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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcgtctcgccttctccttctccggcgatctgtccctctctcgctccgttaatttcttgatcggatttctcgctgtctctccttgcagCTCGTGGTGATCGCCGGCATCGTGTGGAACCCGCCGACCTCCTGCGC

Basic information

species Oryza sativa
transcript LOC_Os10g35644.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35644.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G822098_T03 (Zea mays), 3'ss of exon 2
---------------------------------------------gtctcgtctcgccttctccttctccggcgatctgtccctctctcgctccgttaatttcttgatcggatttctcgctgtctctc-cttgcagCTCGTGGTGATCGCCGGCATCGTGTGGAACCCGCCGACCTCCTGCGC
                                             |   ||  |  |  |||  |  ||| || |  |     ||     | | |   |      || ||     ||   | | |  | | ||||||||||||||||||||||||| ||||||||||||||||||||||||||
gtatactgcctgcgcgcaccgcgcctgccgccgccattggctgctgctgcgggtt-ctatctaatgttcctgcaagattcggttcgacgacccggccgacccaccgaccgacaccctttttttttggcgcctgcagCTCGTGGTGATCGCCGGCATTGTGTGGAACCCGCCGACCTCCTGCGC

upper sequence: LOC_Os10g35644.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G822098_T05 (Zea mays), 3'ss of exon 2
---------------------------------------------gtctcgtctcgccttctccttctccggcgatctgtccctctctcgctccgttaatttcttgatcggatttctcgctgtctctc-cttgcagCTCGTGGTGATCGCCGGCATCGTGTGGAACCCGCCGACCTCCTGCGC-----------------------------------------------------
                                             |   ||  |  |  |||  |  ||| || |  |     ||     | | |   |      || ||     ||   | | |  | | ||||||||||||||||||||||||| ||||||||||||||||||||||||||                                                     
gtatactgcctgcgcgcaccgcgcctgccgccgccattggctgctgctgcgggtt-ctatctaatgttcctgcaagattcggttcgacgacccggccgacccaccgaccgacaccctttttttttggcgcctgcagCTCGTGGTGATCGCCGGCATTGTGTGGAACCCGCCGACCTCCTGCGCGTGAGTTCGCCTTCGCTCCGCTTCATGCCTGCATTGCATTCGCATCTTCTGTG
















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|29689642|gb|CB685917.1|CB685917
EST:     GCATGTTCCTCGCCCGCTACGACGACAGCCCCGCCGGCAAGTTCGACGAG                         CTCGTGGTGATCGCCGGCATCGTGTGGAACCCGCCGACCTCCTGCGC
genomic: GCATGTTCCTCGCCCGCTACGACGACAGCCCCGCCGGCAAGTTCGACGAGgtctcgtctc ... ctccttgcagCTCGTGGTGATCGCCGGCATCGTGTGGAACCCGCCGACCTCCTGCGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctctctcgctccgttaatttcttgatcggatttctcgctgtctctccttgcagCTCGTGGTGATCGCCGGCATCGTGTGGAACCCGCCGACCTCCTGCGC
                     tcttgat  putative branch site (score: 4)
                                tttctcgctgtctctc  putative PPT
               ttaatttctt  TA-rich tract