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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaattgaaaactcaaaaaagaaagagagagctatatcttaaagctggattttgtgagcagCTTTCGCCTTTCTGTAAGATCGTACGAGAAAGGCTGGTTGAATTGGAGCTCCCTCACGTTTACTACAA

Basic information

species Selaginella moellendorffii
transcript EFJ15233
intron # 9
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|169078263|gb|FE487332.1|FE487332
EST:     ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAG                         CTTTCGCCTTTCTGTAAGATCGCACGAGAAAGGCTGGTTGAATTGGAGCTC
genomic: ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAGgtgaattgaa ... ttgtgagcagCTTTCGCCTTTCTGTAAGATCGTACGAGAAAGGCTGGTTGAATTGGAGCTC
EST: gi|70669827|gb|DN838404.1|DN838404
EST:     ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAG                         CTTTCGCCTTTNCTGTA-GATCGCACGAGAA
genomic: ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAGgtgaattgaa ... ttgtgagcagCTTTCGCCTTT-CTGTAAGATCGTACGAGAA
EST: gi|169078264|gb|FE487333.1|FE487333
EST:     CGTTCCTGCGANGAAA-CCAGACAAGCCTCTAAAGATCTGGGCGTACGAG                         CTTTCGCCTTTCTGTAAGATCG
genomic: CGTTCCTGCGA-GAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAGgtgaattgaa ... ttgtgagcagCTTTCGCCTTTCTGTAAGATCG
EST: gi|169042434|gb|FE453437.1|FE453437
EST:     ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAG                         CTTTCGCCTTTCTGTAAGATCGCACGAGAAAGGCTGGTTGAATTGGAGCTC
genomic: ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAGgtgaattgaa ... ttgtgagcagCTTTCGCCTTTCTGTAAGATCGTACGAGAAAGGCTGGTTGAATTGGAGCTC
EST: gi|169065621|gb|FE474328.1|FE474328
EST:     ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAG                         CTTTCGCCTTTCTGTAAGATCG
genomic: ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAGgtgaattgaa ... ttgtgagcagCTTTCGCCTTTCTGTAAGATCG
EST: gi|169065620|gb|FE474327.1|FE474327
EST:     ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAG                         CTTTCGCCTTTCTGTAAGATCGCACGAGAAAGGCTGGTTGAATTGGAGCTC
genomic: ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAGgtgaattgaa ... ttgtgagcagCTTTCGCCTTTCTGTAAGATCGTACGAGAAAGGCTGGTTGAATTGGAGCTC
EST: gi|169062994|gb|FE471100.1|FE471100
EST:     ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAG                         CTTTCGCCTTTCTGTAAGATCGCACGAGAAAGGCTGGTTGAATTGGAGCTC
genomic: ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAGgtgaattgaa ... ttgtgagcagCTTTCGCCTTTCTGTAAGATCGTACGAGAAAGGCTGGTTGAATTGGAGCTC
EST: gi|169045906|gb|FE453920.1|FE453920
EST:     ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAG                         CTTTCGCCTTTCTGTAAGATCGCACGAGAAAGGCTGGTTGAATTGGAGCTC
genomic: ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAGgtgaattgaa ... ttgtgagcagCTTTCGCCTTTCTGTAAGATCGTACGAGAAAGGCTGGTTGAATTGGAGCTC
EST: gi|169049163|gb|FE457151.1|FE457151
EST:     ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAG                         CTTTCGCCTTTCTGTAAGATCGTACGAGAAAGGCTGGTTGAATTGGAGCTC
genomic: ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAGgtgaattgaa ... ttgtgagcagCTTTCGCCTTTCTGTAAGATCGTACGAGAAAGGCTGGTTGAATTGGAGCTC
EST: gi|169062995|gb|FE471101.1|FE471101
EST:     ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAG                         CTTTCGCCTTTCTGNTA-GATCGCACGAGAAAGGCTGGTTGAATTGGAG
genomic: ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAGgtgaattgaa ... ttgtgagcagCTTTCGCCTTTCTG-TAAGATCGTACGAGAAAGGCTGGTTGAATTGGAG
EST: gi|169049164|gb|FE457152.1|FE457152
EST:     ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAG                         CTTTCGCCTTTCTGTAAGATCGTACGAGAAAGGCTGGTTGAATTGGAGCTC
genomic: ACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAGgtgaattgaa ... ttgtgagcagCTTTCGCCTTTCTGTAAGATCGTACGAGAAAGGCTGGTTGAATTGGAGCTC

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: 19 (upstream exon), 26 (downstream exon)
Score: 14

GGATCCCAATACGTTCCTGCGAGAAAACCAGACAAGCCTCTAAAGATCTGGGCGTACGAGgtgaattgaa ... ttgtgagcagCTTTCGCCTTTCTGTAAGATCGTACGAGAAAGGCTGGTTGAATTGGAGCTCCCTCACGTTTACTACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaactcaaaaaagaaagagagagctatatcttaaagctggattttgtgagcagCTTTCGCCTTTCTGTAAGATCGTACGAGAAAGGCTGGTTGAATTGGAGCTCCCTCACGTTTACTACAA
                          tatatcttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaattgaaaactcaaaaaagaaagagagagctatatcttaaagctggattttgtgagcagCTTTCGCCTTTCTGTAAGATCGTACGAGAAAGGCTGGTTGAATTGGAGCTCCCTCACGTTTACTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT