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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGCACGGCGGCGGCGGCGGCGATGGCGCGGTGGCCGTGGAGGTGGAGGGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAGgtactgcgacccccgctttctctctctctctctctctttcttgcgcggcggcgcttcctcttggccccgccacccccagccccaaatggcaaatactgca...

Basic information

species Oryza sativa
transcript LOC_Os01g74580.1
intron # 1
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|33678961|gb|CF307200.1|CF307200
EST:     GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
genomic: GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
EST: gi|218484052|gb|FG943456.1|FG943456
EST:     GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAG                         AGGGGCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
genomic: GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
EST: gi|29616879|gb|CB621891.1|CB621891
EST:     GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
genomic: GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
EST: gi|5004270|gb|AU069419.1|AU069419
EST:     GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
genomic: GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
EST: gi|117246981|gb|CT843770.1|CT843770
EST:     GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
genomic: GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
EST: gi|58677217|gb|CK065904.1|CK065904
EST:     GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
genomic: GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
EST: gi|2310536|gb|C26691.1|C26691
EST:     GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTNCNCCGTCTTCGCGCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
genomic: GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
EST: gi|29679525|gb|CB675800.1|CB675800
EST:     GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
genomic: GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA
EST: gi|33677524|gb|CF305763.1|CF305763
EST:     GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTTAAACGAGCCTCAGAAATGA
genomic: GGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGA

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: 42 (upstream exon), 59 (downstream exon)
Score: 15

GAGAGCACGGCGGCGGCGGCGGCGATGGCGCGGTGGCCGTGGAGGTGGAGGGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTCAGAAATGATGAACCTAAGGAAATATGATGGATCACTTGGTCTGCTAAATGCTGTGTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAGCACGGCGGCGGCGGCGGCGATGGCGCGGTGGCCGTGGAGGTGGAGGGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCGCGCAAGgtactgcgacccccgctttctctctctctctctctctttcttgcgcggcggcgcttcctcttggccccgccacccccagccccaaatggcaaatactgca

- - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcggcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggccccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagcccc