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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggatatgataaaaacgctccattattaaaaccattccgtttcttggggaaatcatcattctaatgataatgctttgctttgtgacattgcagCCTGGAGAAAACACTAAGAAAGTTGTCTTGTATAACCACCGGCGATAGTATCATGGTAGCTTACAACAACAAACAATACTACATTGACATTGTTGAAACA

Basic information

species Oryza sativa
transcript LOC_Os04g48770.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g48770.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G114220_T01 (Zea mays), 3'ss of exon 7
gtgaggatatgataaaaacgctccattatt--------aaaaccattccgtttcttggggaaatcatcattctaatgataatgctttgctttgtgacattgcagCCTGGAGAAAACACTAAGAAAGTTGTCTTGTATAACCACCGGCGATAGTATCATGGTAGCTTACAACAACAAACAATACTACATTGACATTGTTGAAACA
|| |||| |   | ||||   |||  || |        |||  |  | | |||||   || | |   | || | ||  | ||   ||||| |   |  || |||| |||| |||||  ||||||| || || ||  ||||||| || || || ||||||||||| ||||||||||||||||| || ||||| ||||||||||||
gtaaggaaacctttaaaattgtcctataatgatcttgaaaattctcttcatttctcttggcattaggcgttatcattctcattacttgctgttaaattttccagCTTGGAAAAAACTTTAAGAAATTTCTCCTGCTTAACCACGGGAGACAGCATCATGGTAGCCTACAACAACAAACAATATTATATTGATATTGTTGAAACA
















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|88397598|gb|CI684525.1|CI684525
EST:     TTGCAGCCTCACACAACTGACTTTTGGGACATCTCAAATCCGAAGGCCAT                         CCTGGAGAAAACACTAAGAAACTTCTCTTGTTTAACCACCGGCGATAGTAT
genomic: TTGCAGCCTCACACAACTGACTTTTTGGACATCTCAAATCCGAAGGCCATgtgaggatat ... gacattgcagCCTGGAGAAAACACTAAGAAAGTTGTCTTGTATAACCACCGGCGATAGTAT
EST: gi|427856|gb|D23997.1|D23997
EST:     CACAACTGACTTTTTGGACATCTCAAATCCGAA-GCCAT                         CCTGGAGAAAACACTAAGAAACTTCTCTTGTTTAACCACCGGCGATAGTAT
genomic: CACAACTGACTTTTTGGACATCTCAAATCCGAAGGCCATgtgaggatat ... gacattgcagCCTGGAGAAAACACTAAGAAAGTTGTCTTGTATAACCACCGGCGATAGTAT
EST: gi|58687667|gb|CK076354.1|CK076354
EST:     TTGCAGCCTCACACAACTGACTTTTTGGACATCTCAAATCCGAAGGCCAT                         CCTGGAGAAAACACTAAGAAACTTCTCTTGTTTAACCACCGGCGATAGTAT
genomic: TTGCAGCCTCACACAACTGACTTTTTGGACATCTCAAATCCGAAGGCCATgtgaggatat ... gacattgcagCCTGGAGAAAACACTAAGAAAGTTGTCTTGTATAACCACCGGCGATAGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcttggggaaatcatcattctaatgataatgctttgctttgtgacattgcagCCTGGAGAAAACACTAAGAAAGTTGTCTTGTATAACCACCGGCGATAGTATCATGGTAGCTTACAACAACAAACAATACTACATTGACATTGTTGAAACA
                    ttctaat  putative branch site (score: 2)
                   attctaatgataat  TA-rich tract