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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaagaaaactttattttgatatttgttttgtattttctctgaaggttgaaatttgggtggtattaatatatgttcattctttcgttcttagGCAAGGTCCTTGATTCACTCGCTACCTGCTTCAGACAAATCTTTTAGCAAATTTCTGTGTGATGCACCATACTTGCCTGAGTCTATGCTTAAATTACTGG

Basic information

species Oryza sativa
transcript LOC_Os01g49940.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49940.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G466139_T01 (Zea mays), 3'ss of exon 8
gtaagcaag---aaaactttattttgatatttgttttgtattttctctgaaggttgaaatttgggtggtattaatatatgttcattctttcgttcttagGCAAGGTCCTTGATTCACTCGCTACCTGCTTCAGACAAATCTTTTAGCAAATTTCTGTGTGATGCACCATACTTGCCTGAGTCTATGCTTAAATTACTGG
||||||  |   | ||   |||| |  | | | || |  || |||| |      ||| | ||| |   | ||   || | ||  |  | || |   ||||| |||||||||||| | || || ||||||||||||||||||||||||||| || | || |||||||||||  | ||||||||| || ||| ||||||||
gtaagcctgctcataatagtattgtattgtatcttattaatgttcttt-----ctgagagttgagacatcttttcatgtcttt-tgttctcatctctagGCGAGGTCCTTGATTGATTCACTGCCTGCTTCAGACAAATCTTTTAGCAAACTTTTATGCGATGCACCATATCTACCTGAGTCTTTGTTTAGATTACTGG
















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|29628452|gb|CB633463.1|CB633463
EST:     AAAGCACCGCACCTGCTTCTAAAAATTATGAGAACTTCTTTATATCACTT                         GCAAGGTCCTTGATTCACTCGCTACCTGCTTCAGACAAATCTTTTAGCAAA
genomic: AAAGCACCTTACCTGCTTCTAAAAATTATGAGAACTTCTTTATATCACTTgtaagcaaga ... tcgttcttagGCAAGGTCCTTGATTCACTCGCTACCTGCTTCAGACAAATCTTTTAGCAAA
EST: gi|29622214|gb|CB627225.1|CB627225
EST:     AAAGCACCGCACCTGCTTCTAAAAATTATGAGAACTTCTTTATATCACTT                         GCAAGGTCCTTGATTCACTCGCTACCTGCTTCAGACAAATCTTTTAGCAAA
genomic: AAAGCACCTTACCTGCTTCTAAAAATTATGAGAACTTCTTTATATCACTTgtaagcaaga ... tcgttcttagGCAAGGTCCTTGATTCACTCGCTACCTGCTTCAGACAAATCTTTTAGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgaaggttgaaatttgggtggtattaatatatgttcattctttcgttcttagGCAAGGTCCTTGATTCACTCGCTACCTGCTTCAGACAAATCTTTTAGCAAATTTCTGTGTGATGCACCATACTTGCCTGAGTCTATGCTTAAATTACTGG
                        tattaat  putative branch site (score: 2)
                                    ttcattctttcgttct  putative PPT
                        tattaatatatgttca  TA-rich tract