Human Gene TSEN2 (ENST00000444864.6) from GENCODE V44
  Description: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data. (from UniProt H7C2Z3)
RefSeq Summary (NM_001321278): This gene encodes one of the subunits of the tRNA splicing endonuclease. This endonuclease catalyzes the first step in RNA splicing which is the removal of introns. Mutations in this gene have been associated with pontocerebellar hypoplasia type 2. A pseudogene has been identified on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2009].
Gencode Transcript: ENST00000444864.6
Gencode Gene: ENSG00000154743.19
Transcript (Including UTRs)
   Position: hg38 chr3:12,484,563-12,539,610 Size: 55,048 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg38 chr3:12,489,801-12,539,373 Size: 49,573 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:12,484,563-12,539,610)mRNA (may differ from genome)Protein (490 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGencodeGeneCardsHGNC
MalacardsMGIPubMedUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: H7C2Z3_HUMAN
DESCRIPTION: SubName: Full=tRNA-splicing endonuclease subunit Sen2; Flags: Fragment;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: TSEN2
Diseases sorted by gene-association score: pontocerebellar hypoplasia type 2b* (1200), pontocerebellar hypoplasia, type 2e* (143), tsen2-related pontocerebellar hypoplasia* (100), pontocerebellar hypoplasia (33), pontocerebellar hypoplasia, type 6 (10), microcephaly (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.86 RPKM in Nerve - Tibial
Total median expression: 127.07 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -143.20335-0.427 Picture PostScript Text
3' UTR -49.70237-0.210 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  ModBase Predicted Comparative 3D Structure on H7C2Z3
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Descriptions from all associated GenBank mRNAs
  AK225875 - Homo sapiens mRNA for tRNA splicing endonuclease 2 homolog, clone: FCC124A09.
AK074794 - Homo sapiens cDNA FLJ90313 fis, clone NT2RP2001388, weakly similar to TRNA-SPLICING ENDONUCLEASE SUBUNIT SEN2 (EC 3.1.27.9).
AK027821 - Homo sapiens cDNA FLJ14915 fis, clone PLACE1006878, weakly similar to TRNA-SPLICING ENDONUCLEASE SUBUNIT SEN2 (EC 3.1.27.9).
BC004178 - Homo sapiens tRNA splicing endonuclease 2 homolog (S. cerevisiae), mRNA (cDNA clone MGC:2776 IMAGE:2959536), complete cds.
BC004211 - Homo sapiens tRNA splicing endonuclease 2 homolog (S. cerevisiae), mRNA (cDNA clone MGC:4440 IMAGE:2959536), complete cds.
BC019582 - Homo sapiens tRNA splicing endonuclease 2 homolog (S. cerevisiae), mRNA (cDNA clone MGC:24987 IMAGE:3872331), complete cds.
AK300449 - Homo sapiens cDNA FLJ58327 complete cds, highly similar to tRNA-splicing endonuclease subunit Sen2 (EC 3.1.27.9).
AK295508 - Homo sapiens cDNA FLJ55685 complete cds, highly similar to tRNA-splicing endonuclease subunit Sen2 (EC 3.1.27.9).
JD216967 - Sequence 197991 from Patent EP1572962.
JD230529 - Sequence 211553 from Patent EP1572962.
JD192136 - Sequence 173160 from Patent EP1572962.
JD230792 - Sequence 211816 from Patent EP1572962.
AK291183 - Homo sapiens cDNA FLJ76821 complete cds, highly similar to Homo sapiens tRNA splicing endonuclease 2 homolog (SEN2, S. cerevisiae) (TSEN2), mRNA.
JD458975 - Sequence 439999 from Patent EP1572962.
CU676442 - Synthetic construct Homo sapiens gateway clone IMAGE:100018319 5' read TSEN2 mRNA.
HQ447904 - Synthetic construct Homo sapiens clone IMAGE:100071260; CCSB004746_04 tRNA splicing endonuclease 2 homolog (S. cerevisiae) (TSEN2) gene, encodes complete protein.
KJ899649 - Synthetic construct Homo sapiens clone ccsbBroadEn_09043 TSEN2 gene, encodes complete protein.
BC021975 - Homo sapiens tRNA splicing endonuclease 2 homolog (S. cerevisiae), mRNA (cDNA clone IMAGE:3833047), partial cds.
AF086155 - Homo sapiens full length insert cDNA clone ZB55G05.
JD374685 - Sequence 355709 from Patent EP1572962.
JD490086 - Sequence 471110 from Patent EP1572962.
JD490087 - Sequence 471111 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AK027821, ENST00000444864.1, ENST00000444864.2, ENST00000444864.3, ENST00000444864.4, ENST00000444864.5, H7C2Z3, H7C2Z3_HUMAN, uc011auq.1, uc011auq.2, uc011auq.3
UCSC ID: ENST00000444864.6
RefSeq Accession: NM_001321278
Protein: H7C2Z3

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.