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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGACCTCGGTTATGCTCACGAGCTGGGAAACTACGCCGAGTACAGTGGAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactttcactttcatagtgattcccagtcaacgttgttccattgcag

Basic information

species Selaginella moellendorffii
transcript EFJ27687
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ27687 (Selaginella moellendorffii), 5'ss of exon 9
lower sequence: PP1S63_54V6.2 (Physcomitrella patens), 5'ss of exon 11
TGGTGACCTCGGTTATGCTCACGAGCTGGGAAACTACGCCGAGTACAGTGGAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactttcac------tttcatagtg-attcccagtcaacgttgttccattgcag-----------------------------------------
 || || || |||||||| |||||||| || || || || |||||||||||||| ||||  || || |||||| | || ||||| |||||||| |||||||||||  | |  |       |||   |  | ||| | ||||  |  |||    |||                                            
CGGGGATCTTGGTTATGCACACGAGCTTGGCAATTATGCTGAGTACAGTGGAGCTCCAAATGAAGAAGAGACTTTGCAGTATGCCCGTGCTTTGATTGACgtaagtccgtctatagttggttttggacagcatttcaagtcttctatgtagtgttggttctccttccactgaattttggacgttcccttatgatgtctcc
















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:     GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGAC                         TGCGTCACTGCGAATCCAGACGGACGCCGCCGAGCGTTGCTCATCGGTGGC
genomic: GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactt ... tccattgcagTGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
EST: gi|169112109|gb|FE513452.1|FE513452
EST:     GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGAC                         TGCGTCACTGCGAATCCAGACGGACGCCGCCGAGCGTTGCTCATCGGTGGC
genomic: GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactt ... tccattgcagTGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
EST: gi|169082641|gb|FE486200.1|FE486200
EST:     GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGAC                         TGCGTCACTGCGAATCCAGACGGACGCCGCCGAGCGTTGCTCATCGGTGGC
genomic: GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactt ... tccattgcagTGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
EST: gi|169037361|gb|FE443307.1|FE443307
EST:     GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGAC                         TGCGTCACTGCGAATCCAGACGGACGCCGCCGAGCGTTGCTCATCGGTGGC
genomic: GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactt ... tccattgcagTGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
EST: gi|169039921|gb|FE447607.1|FE447607
EST:     GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGAN                         TGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
genomic: GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactt ... tccattgcagTGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
EST: gi|169037362|gb|FE443308.1|FE443308
EST:     GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGAC                         TGCGTCACTGCGAATCCAGACGGACGCCGCCGAGCGTTGCTCATCGGTGGC
genomic: GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactt ... tccattgcagTGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
EST: gi|169071277|gb|FE478409.1|FE478409
EST:     GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGAC                         TGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
genomic: GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactt ... tccattgcagTGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
EST: gi|169112907|gb|FE514659.1|FE514659
EST:     GAGCGCCAAGCGAGGAGGAGACTGTACACTATGCTCGTGCTTTAATTGAC                         TGCGTCGCTGCGAACCCAGTCGGACGTCGCAGAGCTTTGCTCATCGGTGGA
genomic: GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactt ... tccattgcagTGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
EST: gi|169082642|gb|FE486201.1|FE486201
EST:     GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGAC                         TGCGTCACTGCGAATCCAGACGGACGCCGCCGAGCGTTGCTCATCGGTGGC
genomic: GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactt ... tccattgcagTGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
EST: gi|169044046|gb|FE451632.1|FE451632
EST:     GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGAC                         TGCGTCACTGCGAATCCAGACGGACGCCGCCGAGCGTTGCTCATCGGTGGC
genomic: GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactt ... tccattgcagTGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
EST: gi|169102323|gb|FE506547.1|FE506547
EST:     GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGAC                         TGCGTCACTGCGAATCCAGACGGACGCCGCCGAGCGTTGCTCATCGGTGGC
genomic: GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactt ... tccattgcagTGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
EST: gi|169064650|gb|FE471381.1|FE471381
EST:     GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGAC                         TGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC
genomic: GAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactt ... tccattgcagTGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGC

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), 31 (downstream exon)
Score: 35

TGGTGACCTCGGTTATGCTCACGAGCTGGGAAACTACGCCGAGTACAGTGGAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactt ... tccattgcagTGCGTCACTGCGAACCCAGACGGACGTCGCAGAGCTTTGCTCATCGGTGGCGGCATAGCCAACTTCACCGATGTCGCTGCAACGTTTAATGGTATCATCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGACCTCGGTTATGCTCACGAGCTGGGAAACTACGCCGAGTACAGTGGAGCGCCAAGCGAGGAGGAGACTCTACACTATGCTCGTGCTTTAATTGACgtaagaactttcactttcatagtgattcccagtcaacgttgttccattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA