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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgcgtgcgctctcactagattttttgtttcaacttgtatcgtatttcttcattttttttacaccttgcacttttcctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATTGGTGGTACGGCGCCTTAGCACCTGTAATAATGGTAATCCATATGTTCGG

Basic information

species Oryza sativa
transcript LOC_Os11g17610.1
intron # 10
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|88530840|gb|CI459265.1|CI459265
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAG                         CTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
EST: gi|88271211|gb|CI387264.1|CI387264
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAG                         CTTAGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
EST: gi|86427132|gb|CI072229.1|CI072229
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAG                         CTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
EST: gi|86485836|gb|CI128469.1|CI128469
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAG                         CTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
EST: gi|88506305|gb|CI433811.1|CI433811
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAG                         CTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
EST: gi|88485472|gb|CI422743.1|CI422743
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCCAAAG                         CTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
EST: gi|88901816|gb|CI374424.1|CI374424
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAG                         CTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
EST: gi|86598669|gb|CI355286.1|CI355286
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAG                         CGTGGAAGATATATCCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
EST: gi|88479727|gb|CI416998.1|CI416998
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAG                         CTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
EST: gi|86490045|gb|CI132678.1|CI132678
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAG                         CTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
EST: gi|88540023|gb|CI470031.1|CI470031
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAG                         CTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
EST: gi|86883137|gb|CI314316.1|CI314316
EST:     CAAGAGATCAACTTTCACCACTGACATCATTGAGTTACTGGGGCAAAAGG                         CTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCAT
genomic: CAAGAGATCAACTGTCACCACTGACATCATTGAGTTACT-GGGCAAAA-Ggtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCAT
EST: gi|88488080|gb|CI425351.1|CI425351
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAG                         CTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
EST: gi|86887072|gb|CI325887.1|CI325887
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAG                         CTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
EST: gi|218499213|gb|FG962191.1|FG962191
EST:     AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTCCTGGGCAAAAG                         CTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT
genomic: AACAAGAGATCAACTGTCACCACTGACATCATTGAGTTACTGGGCAAAAGgtccgcgtgc ... cctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacttgtatcgtatttcttcattttttttacaccttgcacttttcctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATTGGTGGTACGGCGCCTTAGCACCTGTAATAATGGTAATCCATATGTTCGG
              tttcttcatttttttt  CT-rich tract
            tatttcttcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgcgtgcgctctcactagattttttgtttcaacttgtatcgtatttcttcattttttttacaccttgcacttttcctcttgcagCTTGGAAGATATATGCCCTGCTGGTCATTAGTTTAGATCTTTACCATCATTGGTGGTACGGCGCCTTAGCACCTGTAATAATGGTAATCCATATGTTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG