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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGACCCCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAAgtacatgcctttttcaatttctccttgatactgttgctgaccagttccttcctgtcttctgcag

Basic information

species Selaginella moellendorffii
transcript EFJ34432
intron # 8
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|169048187|gb|FE455459.1|FE455459
EST:     CCCGACAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAGTCAAAAGGTTGGAGACGA
genomic: CCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAAgtacatgcct ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACCA
EST: gi|169039488|gb|FE449163.1|FE449163
EST:     CCCGACAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAGTCAAAAGGTTGGAGACGA
genomic: CCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAAgtacatgcct ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACCA
EST: gi|169030852|gb|FE439797.1|FE439797
EST:     CCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACCA
genomic: CCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAAgtacatgcct ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACCA
EST: gi|169043989|gb|FE451575.1|FE451575
EST:     CCCGACAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAGTCAAAAGGTTGGAGACGA
genomic: CCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAAgtacatgcct ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACCA
EST: gi|169043990|gb|FE451576.1|FE451576
EST:     CCCGACAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAGTCAAAAGGTTGGAGACGA
genomic: CCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAAgtacatgcct ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACCA
EST: gi|169072916|gb|FE482344.1|FE482344
EST:     CCCGACAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAGTCAAAAGGTTGGAGACGA
genomic: CCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAAgtacatgcct ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACCA
EST: gi|169043410|gb|FE451854.1|FE451854
EST:     CCCGACAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAAgtacatgcct ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACCA
EST: gi|169107735|gb|FE511458.1|FE511458
EST:     CCCGACAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAGTCAAAAGGTTGGAGACGA
genomic: CCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAAgtacatgcct ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACCA
EST: gi|169032351|gb|FE440908.1|FE440908
EST:     CCCGACAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAGTCAAAAGGTTGGAGACGA
genomic: CCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAAgtacatgcct ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACCA
EST: gi|169108565|gb|FE510780.1|FE510780
EST:     CCCGACAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAA                         CCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACGA
genomic: CCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAAgtacatgcct ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACCA

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), 34 (downstream exon)
Score: 190

GTGACCCCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAAgtacatgcct ... tcttctgcagCCCACATATTGCGAGTGTGCTGGACAAGGAAAATCAAAAGGTTGGAGACCACGGGCTTTGCTCCGTCTGCGAGATGGCCGTTGTTTCGGTCCAGAACCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGACCCCCGATAAAGTATGTGCTCAAGCTGGGGTCTGCACTCTTCGTAATGACAAgtacatgcctttttcaatttctccttgatactgttgctgaccagttccttcctgtcttctgcag

- - - - - - - - - - - - CAAGCT
- - - - - - - - - - - -  AAGCTG