Q8NCE0 (SEN2_HUMAN) Reviewed, UniProtKB/Swiss-Prot
Last modified
May 1, 2013.
Version 88.
History...
Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | Recommended name: tRNA-splicing endonuclease subunit Sen2 EC=3.1.27.9 Alternative name(s): tRNA-intron endonuclease Sen2 Short name=HsSen2 | ||||
| Gene names |
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| Organism | Homo sapiens (Human) [Reference proteome] | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo![]() |
Protein attributes
| Sequence length | 465 AA. |
| Sequence status | Complete. |
| Protein existence | Evidence 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 | Endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxy and 2',3'-cyclic phosphate termini, and specifically removing the intron. |
| 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. Nucleus › nucleolus. 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. |
| Sequence similarities | Belongs to the tRNA-intron endonuclease family. |
Ontologies
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 key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 465 | 465 | tRNA-splicing endonuclease subunit Sen2 | PRO_0000109452 | |||||
Sites | |||||||||
| Active site | 369 | 1 | By similarity | ||||||
| Active site | 377 | 1 | By similarity | ||||||
| Active site | 416 | 1 | By similarity | ||||||
Amino acid modifications | |||||||||
| Modified residue | 408 | 1 | Phosphoserine By similarity | ||||||
| Modified residue | 411 | 1 | Phosphoserine By similarity | ||||||
| Modified residue | 415 | 1 | Phosphoserine By similarity | ||||||
Natural variations | |||||||||
| Alternative sequence | 173 – 231 | 59 | Missing in isoform 4. | VSP_046192 | |||||
| Alternative sequence | 276 – 301 | 26 | Missing in isoform 5. | VSP_046193 | |||||
| Alternative sequence | 278 – 303 | 26 | Missing in isoform 3. | VSP_010985 | |||||
| Alternative sequence | 304 – 320 | 17 | Missing in isoform 2. | VSP_010986 | |||||
| Alternative sequence | 417 – 465 | 49 | ELMLC…DQDDL → VTQHQLCHWSVT in isoform 5. | VSP_046194 | |||||
| Natural variant | 41 | 1 | R → H. Corresponds to variant rs12495784 [ dbSNP | Ensembl ]. | VAR_048931 | |||||
| Natural variant | 126 | 1 | R → H. Corresponds to variant rs33955793 [ dbSNP | Ensembl ]. | VAR_048932 | |||||
| Natural variant | 309 | 1 | Y → C in PCH2B. Ref.7 | VAR_054810 | |||||
Experimental info | |||||||||
| Sequence conflict | 138 | 1 | H → Q in BAH13287. Ref.2 | ||||||
| Sequence conflict | 208 | 1 | K → E in BAH13287. Ref.2 | ||||||
Sequences
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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. 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. 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. 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. 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. |
| IPI | IPI00427037. IPI00427039. IPI00427040. IPI00790771. IPI00926682. |
| RefSeq | NP_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. |
| UniGene | Hs.335550. |
3D structure databases | |
| ProteinModelPortal | Q8NCE0. |
| ModBase | Search... |
Protein-protein interaction databases | |
| IntAct | Q8NCE0. 1 interaction. |
| STRING | 9606.ENSP00000284995. |
PTM databases | |
| PhosphoSite | Q8NCE0. |
Polymorphism databases | |
| DMDM | 50428914. |
Proteomic databases | |
| PaxDb | Q8NCE0. |
| PRIDE | Q8NCE0. |
Protocols and materials databases | |
| DNASU | 80746. |
| StructuralBiologyKnowledgebase | Search... |
Genome annotation databases | |
| Ensembl | ENST00000284995; ENSP00000284995; ENSG00000154743. ENST00000314571; ENSP00000323188; ENSG00000154743. ENST00000383797; ENSP00000373307; ENSG00000154743. ENST00000402228; ENSP00000385976; ENSG00000154743. ENST00000415684; ENSP00000416510; ENSG00000154743. ENST00000444864; ENSP00000407974; ENSG00000154743. ENST00000454502; ENSP00000392029; ENSG00000154743. |
| GeneID | 80746. |
| KEGG | hsa:80746. |
| UCSC | uc003bxa.3. human. uc003bxb.3. human. |
Organism-specific databases | |
| CTD | 80746. |
| GeneCards | GC03P012504. |
| HGNC | HGNC:28422. TSEN2. |
| HPA | HPA027120. HPA027125. HPA027268. |
| MIM | 608753. gene. 612389. phenotype. |
| neXtProt | NX_Q8NCE0. |
| Orphanet | 2524. Pontocerebellar hypoplasia type 2. |
| PharmGKB | PA142670695. |
| GenAtlas | Search... |
Phylogenomic databases | |
| eggNOG | COG1676. |
| HOGENOM | HOG000154285. |
| HOVERGEN | HBG056610. |
| InParanoid | Q8NCE0. |
| KO | K15322. |
| PhylomeDB | Q8NCE0. |
Gene expression databases | |
| ArrayExpress | Q8NCE0. |
| Bgee | Q8NCE0. |
| CleanEx | HS_TSEN2. |
| Genevestigator | Q8NCE0. |
| GermOnline | ENSG00000154743. Homo sapiens. |
Family and domain databases | |
| Gene3D | 3.40.1350.10. 1 hit. |
| InterPro | IPR011856. tRNA_endonuc-like_dom. IPR006677. tRNA_intron_Endonuc_cat-like. IPR006678. tRNA_intron_Endonuc_N. IPR016589. tRNA_splic_SEN2. [Graphical view] |
| Pfam | PF01974. tRNA_int_endo. 1 hit. PF02778. tRNA_int_endo_N. 1 hit. [Graphical view] |
| PIRSF | PIRSF011789. tRNA_splic_SEN2. 1 hit. |
| SUPFAM | SSF53032. tRNA_int_endo_C. 1 hit. |
| ProtoNet | Search... |
Other | |
| GenomeRNAi | 80746. |
| NextBio | 71098. |
| SOURCE | Search... |
Entry information
| Entry name | SEN2_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q8NCE0 Secondary accession number(s): B7Z6K1 Q9BPU7 | ||||||||
| Entry history |
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| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation program | Chordata Protein Annotation Program | ||||||||
| Disclaimer | Any 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
| Human chromosome 3 Human chromosome 3: entries, gene names and cross-references to MIM |
| Human entries with polymorphisms or disease mutations List of human entries with polymorphisms or disease mutations |
| Human polymorphisms and disease mutations Index of human polymorphisms and disease mutations |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| SIMILARITY comments Index of protein domains and families |

Clusters with
