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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAGAGGATGGGGCAGCGACCAAGCTGCAGAAGGTGTACCGGAGCTACCGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctccacagatcctaccccaatctttcttctcccttcccttttcttttcttttcttttactgatccttctgaagcttcttgctccggatttgtttactgttcggtttcgtggaatttattccataatctaaaaaaaactgcttgatttttaattgagatggtttgtggattggattgttgatgaag

Basic information

species Oryza sativa
transcript LOC_Os12g05420.1
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|88735776|gb|CI759284.1|CI759284
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88409718|gb|CI569008.1|CI569008
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88424648|gb|CI606447.1|CI606447
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88362869|gb|CI614225.1|CI614225
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|58600488|gb|CK011016.1|CK011016
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88827748|gb|CI778313.1|CI778313
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|87023716|gb|CI286467.1|CI286467
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88409692|gb|CI568982.1|CI568982
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88353149|gb|CI624113.1|CI624113
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTAGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88722671|gb|CI746181.1|CI746181
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88761736|gb|CI771292.1|CI771292
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88385913|gb|CI568581.1|CI568581
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88732261|gb|CI757109.1|CI757109
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|29688635|gb|CB684910.1|CB684910
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCATCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGATGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88388290|gb|CI627829.1|CI627829
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88315207|gb|CI611871.1|CI611871
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|58604460|gb|CK014988.1|CK014988
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88826469|gb|CI777034.1|CI777034
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|58677266|gb|CK065953.1|CK065953
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|117240969|gb|CT842912.1|CT842912
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88696332|gb|CI739907.1|CI739907
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|33797243|gb|CF324484.1|CF324484
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT
EST: gi|88315574|gb|CI615446.1|CI615446
EST:     CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTG                         GTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCATTCTT
genomic: CGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTT

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: 55 (upstream exon), 62 (downstream exon)
Score: 22

GAGGAGAGGATGGGGCAGCGACCAAGCTGCAGAAGGTGTACCGGAGCTACCGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctc ... gttgatgaagGTGGCAAGCGTTGGATTTCGCGCGGCTGAGCCACAGCACCGTCTCCTTCTTCGACGACCCGAAACCGGAGACCGTAGCGTCGCGATGGAACCGCGTCAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGAGAGGATGGGGCAGCGACCAAGCTGCAGAAGGTGTACCGGAGCTACCGGACCCGGCGCAAGCTCGCCGACTCCGCCGTCGTCGTCGAGGAGCTCTGgtaaattctccacagatcctaccccaatctttcttctcccttcccttttcttttcttttcttttactgatccttctgaagcttcttgctccggatttgtttactgttcggtttcgtggaatttattccataatctaaaaaaaactgcttgatttttaattgagatggtttgtggattggattgttgatgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT