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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgttctgatttccaaaacaaacagatatgcttccacctgtctgctgttctttcattcggttatcttctgtagtctgatttagcacacgtctag...

Basic information

species Oryza sativa
transcript LOC_Os01g33000.1
intron # 5
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|218493642|gb|FG944469.1|FG944469
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|87006610|gb|CI294993.1|CI294993
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|88222599|gb|CI222555.1|CI222555
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|33680042|gb|CF308281.1|CF308281
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|86503385|gb|CI146018.1|CI146018
EST:     AACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: AACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|29681976|gb|CB678251.1|CB678251
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|88223324|gb|CI223173.1|CI223173
EST:     CAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: CAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|33685867|gb|CF314106.1|CF314106
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|87021808|gb|CI277975.1|CI277975
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|88980037|gb|CI026327.1|CI026327
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|218482382|gb|FG946501.1|FG946501
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|88246392|gb|CI246241.1|CI246241
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|218487332|gb|FG968263.1|FG968263
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGTTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|218493643|gb|FG944470.1|FG944470
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|33810073|gb|CF330924.1|CF330924
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTA-AC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|89169887|gb|CI110246.1|CI110246
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGCCCAGAAGAAG                         ATAGCGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|22307863|gb|BQ909085.1|BQ909085
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|218498668|gb|FG952677.1|FG952677
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|33680411|gb|CF308650.1|CF308650
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|86420866|gb|CI056855.1|CI056855
EST:     ATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCTAACCGACTATAC
genomic: ATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|87028306|gb|CI112000.1|CI112000
EST:     CAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: CAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|86493867|gb|CI136500.1|CI136500
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|87018091|gb|CI275905.1|CI275905
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|86500451|gb|CI143084.1|CI143084
EST:     GGATGCATGCTTTCTCACCGTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
EST: gi|87027175|gb|CI278207.1|CI278207
EST:     GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG                         ATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC
genomic: GGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATAC

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: 72 (upstream exon), 64 (downstream exon)
Score: 22

GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgt ... tcttggccagATAACGGTGGTGCTGTAAAATACTGGGGTCCTGGTAGCAAACCGACTATACCACTATCTGTTTTTGGTATGGCTTCTTACAAGTTCAGCAATTCAATATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAGgtatgatcgttctgatttccaaaacaaacagatatgcttccacctgtctgctgttctttcattcggttatcttctgtagtctgatttagcacacgtctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa