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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggattggtctgatcgttctttcattctcgacgagtttttcttggtctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTGTGGAAGGAGACCCGGTTTACCAAGTCGCCGTTCCAGGAGTTCACGGACT

Basic information

species Selaginella moellendorffii
transcript EFJ24057
intron # 1
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|169037289|gb|FE443287.1|FE443287
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACTCTGGGAAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169101141|gb|FE503485.1|FE503485
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169049580|gb|FE457724.1|FE457724
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATG
EST: gi|169110290|gb|FE510619.1|FE510619
EST:     TTTTCACCTCGTCGCGGGGATCGACCAAGACACTCGGCAATTTCGTCAAG                         GCTACGTACGACTGTTTGTTGAAGACGTATGGGTTCCTCCCCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169044278|gb|FE453008.1|FE453008
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169037290|gb|FE443288.1|FE443288
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACTCTGGGAAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169035202|gb|FE442580.1|FE442580
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169100295|gb|FE501092.1|FE501092
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACTCTGGGAAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
EST: gi|169057178|gb|FE464689.1|FE464689
EST:     TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAG                         GCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG
genomic: TTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTG

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), 34 (downstream exon)
Score: 17

TGCCGCTCGCGTCCCCAAGAAGGTGCTCCAGTTTGCCGGGATCGAGGATGTTTTCACCTCGTCGCGCGGATCGACCAAGACACTCGGCAACTTCGTCAAGgtgaggattg ... tctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTGTGGAAGGAGACCCGGTTTACCAAGTCGCCGTTCCAGGAGTTCACGGACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggattggtctgatcgttctttcattctcgacgagtttttcttggtctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTGTGGAAGGAGACCCGGTTTACCAAGTCGCCGTTCCAGGAGTTCACGGACT
       gtctgat  putative branch site (score: 17)
                                   tttttcttggtctttc  putative PPT
                                   tttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggattggtctgatcgttctttcattctcgacgagtttttcttggtctttcgcagGCTACGTACGACTGTCTGTTGAAGACGTATGGGTTCCTCACCCCGGATCTGTGGAAGGAGACCCGGTTTACCAAGTCGCCGTTCCAGGAGTTCACGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA