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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatatagttcagaaaatacaggagcatgcagtttggaatattagttgcattgaacatttgcactgcttattctgaatatgcattctctacattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCTGAGCTGACCAATGTCAGAACAGAGGATCTCATGGTGATCTGCAGCGTAG

Basic information

species Oryza sativa
transcript LOC_Os04g58700.2
intron # 12
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|87020795|gb|CI269512.1|CI269512
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|86479202|gb|CI121835.1|CI121835
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|86834224|gb|CI343984.1|CI343984
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTTATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|86493569|gb|CI136202.1|CI136202
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|86418514|gb|CI032723.1|CI032723
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|7212756|gb|AU066074.2|AU066074
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|89192799|gb|CI050097.1|CI050097
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|86901194|gb|CI297428.1|CI297428
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|88270634|gb|CI385892.1|CI385892
EST:     TGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|88991542|gb|CI019720.1|CI019720
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACCAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|88907127|gb|CI089921.1|CI089921
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcattgaacatttgcactgcttattctgaatatgcattctctacattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCTGAGCTGACCAATGTCAGAACAGAGGATCTCATGGTGATCTGCAGCGTAG
                                      ttctctac  CT-rich tract
        aacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatatagttcagaaaatacaggagcatgcagtttggaatattagttgcattgaacatttgcactgcttattctgaatatgcattctctacattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCTGAGCTGACCAATGTCAGAACAGAGGATCTCATGGTGATCTGCAGCGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG