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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatattagtctcttaattctgaattaattcctcatctgatcgctcaagtttgatctgctgatcgattttgggttttgaatcaaatcattgcatgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG

Basic information

species Oryza sativa
transcript LOC_Os02g02560.1
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|88370657|gb|CI590235.1|CI590235
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGT-CGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88401596|gb|CI588537.1|CI588537
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88417942|gb|CI596619.1|CI596619
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88371009|gb|CI595121.1|CI595121
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88294742|gb|CI604614.1|CI604614
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88377046|gb|CI597830.1|CI597830
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGGCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88426949|gb|CI601910.1|CI601910
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88433235|gb|CI591675.1|CI591675
EST:     GAGAAGCTCGCCAAGCTGTGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCTGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88415469|gb|CI589061.1|CI589061
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|3090613|gb|C93600.1|C93600
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88391611|gb|CI600800.1|CI600800
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88433205|gb|CI591645.1|CI591645
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCTGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88389523|gb|CI600692.1|CI600692
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88387609|gb|CI585312.1|CI585312
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88314463|gb|CI604947.1|CI604947
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGCTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCG-TCGCCCGCTACCTCAG
EST: gi|88314385|gb|CI604869.1|CI604869
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88300805|gb|CI589797.1|CI589797
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|66922584|gb|CX109432.1|CX109432
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88434257|gb|CI589322.1|CI589322
EST:     AGAAGCTCGCCAAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: AGAAGCTCGCC-AAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88433214|gb|CI591654.1|CI591654
EST:     AGAAGCTCGCCAAGCTTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: AGAAGCTCGCCAAGC-TGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88389649|gb|CI603148.1|CI603148
EST:     GAGAAACTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88370364|gb|CI587754.1|CI587754
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
EST: gi|88405310|gb|CI586131.1|CI586131
EST:     GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAG                         TGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
genomic: GAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 70 (upstream exon), 72 (downstream exon)
Score: 50

GTCTCATCAGATCAGCGTGAAGCAGCGGCAAGAACACAAAAATGGCGGACGAGAAGCTCGCCAAGCTGCGTGAAGCCGTCGCCGGCCTCTCGCAGATCAGgtaattatat ... atgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttgatctgctgatcgattttgggttttgaatcaaatcattgcatgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG
         tgctgat  putative branch site (score: 50)
                          ttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattatattagtctcttaattctgaattaattcctcatctgatcgctcaagtttgatctgctgatcgattttgggttttgaatcaaatcattgcatgcgtgcagTGACAACGAGAAGTCCGGGTTCATCAGCCTCGTCGCCCGCTACCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT