Friday, December 18, 2015

The isoform of Ube3a

The isoform abundances of Ube3a (in colon and brain cortex of adult mice)

Use Tophat for the transcriptome analysis and examined the isoform_exp.diff file 
mRNA_id         gene_id         locus                   fpkm_colon  fpkm_cortex
NM_001033962    Ube3a_isoform_3 chr7:66484119-66562097  0.004558    5.07055
NM_011668       Ube3a_isoform_2 chr7:66484119-66562097  0.230222    0.60659
NM_173010       Ube3a_isoform_1 chr7:66484119-66562097  5.82296     1.36267
It seems that iso3 of Ube3a is the main variant in the mouse cortex. The iso2 of Ube3a encodes the full length protein. Iso1 is considered to be E3-ligase deficient as it lacks 87 amino acids from the C-terminal HECT domain. Both iso1 and iso3 lack 21 amino acids from N-terminus as well. Regarding the localization, Iso1 and Iso2 are ubiquitously found throughout a cell, where Iso3 is confined to the nucleus.