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SAGE Genie
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LT Viewer

Brief Summary of Ludwig Transcript (LT) Viewer

Below is a visual representation of a particular transcript with, at most, four possible virtual SAGE tag locations, starting from the 3' end. Transcripts which overlap this longer transcript are positioned on the display and annotated as either internally primed or alternatively polyadenylated. In addition, there is a table containing information on the influence of Single Nucleotide Polymorphisms (SNPs) in the generation of alternative tags

Transcript NM_004181

#4
#3
#2
#1
5' 
big blue_4 median leg_4 median blue_3 median leg_3 median blue_2 median leg_2 median blue_1 median leg_1 median median  3'
bp number:
1
496
622
786
806
1110


No IP for this gene.
PA transcripts: BQ719597
BQ719597
BG332394
BG332394
BQ021061


No SNP-Associated Alternative Tag for this gene.

Tag Info Summary

The table below summarizes the tag information from above. The tag link enables the user to see which other gene(s) may be represented by the particular tag and the reliability of each mapping. Be aware that it is possible that an internal tag from one gene might, on occasion, have a better match to a different gene and thus the tag frequency is possibly the sum of more than one gene.

Tag Tag Sequence Tag Position BP Number Tag Freq 
leg_1 CAGTCTAAAA 1 806 1472
leg_2 AAAATATATA 2 786 17
leg_3 GCGCCAGTTC 3 622 52
leg_4 ATGCCGTGGC 4 496 26

Notes:

  • A_plus corresponds to A-rich regions, defined as an internal stretch of eight adenosines within a 10 bp region.
  • IP transcripts are "probably" derived from an internal priming of an internal A-rich region.
  • PA transcripts are sequences that have a polyA signal and a poyA tail and therefore are "probably" derived from alternative polyadenylation.