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SAGE Genie
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Cancer Genome Characterization Initiative

Visit the database of genomic characterization data for multiple tumor types.

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 BC011991

#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
983
1358
1379
1460
1584


No IP for this gene.
PA transcripts: BF515162
BG617085
AV649730
BQ064738


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 GGAAAAGTGG 1 1460 2397
leg_2 TCTATCCCCC 2 1379 46
leg_3 TTTTTAGAGG 3 1358 14
leg_4 TTTAACATCC 4 983 34

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.