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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCGGGAGTTCCGCGACCGCTACGTGATCCGCTCGGTCGACGGCGGCGGCGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAGgttaccacttactactcctcccctcaccgtgaagcgcgccgccgccggaatcgttccgtgcaaagcaaaggggaaaacaaatcgcggctatgttccggttttgttggttggtttgagtgctgggctcgtgaaccgatggtggttttactaacctgtgcatttgttcgcgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g18080.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18080.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G047894_T04 (Zea mays), 5'ss of exon 1
CTGCGGGAGTTCCGCGACCGCTACGTGATCCGCTCGGTCGACGGCGGCGGCGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAGgttaccacttactactcctcccctcaccgtgaagcgcgccgccgccggaatcgttccgtgcaaagcaaaggggaaaacaaatcgcggctatgttccggttttgttggt----tggtttgagtgctgggctcgtgaaccgatggtggttttactaacctgtgcatttgttcgcgtgcag
|||||||||||||||||||||||||||||||| ||| ||||||||| || ||| |||||||||   ||||||  ||||||| ||||||| |||||| ||||| |   | |       | |        |||  | ||  |     |||| | ||   ||    |   |  ||         || ||| | ||| | | |||  ||| |    ||| | |      ||  | |||  | |   ||||||| || |       | | | |||| | ||||
CTGCGGGAGTTCCGCGACCGCTACGTGATCCGTTCGCTCGACGGCGCCGCCGCTTTCGCCGTCCTTCGCTCCGGCGGCTCCATCCGCCCTCTCTCCCCAGgtgaagccgtgtagtgacgcgaagggttgtggcgtgcttc-----cggatttgtgttgtattgattgattggtgt----tctcccggatttgtgctgttttgattgatgttatggctcgtcaatcggcgtggtgttctggacgtggttt-acca------tcgtcttttcgtgggcag
















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|88696527|gb|CI740102.1|CI740102
EST:     CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAG                         AGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
genomic: CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAGgttaccactt ... tcgcgtgcagAGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
EST: gi|33675005|gb|CF303244.1|CF303244
EST:     CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAG                         AGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
genomic: CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAGgttaccactt ... tcgcgtgcagAGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
EST: gi|88412895|gb|CI576159.1|CI576159
EST:     CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAG                         AGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
genomic: CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAGgttaccactt ... tcgcgtgcagAGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
EST: gi|88298501|gb|CI563496.1|CI563496
EST:     CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAG                         AGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
genomic: CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAGgttaccactt ... tcgcgtgcagAGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
EST: gi|86888398|gb|CI303680.1|CI303680
EST:     CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAG                         AGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
genomic: CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAGgttaccactt ... tcgcgtgcagAGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
EST: gi|117222519|gb|CT845898.1|CT845898
EST:     CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAG                         AGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
genomic: CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAGgttaccactt ... tcgcgtgcagAGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
EST: gi|29624693|gb|CB629704.1|CB629704
EST:     CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAG                         AGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
genomic: CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAGgttaccactt ... tcgcgtgcagAGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
EST: gi|88403694|gb|CI611349.1|CI611349
EST:     CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAG                         AGGAAGCGGCTGCGGGAAGCGATTGTACGGTGTCGAAGATTTACGGAGTGG
genomic: CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAGgttaccactt ... tcgcgtgcagAGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
EST: gi|86883987|gb|CI309935.1|CI309935
EST:     CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAG                         AGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG
genomic: CGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAGgttaccactt ... tcgcgtgcagAGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGG

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: 64 (upstream exon), 66 (downstream exon)
Score: 8

CTGCGGGAGTTCCGCGACCGCTACGTGATCCGCTCGGTCGACGGCGGCGGCGCCTTCGCCGTCTCCCGCTCCAACGGCTCCCTCCGCCCCCTCTCCGCAGgttaccactt ... tcgcgtgcagAGGAAGCGGCTGCGGGAAGCGATTGTAGGGTGTCGAAGATTTACGGAGTGGCTGGCGTGATCAGGTTGCTCGCCG




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