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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtgttgagcttttggtgacggagagaaagactgttttgtttccagGCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCAAAGGGCCGCAGGAAAAAGCTGCGTGAG

Basic information

species Selaginella moellendorffii
transcript EFJ23006
intron # 6
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|169049297|gb|FE458221.1|FE458221
EST:     GCCGGCGTGTCATTGGGTGCAGCGATCGGGTTTCTTCTCTACGGTGGAAG                         GCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCAAAGGGCCGCAGGAA
genomic: GCCGGCGTGTCATTGGGTGCAGCGATCGGGTTTCTTCTCTACGGTGGAAGgtcggtgttg ... ttgtttccagGCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCAAAGGGCCGCAGGAA
EST: gi|169049298|gb|FE458222.1|FE458222
EST:     GCCGGCGTGTCATTGGGTGCAGCGATCGGGTTTCTTCTCTACGGTGGAAG                         GCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCANAGGGCCGC
genomic: GCCGGCGTGTCATTGGGTGCAGCGATCGGGTTTCTTCTCTACGGTGGAAGgtcggtgttg ... ttgtttccagGCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCAAAGGGCCGC
EST: gi|169087157|gb|FE493104.1|FE493104
EST:     GCCGGCGTGTCATTGGGTGCAGCGATCGGGTTTCTTCTCTACGGTGGAAG                         GCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCAAAGGGCCGCAGGAA
genomic: GCCGGCGTGTCATTGGGTGCAGCGATCGGGTTTCTTCTCTACGGTGGAAGgtcggtgttg ... ttgtttccagGCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCAAAGGGCCGCAGGAA
EST: gi|70670999|gb|DN839576.1|DN839576
EST:     GCCGGCGTGTCATTGGGTGCAGCGATCGGGTTTCTTCTCTACGGTGGAAG                         GCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCAAAGGGCCGCAGGAA
genomic: GCCGGCGTGTCATTGGGTGCAGCGATCGGGTTTCTTCTCTACGGTGGAAGgtcggtgttg ... ttgtttccagGCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCAAAGGGCCGCAGGAA
EST: gi|169087158|gb|FE493105.1|FE493105
EST:     GCCGGCGTGTCATTGGGTGCAGCGATCGGGTTTCTTCTCTACGGTGGAAG                         GCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCANAGGGCCGCAG
genomic: GCCGGCGTGTCATTGGGTGCAGCGATCGGGTTTCTTCTCTACGGTGGAAGgtcggtgttg ... ttgtttccagGCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCAAAGGGCCGCAG

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), 10 (downstream exon)
Score: 4

TCTGGTGGAAGCCACTTGGCCTTCTCGAGAGCTTCTCCAAGATTTTCTTTGCCGGCGTGTCATTGGGTGCAGCGATCGGGTTTCTTCTCTACGGTGGAAGgtcggtgttg ... ttgtttccagGCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCAAAGGGCCGCAGGAAAAAGCTGCGTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcggtgttgagcttttggtgacggagagaaagactgttttgtttccagGCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCAAAGGGCCGCAGGAAAAAGCTGCGTGAG
                                                ttttgtttcc  CT-rich tract
                                           ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtgttgagcttttggtgacggagagaaagactgttttgtttccagGCTGTTCTTGATGCTACAAAGATTTCCCATCGAATCAAAGGGCCGCAGGAAAAAGCTGCGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC