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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcactagagtccttggagagtcttactgatatatctttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG

Basic information

species Selaginella moellendorffii
transcript EFJ22768
intron # 4
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|169028104|gb|FE435956.1|FE435956
EST:     CAACACTAATAGTGAATAACAGGCAGTATAGAG                         GCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
genomic: CAACACTAATAGTGAATAACAGGCAGTATAGAGgtatcactag ... tttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
EST: gi|169096681|gb|FE496811.1|FE496811
EST:     TGAATAACAGGCAGTATAGAG                         GCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
genomic: TGAATAACAGGCAGTATAGAGgtatcactag ... tttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
EST: gi|169096537|gb|FE499449.1|FE499449
EST:     AGTGAATAACAGGCAGTATAGAG                         GCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
genomic: AGTGAATAACAGGCAGTATAGAGgtatcactag ... tttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
EST: gi|169031591|gb|FE439056.1|FE439056
EST:     CAGGCAGTATAGAG                         GCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
genomic: CAGGCAGTATAGAGgtatcactag ... tttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
EST: gi|169096682|gb|FE496812.1|FE496812
EST:     TGACGTTACCATTTTACCAACACTAATCGTGAATAACAGGCAGTATAGAG                         GCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
genomic: TGACGTTACCATTTTGCCAACACTAATAGTGAATAACAGGCAGTATAGAGgtatcactag ... tttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
EST: gi|169096538|gb|FE499450.1|FE499450
EST:     TGACGTTACCATTTTGCCAACACTAATAGTGAATAACAGGCAGTATAGAG                         GCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
genomic: TGACGTTACCATTTTGCCAACACTAATAGTGAATAACAGGCAGTATAGAGgtatcactag ... tttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
EST: gi|169083003|gb|FE488525.1|FE488525
EST:     TAATCGTGAATAACAGGCAGTATAGAG                         GCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
genomic: TAATAGTGAATAACAGGCAGTATAGAGgtatcactag ... tttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
EST: gi|169050286|gb|FE458353.1|FE458353
EST:     TGACGTTACCATTTTGCCAACACTAATAGTGAATAACAGGCAGTATAGAG                         GCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
genomic: TGACGTTACCATTTTGCCAACACTAATAGTGAATAACAGGCAGTATAGAGgtatcactag ... tttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
EST: gi|169081076|gb|FE486141.1|FE486141
EST:     TGACGTTACCATTTTGCCAACACTAATAGTGAATAACAGGCAGTATAGAG                         GCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTTCCA-
genomic: TGACGTTACCATTTTGCCAACACTAATAGTGAATAACAGGCAGTATAGAGgtatcactag ... tttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTT-CCAA
EST: gi|169114821|gb|FE516082.1|FE516082
EST:     TGACGTTACCATTTTGCCAACACTAATAGTGAATAACAGGCAGTATAGAG                         GCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG
genomic: TGACGTTACCATTTTGCCAACACTAATAGTGAATAACAGGCAGTATAGAGgtatcactag ... tttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAG

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: 50

GTGGGACATGGCAGCCGTGGTGACGTTACCATTTTGCCAACACTAATAGTGAATAACAGGCAGTATAGAGgtatcactag ... tttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatcactagagtccttggagagtcttactgatatatctttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG
                                 tactgat  putative branch site (score: 50)
                                         tatcttt  CT-rich tract
                                      atatatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcactagagtccttggagagtcttactgatatatctttggtgcagGCAAGCTGGATAAAGCCGCGGTGCTGAAAGCTATTTGTTCGGGTTTCCAAGAAACTACAGAGCCAGCCGTCTGTTTGAGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA