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Q7Z6J9

- SEN54_HUMAN

UniProt

Q7Z6J9 - SEN54_HUMAN

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
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    • History
      Entry version 95 (01 Oct 2014)
      Sequence version 3 (18 May 2010)
      Previous versions | rss
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    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

    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. nucleolus Source: UniProtKB-SubCell

    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

    ArrayExpressiQ7Z6J9.
    BgeeiQ7Z6J9.
    CleanExiHS_TSEN54.
    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. 9 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.
    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

    MEPEPEPAAV EVPAGRVLSA RELFAARSRS QKLPQRSHGP KDFLPDGSAA    50
    QAERLRRCRE ELWQLLAEQR VERLGSLVAA EWRPEEGFVE LKSPAGKFWQ 100
    TMGFSEQGRQ RLHPEEALYL LECGSIHLFH QDLPLSIQEA YQLLLTDHTV 150
    TFLQYQVFSH LKRLGYVVRR FQPSSVLSPY ERQLNLDASV QHLEDGDGKR 200
    KRSSSSPRSI NKKAKALDNS LQPKSLAASS PPPCSQPSQC PEEKPQESSP 250
    MKGPGGPFQL LGSLGPSPGP AREGVGCSWE SGRAENGVTG AGKRRWNFEQ 300
    ISFPNMASDS RHTLLRAPAP ELLPANVAGR ETDAESWCQK LNQRKEKLSR 350
    REREHHAEAA QFQEDVNADP EVQRCSSWRE YKELLQRRQV QRSQRRAPHL 400
    WGQPVTPLLS PGQASSPAVV LQHISVLQTT HLPDGGARLL EKSGGLEIIF 450
    DVYQADAVAT FRKNNPGKPY ARMCISGFDE PVPDLCSLKR LSYQSGDVPL 500
    IFALVDHGDI SFYSFRDFTL PQDVGH 526
    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.

    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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. 9 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.
    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

    ArrayExpressi Q7Z6J9.
    Bgeei Q7Z6J9.
    CleanExi HS_TSEN54.
    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

    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 1, 2014
    This is version 95 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