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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttaatttacctttttgttggcaatacaatatatatctcattttattctttcatgtttctattagaatcattactctctttttacatcactataactctatccttatgccaacaaactgaaaagacgcttgttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTGCGACGGCCATCACCTTCTGAGAAATGCTTCACCTAGTGAACCAGGAGCT

Basic information

species Oryza sativa
transcript LOC_Os10g38980.1
intron # 7
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|88466556|gb|CI532363.1|CI532363
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGGTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|116875026|gb|EC365534.1|EC365534
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|116875033|gb|EC365541.1|EC365541
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|88522247|gb|CI449992.1|CI449992
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|88554422|gb|CI484602.1|CI484602
EST:     AAATGTCATTGCCTGCATGGCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|88483086|gb|CI420357.1|CI420357
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|29640850|gb|CB645857.1|CB645857
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|88526257|gb|CI453313.1|CI453313
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGGTCAG                         TAGGTATCTCCAGGACTGGAATTGGAATTTTGGCGCCTCTTGTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|88552657|gb|CI482685.1|CI482685
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTGTATTCTTT
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAA-GCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTT
EST: gi|86504223|gb|CI146856.1|CI146856
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|88522672|gb|CI449489.1|CI449489
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGGATTTTGGCGCCTCTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|86500464|gb|CI143097.1|CI143097
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         --G-TATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|88555795|gb|CI486077.1|CI486077
EST:     AAATGTCATTGCCTCCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGGAATTTTGGCNCCTCTTGTATTCTTT
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATT-GGAATTTTGGCGCCTCTTCTATTCTTT
EST: gi|88283178|gb|CI404624.1|CI404624
EST:     AGAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
genomic: AGAAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|88537263|gb|CI465088.1|CI465088
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTTTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|29666973|gb|CB663248.1|CB663248
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         --G-TATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|88546745|gb|CI474415.1|CI474415
EST:     AAATGTCATGGCCTGCATTGCCTGTCGGGCCAACATTTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTGTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|88482069|gb|CI419340.1|CI419340
EST:     TCATTGCCTGCATTCCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTGTATTCTTTG
genomic: TCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|86861783|gb|CI329548.1|CI329548
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
EST: gi|88555527|gb|CI485792.1|CI485792
EST:     AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAG                         TAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG
genomic: AAATGTCATTGCCTGCATTGCCTGTCGCGCCAACATCTGGAAGCTCAGgtacttaatt ... gttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcactataactctatccttatgccaacaaactgaaaagacgcttgttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTGCGACGGCCATCACCTTCTGAGAAATGCTTCACCTAGTGAACCAGGAGCT
    ctataac  putative branch site (score: 3)
     tataact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttaatttacctttttgttggcaatacaatatatatctcattttattctttcatgtttctattagaatcattactctctttttacatcactataactctatccttatgccaacaaactgaaaagacgcttgttatggcagTAGGTATCTCCAGAACTGGAATTGGAATTTTGGCGCCTCTTCTATTCTTTGCGACGGCCATCACCTTCTGAGAAATGCTTCACCTAGTGAACCAGGAGCT

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