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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcatccgttactcagccgcaaactatttctccaaagtgacgatctttttcttttttcttctggaatttgcataaccctagctaggttctcttaaagttctggcttaatttgcttaataaccaatcttataagtgagggagggggactaataacagttttttttgttctaaaaaaagttaaatttctgttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCTAGTATGTGAAACGGATCGATTTCCATTTGAGCAGCAGCAACTGCTGCTG

Basic information

species Oryza sativa
transcript LOC_Os02g21190.3
intron # 1
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|88571737|gb|CI663110.1|CI663110
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88456198|gb|CI565848.1|CI565848
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88726837|gb|CI750492.1|CI750492
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88722727|gb|CI746237.1|CI746237
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|33676405|gb|CF304644.1|CF304644
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88373318|gb|CI614654.1|CI614654
EST:     GGCGGGGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88720476|gb|CI743775.1|CI743775
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88718793|gb|CI742303.1|CI742303
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88454353|gb|CI569925.1|CI569925
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88692210|gb|CI735785.1|CI735785
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88357109|gb|CI615996.1|CI615996
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88302370|gb|CI668216.1|CI668216
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTNTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88576822|gb|CI673349.1|CI673349
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88354559|gb|CI678596.1|CI678596
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88387120|gb|CI577906.1|CI577906
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88731027|gb|CI754640.1|CI754640
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88447518|gb|CI584633.1|CI584633
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
EST: gi|88570056|gb|CI661231.1|CI661231
EST:     GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCG                         GTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT
genomic: GGCGGCGTGGGCGTGGCGATCGAGGCGAGCCGTTGCATCCGCCCTCACCGgtgagcatcc ... gttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggactaataacagttttttttgttctaaaaaaagttaaatttctgttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCTAGTATGTGAAACGGATCGATTTCCATTTGAGCAGCAGCAACTGCTGCTG
                                        tttctgtt  CT-rich tract
     taataacagttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcatccgttactcagccgcaaactatttctccaaagtgacgatctttttcttttttcttctggaatttgcataaccctagctaggttctcttaaagttctggcttaatttgcttaataaccaatcttataagtgagggagggggactaataacagttttttttgttctaaaaaaagttaaatttctgttatgtcagGTTAGATCCGTCCTCGCTAACCCAACGCCGACGAGAAGTTTGCAGTGCTCTAGTATGTGAAACGGATCGATTTCCATTTGAGCAGCAGCAACTGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT