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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgccgttttcaatttctccttgaaactgttgctgaccagttccttcctctcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGACGTGCTTTGCTCCGTCTGCGAGATGGCTGTTGTTTGGGTCCAGAACCAG

Basic information

species Selaginella moellendorffii
transcript EFJ34434
intron # 8
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169113000|gb|FE515480.1|FE515480
EST:     CCCGACAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169031797|gb|FE438482.1|FE438482
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169055215|gb|FE461076.1|FE461076
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGG
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGG
EST: gi|169031872|gb|FE438505.1|FE438505
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169112151|gb|FE513494.1|FE513494
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169060203|gb|FE467565.1|FE467565
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169110929|gb|FE509334.1|FE509334
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169112990|gb|FE515470.1|FE515470
EST:     CCCGACAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169058238|gb|FE466005.1|FE466005
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169031935|gb|FE440661.1|FE440661
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169114468|gb|FE516538.1|FE516538
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169065200|gb|FE474024.1|FE474024
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169039673|gb|FE448607.1|FE448607
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAAGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169112152|gb|FE513495.1|FE513495
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169096046|gb|FE500024.1|FE500024
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169021618|gb|FE432137.1|FE432137
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169096045|gb|FE500023.1|FE500023
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169093446|gb|FE495727.1|FE495727
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169031873|gb|FE438506.1|FE438506
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169039672|gb|FE448606.1|FE448606
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169044448|gb|FE451072.1|FE451072
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169021619|gb|FE432138.1|FE432138
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
EST: gi|169021385|gb|FE431176.1|FE431176
EST:     CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 34 (downstream exon)
Score: 158

GTGACGCCCGACAGAGTATGTGCTCAAGCTGGAGTCTGCTCTCTTCGTAATGACAAgtacatgccg ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGACGTGCTTTGCTCCGTCTGCGAGATGGCTGTTGTTTGGGTCCAGAACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttcaatttctccttgaaactgttgctgaccagttccttcctctcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGACGTGCTTTGCTCCGTCTGCGAGATGGCTGTTGTTTGGGTCCAGAACCAG
                         tgctgac  putative branch site (score: 158)
                               ccagttccttcctctc  CT-rich tract
      aatttct  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgccgttttcaatttctccttgaaactgttgctgaccagttccttcctctcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGACGTGCTTTGCTCCGTCTGCGAGATGGCTGTTGTTTGGGTCCAGAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT