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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacttttcacgaagagatcctcgctttactacttttggtgttcttattctcgctcttcatccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGCCCAAACTACCAGAAAGGCCTGGAAAGGATGAGAACACTTGGCAGGGATA

Basic information

species Selaginella moellendorffii
transcript EFJ27687
intron # 10
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|169067517|gb|FE475259.1|FE475259
EST:     CCGACGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGCCGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169112109|gb|FE513452.1|FE513452
EST:     CCGACGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGCCGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169082641|gb|FE486200.1|FE486200
EST:     CCGACGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGCCGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169037361|gb|FE443307.1|FE443307
EST:     CCGACGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGCCGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169082044|gb|FE487995.1|FE487995
EST:     GTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: GTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169039921|gb|FE447607.1|FE447607
EST:     CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169037362|gb|FE443308.1|FE443308
EST:     CCGACGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGCCGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169071277|gb|FE478409.1|FE478409
EST:     CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169112907|gb|FE514659.1|FE514659
EST:     CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169082642|gb|FE486201.1|FE486201
EST:     CCGACGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGCCGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169044046|gb|FE451632.1|FE451632
EST:     CCGACGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGCCGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169082043|gb|FE487994.1|FE487994
EST:     GTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: GTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169102323|gb|FE506547.1|FE506547
EST:     CCGACGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGCCGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169107924|gb|FE513792.1|FE513792
EST:     CATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: CATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
EST: gi|169064650|gb|FE471381.1|FE471381
EST:     CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAG                         GAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC
genomic: CCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGC

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: 34 (upstream exon), 35 (downstream exon)
Score: 42

AGACGGACGTCGCAGAGCTTTGCTCATCGGTGGCGGCATAGCCAACTTCACCGATGTCGCTGCAACGTTTAATGGTATCATCCGCGCGCTCCGCGAGAAGgtaaactttt ... atccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGCCCAAACTACCAGAAAGGCCTGGAAAGGATGAGAACACTTGGCAGGGATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagatcctcgctttactacttttggtgttcttattctcgctcttcatccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGCCCAAACTACCAGAAAGGCCTGGAAAGGATGAGAACACTTGGCAGGGATA
                           ttcttattctcgctct  CT-rich tract
                           ttcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacttttcacgaagagatcctcgctttactacttttggtgttcttattctcgctcttcatccccgcagGAATCCCAGCTGAAAGTGGCAAAGGTGCACATATTCGTGAGGCGAGGGGGCCCAAACTACCAGAAAGGCCTGGAAAGGATGAGAACACTTGGCAGGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG