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Q7Z6J9

- SEN54_HUMAN

UniProt

Q7Z6J9 - SEN54_HUMAN

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Protein

tRNA-splicing endonuclease subunit Sen54

Gene

TSEN54

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- 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

  1. mRNA processing Source: UniProtKB-KW
  2. tRNA splicing, via endonucleolytic cleavage and ligation Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

mRNA processing, tRNA processing

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
ProteomesiUP000005640: Chromosome 17

Organism-specific databases

HGNCiHGNC:27561. TSEN54.

Subcellular locationi

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

GO - Cellular componenti

  1. nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

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.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti93 – 931S → P in PCH4; associated with S-307 on the other allele. 1 Publication
VAR_054812
Natural varianti307 – 3071A → S in PCH2A and PCH4; associated with P-93 on the other allele. 1 Publication
Corresponds to variant rs113994152 [ dbSNP | Ensembl ].
VAR_054813
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.1 Publication
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti307 – 3071A → S in PCH2A and PCH4; associated with P-93 on the other allele. 1 Publication
Corresponds to variant rs113994152 [ dbSNP | Ensembl ].
VAR_054813

Keywords - Diseasei

Pontocerebellar hypoplasia

Organism-specific databases

MIMi225753. phenotype.
277470. phenotype.
Orphaneti2254. Pontocerebellar hypoplasia type 1.
2524. Pontocerebellar hypoplasia type 2.
166063. Pontocerebellar hypoplasia type 4.
166068. Pontocerebellar hypoplasia type 5.
PharmGKBiPA142670692.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 526526tRNA-splicing endonuclease subunit Sen54PRO_0000194029Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionine2 Publications
Modified residuei178 – 1781Phosphoserine1 Publication
Modified residuei267 – 2671Phosphoserine1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ7Z6J9.
PaxDbiQ7Z6J9.
PRIDEiQ7Z6J9.

PTM databases

PhosphoSiteiQ7Z6J9.

Expressioni

Gene expression databases

BgeeiQ7Z6J9.
CleanExiHS_TSEN54.
ExpressionAtlasiQ7Z6J9. baseline and differential.
GenevestigatoriQ7Z6J9.

Organism-specific databases

HPAiHPA053097.

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

Protein-protein interaction databases

BioGridi129721. 11 interactions.
IntActiQ7Z6J9. 2 interactions.
STRINGi9606.ENSP00000327487.

Structurei

3D structure databases

ProteinModelPortaliQ7Z6J9.
SMRiQ7Z6J9. Positions 102-169.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the SEN54 family.Curated

Phylogenomic databases

eggNOGiNOG327149.
GeneTreeiENSGT00390000004214.
HOGENOMiHOG000049169.
HOVERGENiHBG061211.
InParanoidiQ7Z6J9.
KOiK15326.
OMAiQISFPNM.
PhylomeDBiQ7Z6J9.
TreeFamiTF314691.

Family and domain databases

InterProiIPR024337. tRNA_splic_suSen54.
IPR024336. tRNA_splic_suSen54_N.
[Graphical view]
PANTHERiPTHR21027. PTHR21027. 1 hit.
PfamiPF12928. tRNA_int_end_N2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

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

Sequence cautioni

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

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti4 – 41E → D.4 Publications
Corresponds to variant rs7216673 [ dbSNP | Ensembl ].
VAR_019459
Natural varianti38 – 381H → Q.
Corresponds to variant rs8079373 [ dbSNP | Ensembl ].
VAR_019461
Natural varianti93 – 931S → P in PCH4; associated with S-307 on the other allele. 1 Publication
VAR_054812
Natural varianti137 – 1371I → L.
Corresponds to variant rs11559205 [ dbSNP | Ensembl ].
VAR_057721
Natural varianti307 – 3071A → S in PCH2A and PCH4; associated with P-93 on the other allele. 1 Publication
Corresponds to variant rs113994152 [ dbSNP | Ensembl ].
VAR_054813
Natural varianti347 – 3471K → N.1 Publication
Corresponds to variant rs9911502 [ dbSNP | Ensembl ].
VAR_019462
Natural varianti437 – 4371A → V.1 Publication
Corresponds to variant rs8064529 [ dbSNP | Ensembl ].
VAR_019463
Natural varianti525 – 5251G → R.
Corresponds to variant rs11870627 [ dbSNP | Ensembl ].
VAR_057722

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei157 – 17721VFSHL…PSSVL → PPEEVGLCGSTIPTKLCPVP V in isoform 2. 1 PublicationVSP_010988Add
BLAST
Alternative sequencei178 – 526349Missing in isoform 2. 1 PublicationVSP_010989Add
BLAST

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.
UCSCiuc002joe.1. human. [Q7Z6J9-2]
uc002jof.1. human. [Q7Z6J9-1]

Polymorphism databases

DMDMi296452961.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

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.
CCDSi CCDS11724.1. [Q7Z6J9-1 ]
RefSeqi NP_997229.2. NM_207346.2. [Q7Z6J9-1 ]
UniGenei Hs.378501.

3D structure databases

ProteinModelPortali Q7Z6J9.
SMRi Q7Z6J9. Positions 102-169.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 129721. 11 interactions.
IntActi Q7Z6J9. 2 interactions.
STRINGi 9606.ENSP00000327487.

PTM databases

PhosphoSitei Q7Z6J9.

Polymorphism databases

DMDMi 296452961.

Proteomic databases

MaxQBi Q7Z6J9.
PaxDbi Q7Z6J9.
PRIDEi Q7Z6J9.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000333213 ; ENSP00000327487 ; ENSG00000182173 . [Q7Z6J9-1 ]
GeneIDi 283989.
KEGGi hsa:283989.
UCSCi uc002joe.1. human. [Q7Z6J9-2 ]
uc002jof.1. human. [Q7Z6J9-1 ]

Organism-specific databases

CTDi 283989.
GeneCardsi GC17P073512.
GeneReviewsi TSEN54.
H-InvDB HIX0022516.
HGNCi HGNC:27561. TSEN54.
HPAi HPA053097.
MIMi 225753. phenotype.
277470. phenotype.
608755. gene.
neXtProti NX_Q7Z6J9.
Orphaneti 2254. Pontocerebellar hypoplasia type 1.
2524. Pontocerebellar hypoplasia type 2.
166063. Pontocerebellar hypoplasia type 4.
166068. Pontocerebellar hypoplasia type 5.
PharmGKBi PA142670692.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG327149.
GeneTreei ENSGT00390000004214.
HOGENOMi HOG000049169.
HOVERGENi HBG061211.
InParanoidi Q7Z6J9.
KOi K15326.
OMAi QISFPNM.
PhylomeDBi Q7Z6J9.
TreeFami TF314691.

Miscellaneous databases

ChiTaRSi TSEN54. human.
GenomeRNAii 283989.
NextBioi 94415.
PROi Q7Z6J9.
SOURCEi Search...

Gene expression databases

Bgeei Q7Z6J9.
CleanExi HS_TSEN54.
ExpressionAtlasi Q7Z6J9. baseline and differential.
Genevestigatori Q7Z6J9.

Family and domain databases

InterProi IPR024337. tRNA_splic_suSen54.
IPR024336. tRNA_splic_suSen54_N.
[Graphical view ]
PANTHERi PTHR21027. PTHR21027. 1 hit.
Pfami PF12928. tRNA_int_end_N2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.
    , 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. 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. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, VARIANT [LARGE SCALE ANALYSIS] ASP-4, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. Cited for: VARIANT PCH2A SER-307, VARIANTS PCH4 PRO-93 AND SER-307.

Entry informationi

Entry nameiSEN54_HUMAN
AccessioniPrimary (citable) accession number: Q7Z6J9
Secondary accession number(s): Q86WV3, Q86XE4, Q8N9H2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: May 18, 2010
Last modified: October 29, 2014
This is version 96 of the entry and version 3 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 17
    Human chromosome 17: 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