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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTGATCGTTAAGAGACTGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAGgtacgagcaggctctcaagtttccttccttgttttcatttctctcacgctagactttgtaactttcgtgtgtcaaag

Basic information

species Selaginella moellendorffii
transcript EFJ21638
intron # 10
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|169040804|gb|FE447855.1|FE447855
EST:     TGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAG                         GTCGGGACGCCTAAAACTCACAGACGCTATCTCGCTCGAGACCAAGGAACT
genomic: TGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAGgtacgagcag ... tgtgtcaaagGTCGGGACGCCTAAAACTCACAGACGCTATCTCGCTCGAGACCAAGGAACT
EST: gi|169103946|gb|FE508404.1|FE508404
EST:     TGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAG                         GTCGGGACGCCTAANACTCACAGACGCTATCTCGCTCGAGACCAAGGAACT
genomic: TGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAGgtacgagcag ... tgtgtcaaagGTCGGGACGCCTAAAACTCACAGACGCTATCTCGCTCGAGACCAAGGAACT
EST: gi|169045741|gb|FE453053.1|FE453053
EST:     TGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAG                         GTCGGGACGCCTAAAACTCACAGACGCTATCTCGCTCGAGACCAAGGAACT
genomic: TGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAGgtacgagcag ... tgtgtcaaagGTCGGGACGCCTAAAACTCACAGACGCTATCTCGCTCGAGACCAAGGAACT
EST: gi|169027210|gb|FE435081.1|FE435081
EST:     TGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAG                         GTCGGGACGCCTAAAACTCACAGACGCTATCTCGCTCGAGACCAAGGAACT
genomic: TGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAGgtacgagcag ... tgtgtcaaagGTCGGGACGCCTAAAACTCACAGACGCTATCTCGCTCGAGACCAAGGAACT
EST: gi|169096608|gb|FE499520.1|FE499520
EST:     TGGAAGCGAAACTATTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAG                         GTCGGGACGCCTAAAACTCACAGACGTTTTCTCGCTCGAGACCAAGGAACT
genomic: TGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAGgtacgagcag ... tgtgtcaaagGTCGGGACGCCTAAAACTCACAGACGCTATCTCGCTCGAGACCAAGGAACT
EST: gi|169040805|gb|FE447856.1|FE447856
EST:     TGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAG                         GTCGGGACGCCTAAAACTCACAGACGCTATCTCGCTCGAGACCAAGGAACT
genomic: TGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAGgtacgagcag ... tgtgtcaaagGTCGGGACGCCTAAAACTCACAGACGCTATCTCGCTCGAGACCAAGGAACT
EST: gi|169048503|gb|FE455737.1|FE455737
EST:     TGGAAGCGAAACTATTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAG                         GTCGGGACGCCTAANACTCACAGACGTTTTCTCGCTCGAGACCAAGGAACT
genomic: TGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAGgtacgagcag ... tgtgtcaaagGTCGGGACGCCTAAAACTCACAGACGCTATCTCGCTCGAGACCAAGGAACT
EST: gi|169048502|gb|FE455736.1|FE455736
EST:     TGGAAGCGAAACTATTTCCCGGTCTCAAGGACGCAACAGTTTTTCGAGAG                         GTCGGGACGCCTAAAACTCACAGACGTTTTCTCGCTCGAGACCAAGGAACT
genomic: TGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAGgtacgagcag ... tgtgtcaaagGTCGGGACGCCTAAAACTCACAGACGCTATCTCGCTCGAGACCAAGGAACT

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: 23 (upstream exon), 29 (downstream exon)
Score: 2

GGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTGATCGTTAAGAGACTGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAGgtacgagcag ... tgtgtcaaagGTCGGGACGCCTAAAACTCACAGACGCTATCTCGCTCGAGACCAAGGAACTTACGGACCAATCCCTGTTGGAAAGCCCAAAGGACTTCTCGGGATGCCAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGTACAATGACAAGAAGGAGGCTGTGGCCGATGTGATCGTTAAGAGACTGGAAGCGAAACTGTTTCCCGGTCTCAAGGACGCAACAGTTCTTCGAGAGgtacgagcaggctctcaagtttccttccttgttttcatttctctcacgctagactttgtaactttcgtgtgtcaaag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG