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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCGTCTTCCCGTTCGTCCTCCTGTCCGGTCCGAGTCCCTCTGACGACGCGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgcttgatttcttcccttgccaccgcgatattccgatgtatccgtgatgtgtcgttcatgggtagatcggctagggatttggcggcgttgagg...

Basic information

species Oryza sativa
transcript LOC_Os02g42314.2
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|300216021|gb|HO088647.1|HO088647
EST:     CGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88333562|gb|CI656634.1|CI656634
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88717712|gb|CI741222.1|CI741222
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|86905439|gb|CI285402.1|CI285402
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88334413|gb|CI642658.1|CI642658
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGAACAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|9865085|gb|AU100835.1|AU100835
EST:     CGACTTTCCCCACNCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88581898|gb|CI699113.1|CI699113
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88386007|gb|CI570642.1|CI570642
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88676847|gb|CI730960.1|CI730960
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88387401|gb|CI582919.1|CI582919
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88595265|gb|CI714086.1|CI714086
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|55438029|gb|CV732308.1|CV732308
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGTTTGACAG                  
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGC----T----Ggtacgtacgc ... att
EST: gi|313080048|gb|HO213368.1|HO213368
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88308370|gb|CI649585.1|CI649585
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|33655538|gb|CF278152.1|CF278152
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88342554|gb|CI637130.1|CI637130
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88337710|gb|CI632212.1|CI632212
EST:     CGACTTTCCC-ACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88729548|gb|CI751351.1|CI751351
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|163919981|gb|EG714923.1|EG714923
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88730413|gb|CI754026.1|CI754026
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88393637|gb|CI619929.1|CI619929
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88348941|gb|CI653985.1|CI653985
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88595236|gb|CI714057.1|CI714057
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88692966|gb|CI736541.1|CI736541
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGAACAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88760639|gb|CI770195.1|CI770195
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|25806709|gb|CA762670.1|CA762670
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|33823074|gb|CF337340.1|CF337340
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88345516|gb|CI629777.1|CI629777
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88729270|gb|CI752780.1|CI752780
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCACATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88383885|gb|CI631775.1|CI631775
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|86900317|gb|CI296360.1|CI296360
EST:     CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: CGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
EST: gi|88592549|gb|CI710658.1|CI710658
EST:     GACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTG                         AAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG
genomic: GACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG

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: 74 (upstream exon), 71 (downstream exon)
Score: 43

GCGCGTCTTCCCGTTCGTCCTCCTGTCCGGTCCGAGTCCCTCTGACGACGCGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgc ... attttgacagAAACACTTTGTCATATCAGTCAACAGTAGAGAGGAGACCAGATGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCGTCTTCCCGTTCGTCCTCCTGTCCGGTCCGAGTCCCTCTGACGACGCGACTTTCCCCACGCCGGGATCGAGCTCCGGGGAGGGGAGCTGCGAGCTGgtacgtacgcttgatttcttcccttgccaccgcgatattccgatgtatccgtgatgtgtcgttcatgggtagatcggctagggatttggcggcgttgagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcggcg