SEN15; SEN54 AND CLP1.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT VAL-112.
    Tissue: Kidney epithelium.
  3. "The DNA sequence and biology of human chromosome 19."
    Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V.
    , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M.
    Nature 428:529-535(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain and Eye.
  6. "Extensive gene duplications and a large inversion characterize the human leukocyte receptor cluster."
    Wende H., Volz A., Ziegler A.
    Immunogenetics 51:703-713(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE LRC.
  7. Erratum
    Wende H., Volz A., Ziegler A.
    Immunogenetics 52:3-4(2001)
  8. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. Cited for: VARIANT PCH2C TRP-58.

Entry informationi

Entry nameiSEN34_HUMAN
AccessioniPrimary (citable) accession number: Q9BSV6
Secondary accession number(s): A6NNB1
, B0V3J1, Q9BVT1, Q9H6H5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: June 1, 2001
Last modified: February 4, 2015
This is version 112 of the entry and version 1 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

Miscellaneous

Belongs to the leukocyte receptor cluster (LRC) present on 19q13.4.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: 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

External Data

Dasty 3

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 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.