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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCTTACTGCGCCTGATTCTGGGTTATGAGAAACCAACCCGTGGAGATATAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggttcttctcccagcgaagaaatggcttctcactgttagtgatgccag

Basic information

species Selaginella moellendorffii
transcript EFJ10635
intron # 4
splice site 5'
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|169115175|gb|FE515604.1|FE515604
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|169026960|gb|FE434272.1|FE434272
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|169028378|gb|FE439897.1|FE439897
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|169052592|gb|FE461659.1|FE461659
EST:     CGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: CGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|169036614|gb|FE444159.1|FE444159
EST:     TCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: TCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|169056801|gb|FE465404.1|FE465404
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAAC
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAAC
EST: gi|169078769|gb|FE489619.1|FE489619
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|169078770|gb|FE489620.1|FE489620
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|169105691|gb|FE508457.1|FE508457
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|169027273|gb|FE436145.1|FE436145
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|169115176|gb|FE515605.1|FE515605
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTT
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTT
EST: gi|169116429|gb|FE518195.1|FE518195
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|169087542|gb|FE494633.1|FE494633
EST:     AGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: AGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|169056802|gb|FE465405.1|FE465405
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|70671002|gb|DN839579.1|DN839579
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|169027733|gb|FE433219.1|FE433219
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
EST: gi|169075650|gb|FE482036.1|FE482036
EST:     TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTNTGAGCAGAATCAG                         GCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA
genomic: TAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTA

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: 14

CACCTTACTGCGCCTGATTCTGGGTTATGAGAAACCAACCCGTGGAGATATAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggt ... gtgatgccagGCTGAGGCATTGGATCTTAACAAAACGGTCTTGGAAACAGTGGAAGAAGTAGCCGAGGACTGGAGGCTCGACGACATCAAAGGCCTGCTTGGAAAGTGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCTTACTGCGCCTGATTCTGGGTTATGAGAAACCAACCCGTGGAGATATAACTCTCGGCGAGCATCGAGTTGTACCCAACTACTTTGAGCAGAATCAGgttctttggttcttctcccagcgaagaaatggcttctcactgttagtgatgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG