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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcattcattcttttttcgttttcctattagttcatccaaaactaatggatcaacagGTGTGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACGTGCGCACAGATCTTCGAGGAGGCTGGATGCGACACTCCCGCTTCTCCCT

Basic information

species Selaginella moellendorffii
transcript EFJ16666
intron # 12
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|169075245|gb|FE484114.1|FE484114
EST:     GGCCAAAAAGTCAAAGTTCCAACGTTCCTCGTGCCGGCAACACAAAAG                         GTATGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG
genomic: GGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAGgttcattcat ... ggatcaacagGTGTGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG
EST: gi|169111211|gb|FE511371.1|FE511371
EST:     GGCCAAAAAGTCAAAGTTCCAACGTTCCTCGTGCCGGCAACACAAAAG                         GTATGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG
genomic: GGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAGgttcattcat ... ggatcaacagGTGTGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG
EST: gi|169099806|gb|FE500811.1|FE500811
EST:     GGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAG                         GTGTGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG
genomic: GGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAGgttcattcat ... ggatcaacagGTGTGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG
EST: gi|169075231|gb|FE484113.1|FE484113
EST:     GGCCAAAAAGTCAAAGTTCCAACGTTCCTCGTGCCGGCAACACAAAAG                         GTATGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG
genomic: GGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAGgttcattcat ... ggatcaacagGTGTGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG
EST: gi|169100312|gb|FE501109.1|FE501109
EST:     GGCCAAAAAGTCAAAGTTCCAACGTTCCTCGTGCCGGCAACACAAAAG                         GTATGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG
genomic: GGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAGgttcattcat ... ggatcaacagGTGTGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG
EST: gi|169100311|gb|FE501108.1|FE501108
EST:     GGCCAAAAAGTCAAAGTTCCAACGTTCCTCGTGCCGGCAACACAAAAG                         GTATGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG
genomic: GGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAGgttcattcat ... ggatcaacagGTGTGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG
EST: gi|169035258|gb|FE442610.1|FE442610
EST:     GGCCAAAAAGTCAAAGTTCCAACGTTCCTCGTGCCGGCAACACAAAAG                         GTATGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG
genomic: GGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAGgttcattcat ... ggatcaacagGTGTGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACG

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: 50

GGCCAAAAAGTCAAGGTTCCAACCTTCCTCGTGCCGGCAACACAAAAGgttcattcat ... ggatcaacagGTGTGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACGTGCGCACAGATCTTCGAGGAGGCTGGATGCGACACTCCCGCTTCTCCCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcattcttttttcgttttcctattagttcatccaaaactaatggatcaacagGTGTGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACGTGCGCACAGATCTTCGAGGAGGCTGGATGCGACACTCCCGCTTCTCCCT
                                      aactaat  putative branch site (score: 50)
     attctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcattcattcttttttcgttttcctattagttcatccaaaactaatggatcaacagGTGTGGGTGGACTTGTACGCAATGCCACTCCCCGAGGCAGACGGGAAAACGTGCGCACAGATCTTCGAGGAGGCTGGATGCGACACTCCCGCTTCTCCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA