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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagccttctgtttgcactgttacaacctgctttctcttttttctgttctctttcactaagactagaactttataattaaaccacatgtttgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGACGCTCCACCACTTGAATCCGTTGGACCGCAGAAGTGTCTTGCTTTTAGC

Basic information

species Oryza sativa
transcript LOC_Os07g09000.1
intron # 2
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|58657329|gb|CK046009.1|CK046009
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAATGGGTGCAT                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|58606203|gb|CK034236.1|CK034236
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GTTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|88413396|gb|CI581411.1|CI581411
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|58674632|gb|CK063319.1|CK063319
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCGCTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|58666909|gb|CK055595.1|CK055595
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|58592567|gb|CF990875.1|CF990875
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GTTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|117233168|gb|CT848021.1|CT848021
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GTTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|86904427|gb|CI308637.1|CI308637
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAG
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAG
EST: gi|87005363|gb|CI285585.1|CI285585
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|30228290|gb|CB966181.1|CB966181
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|58683603|gb|CK072290.1|CK072290
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|58600783|gb|CK011311.1|CK011311
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTG
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTG
EST: gi|58605016|gb|CK033049.1|CK033049
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GTTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|29640028|gb|CB645037.1|CB645037
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|88363482|gb|CI618043.1|CI618043
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|58684449|gb|CK073136.1|CK073136
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|58668962|gb|CK057648.1|CK057648
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|29636208|gb|CB641217.1|CB641217
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|29627838|gb|CB632849.1|CB632849
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GTTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|87005434|gb|CI285656.1|CI285656
EST:     GTGCACCCCAGCGGAGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|88425533|gb|CI567253.1|CI567253
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGTGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTGACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|58695857|gb|CK084544.1|CK084544
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|58666737|gb|CK055423.1|CK055423
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|33796125|gb|CF323928.1|CF323928
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|88424456|gb|CI608042.1|CI608042
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
EST: gi|29674145|gb|CB670420.1|CB670420
EST:     GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAG                         GCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA
genomic: GTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGA

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: 37 (upstream exon), 75 (downstream exon)
Score: 12

CGAGGGCGGAGCTCGGGGAGGAGCCGGGCGACGCGCCGCGTGGCATCACGGTGCACCCCAGCGGCGACGAGCTCGTCTGCGCCACGGCCAAGGGGTGCAGgtgcgtgcct ... tgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGACGCTCCACCACTTGAATCCGTTGGACCGCAGAAGTGTCTTGCTTTTAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctctttcactaagactagaactttataattaaaccacatgtttgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGACGCTCCACCACTTGAATCCGTTGGACCGCAGAAGTGTCTTGCTTTTAGC
                  tagaactttataatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagccttctgtttgcactgttacaacctgctttctcttttttctgttctctttcactaagactagaactttataattaaaccacatgtttgaactgaagGCTATTCAAGCTGATTTTTGAAGAGTTCACTGTTCGACTTATTTCAAGAGACGCTCCACCACTTGAATCCGTTGGACCGCAGAAGTGTCTTGCTTTTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - ccttctg
- - - - - - -tgcactg
- - - - - - - - - - - - - cctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgtt