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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaggcacatgacttcaggttcttctaattttctttcgttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGCCTTCTGTTTCCTCCTGACGCTGTTGCGAGAGCCAAGCACTACCTCTCAA

Basic information

species Selaginella moellendorffii
transcript EFJ30498
intron # 2
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|169066246|gb|FE475200.1|FE475200
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169046058|gb|FE453955.1|FE453955
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169054115|gb|FE462350.1|FE462350
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169056997|gb|FE466224.1|FE466224
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169100333|gb|FE501130.1|FE501130
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169098675|gb|FE497249.1|FE497249
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169020174|gb|FE428236.1|FE428236
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169047621|gb|FE455205.1|FE455205
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169111758|gb|FE511957.1|FE511957
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169067097|gb|FE474475.1|FE474475
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169045644|gb|FE452605.1|FE452605
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169042323|gb|FE452871.1|FE452871
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169057473|gb|FE465777.1|FE465777
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169036858|gb|FE444975.1|FE444975
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169097504|gb|FE497946.1|FE497946
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169106601|gb|FE504636.1|FE504636
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
EST: gi|169065718|gb|FE476206.1|FE476206
EST:     TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAG                         GTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC
genomic: TTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGC

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), 31 (downstream exon)
Score: 57

ATAATCTTTACAAACGTTGGAAACCCACACGCTCTAGGACAGAAGCCATTGACGTTTCCTCGCCAGgtactaggca ... gttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGCCTTCTGTTTCCTCCTGACGCTGTTGCGAGAGCCAAGCACTACCTCTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactaggcacatgacttcaggttcttctaattttctttcgttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGCCTTCTGTTTCCTCCTGACGCTGTTGCGAGAGCCAAGCACTACCTCTCAA
                              ttctaat  putative branch site (score: 57)
                           ttcttctaattttctt  CT-rich tract
                                 taattttctttcgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactaggcacatgacttcaggttcttctaattttctttcgttttttaagGTCATGGCTTTGTGCCAAGCTCCATTTCTTATGGACGACCCCAACGTAGGCCTTCTGTTTCCTCCTGACGCTGTTGCGAGAGCCAAGCACTACCTCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT