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Q7Z6J9 (SEN54_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 94. 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 Sen54
Alternative name(s):
SEN54 homolog
Short name=HsSEN54
tRNA-intron endonuclease Sen54
Gene names
Name:TSEN54
Synonyms:SEN54
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length526 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.4

Subunit structure

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. Also belongs to a complex containing isoform 2 of SEN2.

Subcellular location

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

Involvement in disease

Pontocerebellar hypoplasia 4 (PCH4) [MIM:225753]: A 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.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.9

Pontocerebellar hypoplasia 2A (PCH2A) [MIM:277470]: 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.9

Sequence similarities

Belongs to the SEN54 family.

Sequence caution

The sequence AAH53643.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
   Biological processmRNA processing
tRNA processing
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   DiseasePontocerebellar hypoplasia
   PTMAcetylation
Phosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processmRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

tRNA splicing, via endonucleolytic cleavage and ligation

Inferred from direct assay PubMed 17495927. Source: UniProtKB

   Cellular_componentnucleolus

Inferred from electronic annotation. Source: UniProtKB-SubCell

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q7Z6J9-1)

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: Q7Z6J9-2)

The sequence of this isoform differs from the canonical sequence as follows:
     157-177: VFSHLKRLGYVVRRFQPSSVL → PPEEVGLCGSTIPTKLCPVPV
     178-526: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 526526tRNA-splicing endonuclease subunit Sen54
PRO_0000194029

Amino acid modifications

Modified residue11N-acetylmethionine Ref.6 Ref.8
Modified residue1781Phosphoserine Ref.7
Modified residue2671Phosphoserine Ref.7

Natural variations

Alternative sequence157 – 17721VFSHL…PSSVL → PPEEVGLCGSTIPTKLCPVP V in isoform 2.
VSP_010988
Alternative sequence178 – 526349Missing in isoform 2.
VSP_010989
Natural variant41E → D. Ref.1 Ref.3 Ref.6 Ref.8
Corresponds to variant rs7216673 [ dbSNP | Ensembl ].
VAR_019459
Natural variant381H → Q.
Corresponds to variant rs8079373 [ dbSNP | Ensembl ].
VAR_019461
Natural variant931S → P in PCH4; associated with S-307 on the other allele. Ref.9
VAR_054812
Natural variant1371I → L.
Corresponds to variant rs11559205 [ dbSNP | Ensembl ].
VAR_057721
Natural variant3071A → S in PCH2A and PCH4; associated with P-93 on the other allele. Ref.9
Corresponds to variant rs113994152 [ dbSNP | Ensembl ].
VAR_054813
Natural variant3471K → N. Ref.3
Corresponds to variant rs9911502 [ dbSNP | Ensembl ].
VAR_019462
Natural variant4371A → V. Ref.3
Corresponds to variant rs8064529 [ dbSNP | Ensembl ].
VAR_019463
Natural variant5251G → R.
Corresponds to variant rs11870627 [ dbSNP | Ensembl ].
VAR_057722

Sequences

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

Last modified May 18, 2010. Version 3.
Checksum: 857D95C8F7C39461

FASTA52658,819
        10         20         30         40         50         60 
MEPEPEPAAV EVPAGRVLSA RELFAARSRS QKLPQRSHGP KDFLPDGSAA QAERLRRCRE 

        70         80         90        100        110        120 
ELWQLLAEQR VERLGSLVAA EWRPEEGFVE LKSPAGKFWQ TMGFSEQGRQ RLHPEEALYL 

       130        140        150        160        170        180 
LECGSIHLFH QDLPLSIQEA YQLLLTDHTV TFLQYQVFSH LKRLGYVVRR FQPSSVLSPY 

       190        200        210        220        230        240 
ERQLNLDASV QHLEDGDGKR KRSSSSPRSI NKKAKALDNS LQPKSLAASS PPPCSQPSQC 

       250        260        270        280        290        300 
PEEKPQESSP MKGPGGPFQL LGSLGPSPGP AREGVGCSWE SGRAENGVTG AGKRRWNFEQ 

       310        320        330        340        350        360 
ISFPNMASDS RHTLLRAPAP ELLPANVAGR ETDAESWCQK LNQRKEKLSR REREHHAEAA 

       370        380        390        400        410        420 
QFQEDVNADP EVQRCSSWRE YKELLQRRQV QRSQRRAPHL WGQPVTPLLS PGQASSPAVV 

       430        440        450        460        470        480 
LQHISVLQTT HLPDGGARLL EKSGGLEIIF DVYQADAVAT FRKNNPGKPY ARMCISGFDE 

       490        500        510        520 
PVPDLCSLKR LSYQSGDVPL IFALVDHGDI SFYSFRDFTL PQDVGH 

« Hide

Isoform 2 [UniParc].

Checksum: 68B620EF98884157
Show »

FASTA17719,981

References

« Hide 'large scale' references
[1]"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] (ISOFORM 2), VARIANT ASP-4.
Tissue: Cerebellum.
[2]"DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage."
Zody M.C., Garber M., Adams D.J., Sharpe T., Harrow J., Lupski J.R., Nicholson C., Searle S.M., Wilming L., Young S.K., Abouelleil A., Allen N.R., Bi W., Bloom T., Borowsky M.L., Bugalter B.E., Butler J., Chang J.L. expand/collapse author list , Chen C.-K., Cook A., Corum B., Cuomo C.A., de Jong P.J., DeCaprio D., Dewar K., FitzGerald M., Gilbert J., Gibson R., Gnerre S., Goldstein S., Grafham D.V., Grocock R., Hafez N., Hagopian D.S., Hart E., Norman C.H., Humphray S., Jaffe D.B., Jones M., Kamal M., Khodiyar V.K., LaButti K., Laird G., Lehoczky J., Liu X., Lokyitsang T., Loveland J., Lui A., Macdonald P., Major J.E., Matthews L., Mauceli E., McCarroll S.A., Mihalev A.H., Mudge J., Nguyen C., Nicol R., O'Leary S.B., Osoegawa K., Schwartz D.C., Shaw-Smith C., Stankiewicz P., Steward C., Swarbreck D., Venkataraman V., Whittaker C.A., Yang X., Zimmer A.R., Bradley A., Hubbard T., Birren B.W., Rogers J., Lander E.S., Nusbaum C.
Nature 440:1045-1049(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]"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), VARIANTS ASP-4; ASN-347 AND VAL-437.
Tissue: Blood and Uterus.
[4]"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: FUNCTION, COMPONENT OF A COMPLEX WITH SEN2; SEN15; SEN34 AND CLP1.
[5]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[6]"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: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, VARIANT [LARGE SCALE ANALYSIS] ASP-4, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[7]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-178 AND SER-267, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[8]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, VARIANT [LARGE SCALE ANALYSIS] ASP-4, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[9]"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 PCH2A SER-307, VARIANTS PCH4 PRO-93 AND SER-307.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AK094466 mRNA. Translation: BAC04362.1.
BC047793 mRNA. Translation: AAH47793.1.
AC100787 Genomic DNA. No translation available.
BC053643 mRNA. Translation: AAH53643.1. Different initiation.
CCDSCCDS11724.1. [Q7Z6J9-1]
RefSeqNP_997229.2. NM_207346.2. [Q7Z6J9-1]
UniGeneHs.378501.

3D structure databases

ProteinModelPortalQ7Z6J9.
SMRQ7Z6J9. Positions 102-169.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid129721. 9 interactions.
IntActQ7Z6J9. 2 interactions.
STRING9606.ENSP00000327487.

PTM databases

PhosphoSiteQ7Z6J9.

Polymorphism databases

DMDM296452961.

Proteomic databases

MaxQBQ7Z6J9.
PaxDbQ7Z6J9.
PRIDEQ7Z6J9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000333213; ENSP00000327487; ENSG00000182173. [Q7Z6J9-1]
GeneID283989.
KEGGhsa:283989.
UCSCuc002joe.1. human. [Q7Z6J9-2]
uc002jof.1. human. [Q7Z6J9-1]

Organism-specific databases

CTD283989.
GeneCardsGC17P073512.
GeneReviewsTSEN54.
H-InvDBHIX0022516.
HGNCHGNC:27561. TSEN54.
HPAHPA053097.
MIM225753. phenotype.
277470. phenotype.
608755. gene.
neXtProtNX_Q7Z6J9.
Orphanet2254. Pontocerebellar hypoplasia type 1.
2524. Pontocerebellar hypoplasia type 2.
166063. Pontocerebellar hypoplasia type 4.
166068. Pontocerebellar hypoplasia type 5.
PharmGKBPA142670692.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG327149.
HOGENOMHOG000049169.
HOVERGENHBG061211.
InParanoidQ7Z6J9.
KOK15326.
OMAQISFPNM.
PhylomeDBQ7Z6J9.
TreeFamTF314691.

Gene expression databases

ArrayExpressQ7Z6J9.
BgeeQ7Z6J9.
CleanExHS_TSEN54.
GenevestigatorQ7Z6J9.

Family and domain databases

InterProIPR024337. tRNA_splic_suSen54.
IPR024336. tRNA_splic_suSen54_N.
[Graphical view]
PANTHERPTHR21027. PTHR21027. 1 hit.
PfamPF12928. tRNA_int_end_N2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSTSEN54. human.
GenomeRNAi283989.
NextBio94415.
PROQ7Z6J9.
SOURCESearch...

Entry information

Entry nameSEN54_HUMAN
AccessionPrimary (citable) accession number: Q7Z6J9
Secondary accession number(s): Q86WV3, Q86XE4, Q8N9H2
Entry history
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: May 18, 2010
Last modified: July 9, 2014
This is version 94 of the entry and version 3 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 17

Human chromosome 17: entries, gene names and cross-references to MIM