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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccccatataaacgtttgaaactaaaaacaagtgatatatcctcctcttcacgaatgatcaacatttgaaaaaaaaaaaaactaagcatgggcatgttgttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGGAGCCTGGAGGATGTGTTAGCAAGGGCCTGCCCGGAGAGAAGTAGATTGT

Basic information

species Oryza sativa
transcript LOC_Os01g49060.1
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|88517974|gb|CI445628.1|CI445628
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|86546165|gb|CI186371.1|CI186371
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|88521732|gb|CI448399.1|CI448399
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|88903649|gb|CI089187.1|CI089187
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|88506055|gb|CI433561.1|CI433561
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|88474329|gb|CI411600.1|CI411600
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|88322408|gb|CI540376.1|CI540376
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|10931454|gb|AU161728.1|AU161728
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|88477739|gb|CI415010.1|CI415010
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|89196186|gb|CI397188.1|CI397188
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|88433688|gb|CI557424.1|CI557424
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|86594939|gb|CI258193.1|CI258193
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|9866010|gb|AU101760.1|AU101760
EST:     CATNTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|88471934|gb|CI409205.1|CI409205
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|88286930|gb|CI520240.1|CI520240
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|88509990|gb|CI437496.1|CI437496
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|88964723|gb|CI070069.1|CI070069
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|109712884|gb|CI105492.1|CI105492
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
EST: gi|29681676|gb|CB677951.1|CB677951
EST:     CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAG                         CAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG
genomic: CATGTGTCCAATCTGAACTTGCAGCCCTCTACATTCTCTGGATATCAAAGgtaaccccat ... ttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatcaacatttgaaaaaaaaaaaaactaagcatgggcatgttgttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGGAGCCTGGAGGATGTGTTAGCAAGGGCCTGCCCGGAGAGAAGTAGATTGT
      aacatttgaaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccccatataaacgtttgaaactaaaaacaagtgatatatcctcctcttcacgaatgatcaacatttgaaaaaaaaaaaaactaagcatgggcatgttgttacttgcagCAAGTTCCGGCTGTGAAACTAAAGCTGGAAGAAAGGCTACATTCGTTGGGGAGCCTGGAGGATGTGTTAGCAAGGGCCTGCCCGGAGAGAAGTAGATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT