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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcagtagtgaccaatcgattttttctttccttttttttctctataagcctgtgaattttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG

Basic information

species Selaginella moellendorffii
transcript EFJ30498
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23041 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT1G23310.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------gtaaa---gcagtagtgaccaatcgattttttctttccttttttttctctataagcctgtgaattttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG
                           ||  |   ||| |  ||| | | |  ||  ||  | | |  || ||  |  |       |     |   | |||| || || ||||||||||| ||||| || ||| ||||||||||||||||||| ||||||||||||
tggtcctttgttggttagggacttgatgtgcatttgcaattatgatctagcacttgatttgtccatagttattggcagttcctaacttgggctataacagATTATTTTCACAAACGTTGGGAACCCTCATGCTTTAGGACAGAAGCCATTGACATTTCCTCGCCAG

upper sequence: EFJ23041 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv00s0225g00130.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------gtaaagcagtagtgaccaatcgattttttctttcct----tttttttctctataagcctgtgaattttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG
                          || ||   |     |  |||  | |||||| |   |    || ||||   |||   |   | |  | || | |||| || || |||||||| || ||||| || |||||||||||||| ||| |||| ||||||||||||
gcattggcttttgcattctttttgaggttaaatggatcaaaataatttaatttttcatatttgatattgttttgattattttctaattacctgtctacagATTATTTTCACAAACGTGGGCAACCCTCATGCTCTAGGACAGAAACCACTGACTTTTCCTCGCCAG
















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|169066246|gb|FE475200.1|FE475200
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
EST: gi|169054115|gb|FE462350.1|FE462350
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
EST: gi|169100333|gb|FE501130.1|FE501130
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
EST: gi|169098675|gb|FE497249.1|FE497249
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
EST: gi|169020174|gb|FE428236.1|FE428236
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
EST: gi|169047621|gb|FE455205.1|FE455205
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
EST: gi|169111758|gb|FE511957.1|FE511957
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
EST: gi|169067097|gb|FE474475.1|FE474475
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
EST: gi|169042323|gb|FE452871.1|FE452871
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
EST: gi|169057473|gb|FE465777.1|FE465777
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
EST: gi|169036858|gb|FE444975.1|FE444975
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
EST: gi|169097504|gb|FE497946.1|FE497946
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
EST: gi|169106601|gb|FE504636.1|FE504636
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
EST: gi|169065718|gb|FE476206.1|FE476206
EST:     GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAG                         ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG
genomic: GAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTG

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: 33 (upstream exon), 35 (downstream exon)
Score: 48

GGATCCAGACAACATCAACGAGAATGTGAAGAAATGCGTGTATGCGGTGAGAGGGGAGCTCTACTTGCGAGCATCGGAGCTCCAGAAGGAAGGTAAAAAGgtaaagcagt ... ttttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaatcgattttttctttccttttttttctctataagcctgtgaattttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG
                                             ttttccat  CT-rich tract
       attttttctttccttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagcagtagtgaccaatcgattttttctttccttttttttctctataagcctgtgaattttccatagATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC