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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctgagttttctctatgtaattttgtttttctcatgctcttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG

Basic information

species Selaginella moellendorffii
transcript EFJ08399
intron # 5
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|169115001|gb|FE516366.1|FE516366
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169087065|gb|FE495157.1|FE495157
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169115002|gb|FE516367.1|FE516367
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169062456|gb|FE469515.1|FE469515
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGC
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGC
EST: gi|169065055|gb|FE474503.1|FE474503
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169023042|gb|FE431590.1|FE431590
EST:     AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169063746|gb|FE472476.1|FE472476
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCNNAACA-GGATGAGAAAGACTC
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCA-AACAAGGATGAGAAAGACTC
EST: gi|169108039|gb|FE511021.1|FE511021
EST:     AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169099405|gb|FE500488.1|FE500488
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTC
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTC
EST: gi|169072467|gb|FE483863.1|FE483863
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCANACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169072466|gb|FE483862.1|FE483862
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169106626|gb|FE504648.1|FE504648
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169065054|gb|FE474502.1|FE474502
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169067484|gb|FE475239.1|FE475239
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169072328|gb|FE479408.1|FE479408
EST:     AAGAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169063745|gb|FE472475.1|FE472475
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169062455|gb|FE469514.1|FE469514
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169048080|gb|FE456795.1|FE456795
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169054112|gb|FE462347.1|FE462347
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169099404|gb|FE500487.1|FE500487
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169106627|gb|FE504649.1|FE504649
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGT-GAAAGTTCTTCTAGCAGACGGTGCAAACAAGGATGAGAAAGACTC
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTC
EST: gi|169087066|gb|FE495158.1|FE495158
EST:     A-GAGGAGGAACTGACCCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCAGACGGTGNCAA-CAAGGATGAGAAAGACTC
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTG-CAAACAAGGATGAGAAAGACTC
EST: gi|169058747|gb|FE464785.1|FE464785
EST:     AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169108040|gb|FE511022.1|FE511022
EST:     AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCG
EST: gi|169023043|gb|FE431591.1|FE431591
EST:     AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAG                         GGGTTGAAAGTTCTTCTAGCGGACGGTGC
genomic: AAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGC

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: 111

CTTGCCAAGGGAGGAAGTCGAAGAAGCGGAGGCCGAGGGCGAGGGCGAGGAAGAGGAGGAACTGACGCTTCATCACACCGCTAGCACTGGCGACATTGAGgtacctgagt ... ttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacctgagttttctctatgtaattttgtttttctcatgctcttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG
                            ttttgtttttctcatg  CT-rich tract
                   tatgtaattttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctgagttttctctatgtaattttgtttttctcatgctcttcatgccagGGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA