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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggtgcttttctccagcctaagttgagtgtagaactaaactttttaaggagttggttgaactcctctcattgccttcaaactcttcctactattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAAGAAGGGTCCAACAAAAGAGAAGGACTTCCTCCTCAACTCCTAGATCTCA

Basic information

species Oryza sativa
transcript LOC_Os01g53880.1
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|33655776|gb|CF278390.1|CF278390
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|29675173|gb|CB671448.1|CB671448
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|88300117|gb|CI582351.1|CI582351
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|88355017|gb|CI615898.1|CI615898
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|4714666|gb|AU055783.1|AU055783
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|13420517|gb|AU174607.1|AU174607
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|4715020|gb|AU056137.1|AU056137
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|88825683|gb|CI776248.1|CI776248
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|58662812|gb|CK051498.1|CK051498
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|29672642|gb|CB668917.1|CB668917
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|29679027|gb|CB675302.1|CB675302
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|88762435|gb|CI771991.1|CI771991
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTNACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|66913500|gb|CX100348.1|CX100348
EST:     AGTTCTAGACTCTAGCTCCGGCTACGTATGCAACTGTAGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: AGTTCTAG-CTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|88367358|gb|CI566324.1|CI566324
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|33682755|gb|CF310994.1|CF310994
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|58658772|gb|CK047452.1|CK047452
EST:     TAGTTCTAGCTCTAGCTCCGGCTACG-TTGCAGCTG-TGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|88741612|gb|CI765120.1|CI765120
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTNACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|29675175|gb|CB671450.1|CB671450
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
EST: gi|33655772|gb|CF278386.1|CF278386
EST:     TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTG                         GTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA
genomic: TAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaggagttggttgaactcctctcattgccttcaaactcttcctactattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAAGAAGGGTCCAACAAAAGAGAAGGACTTCCTCCTCAACTCCTAGATCTCA
                                     ctcttcctactattct  CT-rich tract
                                            tactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggtgcttttctccagcctaagttgagtgtagaactaaactttttaaggagttggttgaactcctctcattgccttcaaactcttcctactattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAAGAAGGGTCCAACAAAAGAGAAGGACTTCCTCCTCAACTCCTAGATCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC