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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaactgaagctactgtcacaaattcagatttatagaacactgtcacaatctttccgatgcaaaattgatgctgttccaatttttcaatgtag

Basic information

species Oryza sativa
transcript LOC_Os12g08830.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g08830.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G087590_T05 (Zea mays), 5'ss of exon 2
GAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaactgaagctactgtcacaaattcagatttatagaacactgtcacaatctttccgatgcaaaattgatgctgttccaatttttcaatgtag
|||||| ||||| ||||||||||||||||||||||| || |||||||| |||||||| ||||| || ||||||||||||||||  || |||||||| |||||    | |||    | || |  |   ||| |||    |||  | |||  |  |      |   | || ||                          
GAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCTGGGATGAGgtttccacctgg---tgctttttctgtttctgatgcggagactagtgtttctcttaccatggctccaacttag------------------------

upper sequence: LOC_Os12g08830.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA04G42010.1 (Glycine max), 5'ss of exon 2
GAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaactgaagctactgtcacaaattcagatttatagaacactgtcacaatctttccgatgcaaaattgatgctgt---tccaattt--ttcaatgtag--
||| || || || ||||| || || ||||| || |||||||| ||||||||||| || || ||||| |||||||||| ||| | ||| |  |||||||||||||    || ||  |  | ||    | | | | ||  | || | | |   | | |         || | | |||   |   ||| ||||   ||  | | |  
GAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgat--gcttaa--tgatctcttctagttaaagttggaaaaaagtttttaagtatacagtggaaaagactaatgaaataactcctatttgtctcgttttgggt

upper sequence: LOC_Os12g08830.2 (Oryza sativa), 5'ss of exon 2
lower sequence: AT1G77090.1 (Arabidopsis thaliana), 5'ss of exon 2
GAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaactgaagctactgtcacaaattcagatttatagaacactgtcacaatctttccgatgcaaaattgatgctgttccaatttttcaatgtag
||||||||||||||| |||||||| ||||| || || ||||| ||||| ||||| || || || || |||  |||    |||| | | |  ||| | |||||      |    |||  |||  |   |||   | ||| |      |||| |  ||||  ||| |    |   || |||  ||| |||         
GAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAATGAGgttttgtcccttggctcttgtttc---ttcgtttctatggtttttagtcata--ctttgagattcttt-tcattgttgtatcaaatttag-------

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

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaactgaagctactgtcacaaattcagatttatagaacactgtcacaatctttccgatgcaaaattgatgctgttccaatttttcaatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA