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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCACTTGGCCATTTCCCATCTGCCTCCTGGAGCTTTAGCTCTAACTCTAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctcctgtcatgttagccgtagattttggccggagcacaaggtgtttttgttgcttgctgattttacaggttgcaggttgttcttctctttcct...

Basic information

species Oryza sativa
transcript LOC_Os01g53880.7
intron # 1
splice site 5'
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

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: 67 (upstream exon), 52 (downstream exon)
Score: 12

CTTCCACTTGGCCATTTCCCATCTGCCTCCTGGAGCTTTAGCTCTAACTCTAGTTCTAGCTCTAGCTCCGGCTACGTTTGCAACTGTTGTTTATCTCCTGgtgagtcctc ... actattctagGTGGATAGCATTTAGACTCTTGAAGACTTTGAGCTAGTTAACCTTATGGAAGAAGGGTCCAACAAAAGAGAAGGACTTCCTCCTCAACTCCTAGATCTCA




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