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Q8NCE0 (SEN2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 98. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
tRNA-splicing endonuclease subunit Sen2

EC=4.6.1.16
Alternative name(s):
tRNA-intron endonuclease Sen2
Short name=HsSen2
Gene names
Name:TSEN2
Synonyms:SEN2
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length465 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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. Ref.1

Catalytic activity

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.

Subunit structure

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.

Subcellular location

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

Tissue specificity

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

Involvement in disease

Pontocerebellar hypoplasia 2B (PCH2B) [MIM:612389]: A 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.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.7

Sequence similarities

Belongs to the tRNA-intron endonuclease family.

Alternative products

This entry describes 5 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q8NCE0-1)

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.
Isoform 2 (identifier: Q8NCE0-2)

Also known as: SEN2deltaEx8; DeltaEx8;

The sequence of this isoform differs from the canonical sequence as follows:
     304-320: Missing.
Isoform 3 (identifier: Q8NCE0-3)

The sequence of this isoform differs from the canonical sequence as follows:
     278-303: Missing.
Note: No experimental confirmation available.
Isoform 4 (identifier: Q8NCE0-4)

The sequence of this isoform differs from the canonical sequence as follows:
     173-231: Missing.
Note: No experimental confirmation available.
Isoform 5 (identifier: Q8NCE0-5)

The sequence of this isoform differs from the canonical sequence as follows:
     276-301: Missing.
     417-465: ELMLCYLIKPSTMTDKEMESPECMKRIKVQEVILSRWVSSRERSDQDDL → VTQHQLCHWSVT
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 465465tRNA-splicing endonuclease subunit Sen2
PRO_0000109452

Sites

Active site3691 By similarity
Active site3771 By similarity
Active site4161 By similarity

Amino acid modifications

Modified residue4081Phosphoserine By similarity
Modified residue4111Phosphoserine By similarity
Modified residue4151Phosphoserine By similarity

Natural variations

Alternative sequence173 – 23159Missing in isoform 4.
VSP_046192
Alternative sequence276 – 30126Missing in isoform 5.
VSP_046193
Alternative sequence278 – 30326Missing in isoform 3.
VSP_010985
Alternative sequence304 – 32017Missing in isoform 2.
VSP_010986
Alternative sequence417 – 46549ELMLC…DQDDL → VTQHQLCHWSVT in isoform 5.
VSP_046194
Natural variant411R → H.
Corresponds to variant rs12495784 [ dbSNP | Ensembl ].
VAR_048931
Natural variant1261R → H.
Corresponds to variant rs33955793 [ dbSNP | Ensembl ].
VAR_048932
Natural variant3091Y → C in PCH2B. Ref.7
Corresponds to variant rs113994149 [ dbSNP | Ensembl ].
VAR_054810

Experimental info

Sequence conflict1381H → Q in BAH13287. Ref.2
Sequence conflict2081K → E in BAH13287. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified July 19, 2004. Version 2.
Checksum: FF523229B05A1345

FASTA46553,247
        10         20         30         40         50         60 
MAEAVFHAPK RKRRVYETYE SPLPIPFGQD HGPLKEFKIF RAEMINNNVI VRNAEDIEQL 

        70         80         90        100        110        120 
YGKGYFGKGI LSRSRPSFTI SDPKLVAKWK DMKTNMPIIT SKRYQHSVEW AAELMRRQGQ 

       130        140        150        160        170        180 
DESTVRRILK DYTKPLEHPP VKRNEEAQVH DKLNSGMVSN MEGTAGGERP SVVNGDSGKS 

       190        200        210        220        230        240 
GGVGDPREPL GCLQEGSGCH PTTESFEKSV REDASPLPHV CCCKQDALIL QRGLHHEDGS 

       250        260        270        280        290        300 
QHIGLLHPGD RGPDHEYVLV EEAECAMSER EAAPNEELVQ RNRLICRRNP YRIFEYLQLS 

       310        320        330        340        350        360 
LEEAFFLVYA LGCLSIYYEK EPLTIVKLWK AFTVVQPTFR TTYMAYHYFR SKGWVPKVGL 

       370        380        390        400        410        420 
KYGTDLLLYR KGPPFYHASY SVIIELVDDH FEGSLRRPLS WKSLAALSRV SVNVSKELML 

       430        440        450        460 
CYLIKPSTMT DKEMESPECM KRIKVQEVIL SRWVSSRERS DQDDL 

« Hide

Isoform 2 (SEN2deltaEx8) (DeltaEx8) [UniParc].

Checksum: B616BDFCDA590E32
Show »

FASTA44851,265
Isoform 3 [UniParc].

Checksum: 97A9E847199BDE08
Show »

FASTA43949,942
Isoform 4 [UniParc].

Checksum: 61FD06EBE21EEEFD
Show »

FASTA40647,124
Isoform 5 [UniParc].

Checksum: 8B231F84B72FA227
Show »

FASTA40245,532

References

« Hide 'large scale' references
[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] (ISOFORMS 1 AND 2), ALTERNATIVE SPLICING, FUNCTION, SUBCELLULAR LOCATION, COMPONENT OF A COMPLEX WITH SEN15; SEN34; SEN54 AND CLP1, TISSUE SPECIFICITY.
[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. expand/collapse author list , 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] (ISOFORMS 3 AND 5).
Tissue: Placenta and Teratocarcinoma.
[3]Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.
Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
[4]"The DNA sequence, annotation and analysis of human chromosome 3."
Muzny D.M., Scherer S.E., Kaul R., Wang J., Yu J., Sudbrak R., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J. expand/collapse author list , Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R., Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Morgan M.B., Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Wei S., Wheeler D.A., Wright M.W., Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z., Clendenning J., Clerc-Blankenburg K.P., Chen R., Chen Z., Davis C., Delgado O., Dinh H.H., Dong W., Draper H., Ernst S., Fu G., Gonzalez-Garay M.L., Garcia D.K., Gillett W., Gu J., Hao B., Haugen E., Havlak P., He X., Hennig S., Hu S., Huang W., Jackson L.R., Jacob L.S., Kelly S.H., Kube M., Levy R., Li Z., Liu B., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Palmeiri A., Pasternak S., Perez L.M., Phelps K.A., Plopper F.J., Qiang B., Raymond C., Rodriguez R., Saenphimmachak C., Santibanez J., Shen H., Shen Y., Subramanian S., Tabor P.E., Verduzco D., Waldron L., Wang J., Wang J., Wang Q., Williams G.A., Wong G.K.-S., Yao Z., Zhang J., Zhang X., Zhao G., Zhou J., Zhou Y., Nelson D., Lehrach H., Reinhardt R., Naylor S.L., Yang H., Olson M., Weinstock G., Gibbs R.A.
Nature 440:1194-1198(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]"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] (ISOFORM 1).
Tissue: Colon, Eye and Skin.
[7]"tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia."
Budde B.S., Namavar Y., Barth P.G., Poll-The B.T., Nuernberg G., Becker C., van Ruissen F., Weterman M.A.J., Fluiter K., te Beek E.T., Aronica E., van der Knaap M.S., Hoehne W., Toliat M.R., Crow Y.J., Steinling M., Voit T., Roelenso F. expand/collapse author list , Brussel W., Brockmann K., Kyllerman M., Boltshauser E., Hammersen G., Willemsen M., Basel-Vanagaite L., Kraegeloh-Mann I., de Vries L.S., Sztriha L., Muntoni F., Ferrie C.D., Battini R., Hennekam R.C.M., Grillo E., Beemer F.A., Stoets L.M.E., Wollnik B., Nuernberg P., Baas F.
Nat. Genet. 40:1113-1118(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT PCH2B CYS-309.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_001138864.1. NM_001145392.1.
NP_001138865.1. NM_001145393.1.
NP_001138866.1. NM_001145394.1.
NP_001138867.1. NM_001145395.1.
NP_079541.1. NM_025265.3.
XP_005265552.1. XM_005265495.1.
XP_005265554.1. XM_005265497.1.
UniGeneHs.335550.

3D structure databases

ProteinModelPortalQ8NCE0.
SMRQ8NCE0. Positions 279-455.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid123288. 13 interactions.
IntActQ8NCE0. 1 interaction.
STRING9606.ENSP00000284995.

PTM databases

PhosphoSiteQ8NCE0.

Polymorphism databases

DMDM50428914.

Proteomic databases

PaxDbQ8NCE0.
PRIDEQ8NCE0.

Protocols and materials databases

DNASU80746.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000284995; ENSP00000284995; ENSG00000154743. [Q8NCE0-1]
ENST00000314571; ENSP00000323188; ENSG00000154743. [Q8NCE0-3]
ENST00000383797; ENSP00000373307; ENSG00000154743. [Q8NCE0-2]
ENST00000402228; ENSP00000385976; ENSG00000154743. [Q8NCE0-1]
ENST00000415684; ENSP00000416510; ENSG00000154743. [Q8NCE0-3]
ENST00000444864; ENSP00000407974; ENSG00000154743. [Q8NCE0-5]
ENST00000454502; ENSP00000392029; ENSG00000154743. [Q8NCE0-4]
GeneID80746.
KEGGhsa:80746.
UCSCuc003bxa.3. human. [Q8NCE0-3]
uc003bxb.3. human. [Q8NCE0-1]
uc011auq.1. human.

Organism-specific databases

CTD80746.
GeneCardsGC03P012525.
HGNCHGNC:28422. TSEN2.
HPAHPA027120.
HPA027125.
HPA027268.
MIM608753. gene.
612389. phenotype.
neXtProtNX_Q8NCE0.
Orphanet2524. Pontocerebellar hypoplasia type 2.
PharmGKBPA142670695.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1676.
HOGENOMHOG000154285.
HOVERGENHBG056610.
InParanoidQ8NCE0.
KOK15322.
PhylomeDBQ8NCE0.
TreeFamTF314679.

Gene expression databases

ArrayExpressQ8NCE0.
BgeeQ8NCE0.
CleanExHS_TSEN2.
GenevestigatorQ8NCE0.

Family and domain databases

Gene3D3.40.1350.10. 1 hit.
InterProIPR011856. tRNA_endonuc-like_dom.
IPR006677. tRNA_intron_Endonuc_cat-like.
IPR006678. tRNA_intron_Endonuc_N.
IPR016589. tRNA_splic_SEN2.
[Graphical view]
PfamPF01974. tRNA_int_endo. 1 hit.
PF02778. tRNA_int_endo_N. 1 hit.
[Graphical view]
PIRSFPIRSF011789. tRNA_splic_SEN2. 1 hit.
SUPFAMSSF53032. SSF53032. 1 hit.
ProtoNetSearch...

Other

GeneWikiTSEN2.
GenomeRNAi80746.
NextBio71098.
PROQ8NCE0.
SOURCESearch...

Entry information

Entry nameSEN2_HUMAN
AccessionPrimary (citable) accession number: Q8NCE0
Secondary accession number(s): B7Z6K1 expand/collapse secondary AC list , C9IZI7, G5E9Q3, Q8WTW7, Q9BPU7
Entry history
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: July 19, 2004
Last modified: April 16, 2014
This is version 98 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 3

Human chromosome 3: entries, gene names and cross-references to MIM