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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctccttaggaattgccagtggtatcatcattttacttacattcatttattgttgcatttgtaatgacattttcttcttccaaaatgaattcccctccagGATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGTTCTGACTACAGCAGGATGACATGTTCCATCCACCGAGGCAAATAGATAT

Basic information

species Oryza sativa
transcript LOC_Os01g56630.1
intron # 17
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|33683149|gb|CF311388.1|CF311388
EST:     CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGAT                         GATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
genomic: CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGATgtaagttact ... tcccctccagGATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
EST: gi|88458795|gb|CI558456.1|CI558456
EST:     CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGAT                         GATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
genomic: CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGATgtaagttact ... tcccctccagGATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
EST: gi|5004229|gb|AU069378.1|AU069378
EST:     CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGAT                         GATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
genomic: CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGATgtaagttact ... tcccctccagGATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
EST: gi|89167227|gb|CI104513.1|CI104513
EST:     CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGAT                         GATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
genomic: CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGATgtaagttact ... tcccctccagGATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
EST: gi|33800537|gb|CF326139.1|CF326139
EST:     CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGAT                         GATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
genomic: CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGATgtaagttact ... tcccctccagGATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
EST: gi|88438333|gb|CI541077.1|CI541077
EST:     CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGAT                         GATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
genomic: CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGATgtaagttact ... tcccctccagGATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
EST: gi|12622135|gb|AU172348.1|AU172348
EST:     CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGAT                         GATGAACCATCCGGTGAACAAAAGGTNTAAGAATAATCTTGAATGTTGAGT
genomic: CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGATgtaagttact ... tcccctccagGATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
EST: gi|5004218|gb|AU069367.1|AU069367
EST:     CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGAT                         GATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
genomic: CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGATgtaagttact ... tcccctccagGATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
EST: gi|86497820|gb|CI140453.1|CI140453
EST:     CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGAT                         GATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
genomic: CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGATgtaagttact ... tcccctccagGATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
EST: gi|38479720|gb|CF963809.1|CF963809
EST:     CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGAT                         GATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT
genomic: CTTTCAATCCTGGTGCAATAAATCTGTTCCCTGTGGAGATTCATGTTGATgtaagttact ... tcccctccagGATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattgttgcatttgtaatgacattttcttcttccaaaatgaattcccctccagGATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGTTCTGACTACAGCAGGATGACATGTTCCATCCACCGAGGCAAATAGATAT
                                            ttcccctcc  CT-rich tract
                                    aaaatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctccttaggaattgccagtggtatcatcattttacttacattcatttattgttgcatttgtaatgacattttcttcttccaaaatgaattcccctccagGATGAACCATCCGGTGAACAAAAGGTCTAAGAATAATCTTGAATGTTGAGTTCTGACTACAGCAGGATGACATGTTCCATCCACCGAGGCAAATAGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG