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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaacttgactgctgttattctttacctattattcttttacatattcttctctttgattaactgtttggattgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCACTTGATGCTTTCCCAGCTTTG

Basic information

species Oryza sativa
transcript LOC_Os01g49940.2
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49940.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G466139_T01 (Zea mays), 3'ss of exon 19
gtactaacttgactgctgttattctttacctattattcttttacatattcttctctttgattaactgtttggattgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCACTTGATGCTTTCCCAGCTTTG
||||  || | || |||| ||||       |     |||||       | |||   |||  |||     || | |||  || |||||||||   |||||||||| |||||||| |||||||||||||||||||| ||||||||||| || ||||||
gtacatacattaccgctgctattggagttttgcgtgtcttta------ttttcatcttgcctaataagctgaactgtcttgcagGTTGACAGAATACCAATTCCTCTTCTTTTTATGAGAACAGTTATTCAAGCGCTTGATGCTTTTCCTGCTTTG

upper sequence: LOC_Os01g49940.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA04G09480.1 (Glycine max), 3'ss of exon 21
gtactaacttgactgctgttattctttacctattattcttttacatattcttctctttgattaactgtttggattgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCACTTGATGCTTTCCCAGCTTTG
    |||   || |     ||||    |   ||  |   ||||| |    |  |  | | |  | |||||  ||| |     |||||||  |    ||  | || || ||||||||||||||||||||||| ||| |||||||||| || ||  ||
---gtaaggagattctgtgtattgggcaataatactggatttacttcaaatcttaatggctatattgtttaaattttc----agGTTGATCAAACTCCGCTGCCTCTACTTTTCATGAGAACAGTTATTCAGGCAATTGATGCTTTTCCTGCAATG

upper sequence: LOC_Os01g49940.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA06G09580.1 (Glycine max), 3'ss of exon 20
gtactaacttgactgctgttattctttacctattattcttttacatattcttctctttgattaactgtttggattgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCACTTGATGCTTTCCCAGCTTTG
    |||   || |      |||    |   ||  |   ||||| |    |  || | | |  | |||||  ||| |     |||||||  |    ||| | || || ||||||||||||||||||||||| ||| |||||||||| || ||  ||
---gtaaggagattcagtgcattggccaataatactggatttacttcaaatcttcatggctctattgtttaaattttc----agGTTGATCAAACTCCACTGCCGCTACTTTTCATGAGAACAGTTATTCAGGCAATTGATGCTTTTCCTGCACTG

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|29644685|gb|CB649692.1|CB649692
EST:     AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTG                         GTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
genomic: AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTGgtactaactt ... tgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
EST: gi|27577961|gb|CB000656.1|CB000656
EST:     AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTG                         GTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
genomic: AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTGgtactaactt ... tgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
EST: gi|87004655|gb|CI300977.1|CI300977
EST:     CACTGAATAAATTG                         GTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
genomic: CACTGAATAAATTGgtactaactt ... tgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
EST: gi|163925961|gb|EG714989.1|EG714989
EST:     AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTG                         GTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
genomic: AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTGgtactaactt ... tgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
EST: gi|33794819|gb|CF323289.1|CF323289
EST:     AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTG                         GTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
genomic: AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTGgtactaactt ... tgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
EST: gi|300215772|gb|HO088398.1|HO088398
EST:     AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTG                         GTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA
genomic: AGCGCACGGTATTTACTCAGCAAGTTTTGGAGAAGTCACTGAATAAATTGgtactaactt ... tgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattattcttttacatattcttctctttgattaactgtttggattgttatgtagGTTGACAATGTACCAATTCCACTTCTTTTCATGAGAACAGTTATTCAAGCACTTGATGCTTTCCCAGCTTTG
                             gattaac  putative branch site (score: 2)
     attcttttacatatt  TA-rich tract