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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaaaactgaagctactgtcacaaattcagatttatagaacactgtcacaatctttccgatgcaaaattgatgctgttccaatttttcaatgtagGTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTTGCGAATTCCAAGCAGGGACGTTTGTTCGTCGTTGTAGCACCGGTTCGCA

Basic information

species Oryza sativa
transcript LOC_Os12g08830.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G087590_T05 (Zea mays), 3'ss of exon 2
gtgaaaaactgaagctactgtcacaaattcagatttatagaacactgtcacaatctttccgatgcaaa-attgatgctgttccaatt----tttcaatgtagGTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTTGCGAATTCCAAGCAGGGACGTTTGTTCGTCGTTGTAGCACCGGTTCGCA
                                 |  |       || |  |  | |||| |||||  | | |  || |  ||  |       | |||  |||||||||||||| ||||||||||| || ||||| |||||||||||||| || || ||  ||||| | || ||  |||||||| | || || || |||||| 
------------------------------gtttccacctggtgctttttc--tgtttctgatgcggagactagtgtttctcttaccatggctccaacttagGTCCCGGTGTCCATTGCTGATCTGGGCGGCACGGAGATCGACCTGCGCTTCGCAAACCCCAAGGAAGGCCGGCTGTTCGTCATCGTGGCCCCAGTTCGCC

upper sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G087590_T04 (Zea mays), 3'ss of exon 2
gtgaaaaactgaagctactgtcacaaattcagatttatagaacactgtcacaatctttccgatgcaaa-attgatgctgttccaatt----tttcaatgtagGTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTTGCGAATTCCAAGCAGGGACGTTTGTTCGTCGTTGTAGCACCGGTTCGCA
                                 |  |       || |  |  | |||| |||||  | | |  || |  ||  |       | |||  |||||||||||||| ||||||||||| || ||||| |||||||||||||| || || ||  ||||| | || ||  |                          
------------------------------gtttccacctggtgctttttc--tgtttctgatgcggagactagtgtttctcttaccatggctccaacttagGTCCCGGTGTCCATTGCTGATCTGGGCGGCACGGAGATCGACCTGCGCTTCGCAAACCCCAAGGAAGGCCGGCT--------------------------

upper sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgaaaaactgaagctactgtcacaaattcagatttatagaacactgtcacaatctttccgatgcaaaattgatgctgttccaatttttcaatgtagGTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTTGCGAATTCCAAGCAGGGACGTTTGTTCGTCGTTGTAGCACCGGTTCGCA
||      |    |||  |||  |   |||   | ||| |      |||| |  ||||  ||| |    ||     ||||  |    |  ||| ||||| || || ||||| ||||||||||||||||||||||| ||| || | ||||| | | | ||  | || |||||||  ||  ||||||| || ||||  |
gttttgtcccttggctcttgtttc---ttcgtttctatggtttttagtcata--ctttgagattc----ttttcattgttgta----tcaaatttagGTACCTGTATCGATCGCTGATCTTGGTGGCACCGAGATTGACTTGAGATTTGCTAGTCCTAAAGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTA

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|33801711|gb|CF326727.1|CF326727
EST:     GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAG                         GTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT
genomic: GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaact ... ttcaatgtagGTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT
EST: gi|27547203|gb|CA765413.2|CA765413
EST:     GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAG                         GTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT
genomic: GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaact ... ttcaatgtagGTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT
EST: gi|33664741|gb|CF295708.1|CF295708
EST:     GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAG                         GTCCCGGTGTCGATTGCTGATCTTG
genomic: GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaact ... ttcaatgtagGTCCCGGTGTCGATTGCTGATCTTG
EST: gi|58607456|gb|CK035489.1|CK035489
EST:     GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAG                         GTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT
genomic: GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaact ... ttcaatgtagGTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT
EST: gi|33673774|gb|CF302013.1|CF302013
EST:     GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAG                         GTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT
genomic: GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaact ... ttcaatgtagGTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT
EST: gi|14571429|gb|BI118797.1|BI118797
EST:     GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAG                         GTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT
genomic: GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaact ... ttcaatgtagGTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT
EST: gi|88839416|gb|CI005204.1|CI005204
EST:     GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAG                         GTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT
genomic: GGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaact ... ttcaatgtagGTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT
EST: gi|88965272|gb|CI009308.1|CI009308
EST:     TTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAG                         GTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT
genomic: TTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaact ... ttcaatgtagGTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgtcacaatctttccgatgcaaaattgatgctgttccaatttttcaatgtagGTCCCGGTGTCGATTGCTGATCTTGGTGGCACCGAGATCGACCTGCGGTTTGCGAATTCCAAGCAGGGACGTTTGTTCGTCGTTGTAGCACCGGTTCGCA
                         aattgat  putative branch site (score: 4)
                                          tttttc  putative PPT
                                        aatttttcaatgta  TA-rich tract