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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAGCAACTCGAGGCACGCATGTCGCAAATCAGAGAGGATCCCGCTTTGAAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcctctttatctgattctctctcactcgtgcaagtgactgacttttgtgatgtgaacttttgccag

Basic information

species Selaginella moellendorffii
transcript EFJ08399
intron # 4
splice site 5'
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|169115001|gb|FE516366.1|FE516366
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169087065|gb|FE495157.1|FE495157
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169101055|gb|FE500643.1|FE500643
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAAACA-GCTAGGAC
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAA-CAAGCTAGGAC
EST: gi|169058746|gb|FE464784.1|FE464784
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169043618|gb|FE452686.1|FE452686
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169115002|gb|FE516367.1|FE516367
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169062456|gb|FE469515.1|FE469515
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169048081|gb|FE456796.1|FE456796
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169065055|gb|FE474503.1|FE474503
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169023042|gb|FE431590.1|FE431590
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169063746|gb|FE472476.1|FE472476
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169108039|gb|FE511021.1|FE511021
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169099405|gb|FE500488.1|FE500488
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169072467|gb|FE483863.1|FE483863
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169072466|gb|FE483862.1|FE483862
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169106626|gb|FE504648.1|FE504648
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169065054|gb|FE474502.1|FE474502
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169067484|gb|FE475239.1|FE475239
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169063745|gb|FE472475.1|FE472475
EST:     AAGCCAGTCCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169062455|gb|FE469514.1|FE469514
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169048080|gb|FE456795.1|FE456795
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169054112|gb|FE462347.1|FE462347
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169099404|gb|FE500487.1|FE500487
EST:     CAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: CAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169106627|gb|FE504649.1|FE504649
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169087066|gb|FE495158.1|FE495158
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169058747|gb|FE464785.1|FE464785
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169108040|gb|FE511022.1|FE511022
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
EST: gi|169023043|gb|FE431591.1|FE431591
EST:     AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAA                         GTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT
genomic: AAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGT

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), 35 (downstream exon)
Score: 157

AGGAGCAACTCGAGGCACGCATGTCGCAAATCAGAGAGGATCCCGCTTTGAAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcct ... cttttgccagGTACTGGAATGATCCCGATGTTCTTAACAAGCTAGGACGGGCAATGGGAGTAGGGGGTCCGCAGCACTTTGGCTTGCCAAGGGAGGAAGTCGAAGAAGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAGCAACTCGAGGCACGCATGTCGCAAATCAGAGAGGATCCCGCTTTGAAGCCAGTTCTCGACGAGATCGAGCAAGGAGGCCCAGCAGCTATGATGAAgtacgatcctctttatctgattctctctcactcgtgcaagtgactgacttttgtgatgtgaacttttgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT