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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttaatttttttttgctcttaaagtttgaaattctatgaattatcctcacttaatgtgaaaagcagatatttggagacgtaatgtgtatggattcacttgttagtaacccatctcattaactgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG

Basic information

species Oryza sativa
transcript LOC_Os03g24220.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 20
gtacgttaatttttttttgctcttaaagtttgaaattctatgaattatcctcacttaatgtgaaaagcagatatttggagacgtaatgtgtatggattcacttgttagtaacccatctcattaactgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG
                    | |   | |  |   |||   |     ||| |  ||  | |  ||        ||   |  ||| ||   | |   ||  | |  |  |      ||   ||||||| |||||| ||||   |||| | |||||||||||||| |||||||| ||||||||||| ||||| ||||||||||||||||| || ||||| || |||   ||  ||
------------------cttttcggaatgcg---ttcagaggcaagtccacttttgctattcaa-------tttacaaagcgtgatacatgttatttttccttcttat------tccttttaactgcttgcagGGTGGCAATAAGGGCTCAGGTGATGGTGGGCCAACTCAAAGGGCATCAGCCTTGGCCGCTCTTTCATCTGCATTGAATCCATCGTCGCAAGGAAAACAG

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G359566_T01 (Zea mays), 3'ss of exon 5
gtacgttaatttttttttgctcttaaagtttgaaattctatgaattatcctcacttaatgtgaaaagcagatatttggagacgtaatgtgtatggattcacttgttagtaacccatctcattaactgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG
                         ||||    | || |   | | |   | ||  |  |||| |  || ||  ||          | | |||    || ||   | |   |    ||  ||||||  |||||| ||||   |||||| ||||||||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||| || ||||| || |||   ||  ||
-----------------------gtaagtcc--acttttgctattcaat-ttacaaagcgtgatactcatatggtttttccatctctctctat---ctctctctcttgcttcatgcctttttaactccttgcagGGTGGCAATAAGAGCTCAGGTGATGGTGGACCAACTCAAAGGGCATCAGCCTTGGCAGCTCTTTCATCCGCATTGAATCCATCGTCGCAAGGAAAACAG
















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|88694289|gb|CI738327.1|CI738327
EST:     GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG                         AGTGGATCTAAGAGTT
genomic: GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAGgtacgttaat ... ctgtttgcagAGTGGATCTAAGAGTT
EST: gi|58596217|gb|CK006745.1|CK006745
EST:     GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG                         AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
genomic: GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAGgtacgttaat ... ctgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
EST: gi|58677092|gb|CK065779.1|CK065779
EST:     GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG                         AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
genomic: GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAGgtacgttaat ... ctgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
EST: gi|25798468|gb|CA754429.1|CA754429
EST:     GAAATTCATTTCAGAAGAAACTTTCACTTCTTTTCGGGATGCGCTCAGAG                         AGTGGATCTAAGAG
genomic: GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAGgtacgttaat ... ctgtttgcagAGTGGATCTAAGAG
EST: gi|396941448|gb|HO188657.1|HO188657
EST:     GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG                         AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
genomic: GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAGgtacgttaat ... ctgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
EST: gi|88718464|gb|CI741974.1|CI741974
EST:     GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG                         AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
genomic: GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAGgtacgttaat ... ctgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
EST: gi|58661440|gb|CK050120.1|CK050120
EST:     GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG                         AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
genomic: GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAGgtacgttaat ... ctgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
EST: gi|33674859|gb|CF303098.1|CF303098
EST:     GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG                         AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
genomic: GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAGgtacgttaat ... ctgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
EST: gi|58674368|gb|CK063054.1|CK063054
EST:     GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG                         AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTC
genomic: GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAGgtacgttaat ... ctgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTC
EST: gi|58610643|gb|CK038355.1|CK038355
EST:     GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG                         AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
genomic: GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAGgtacgttaat ... ctgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
EST: gi|58652740|gb|CK041420.1|CK041420
EST:     GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG                         AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
genomic: GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAGgtacgttaat ... ctgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
EST: gi|56157785|gb|C26501.2|C26501
EST:     GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG                         AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
genomic: GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAGgtacgttaat ... ctgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
EST: gi|58652765|gb|CK041445.1|CK041445
EST:     GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG                         AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA
genomic: GAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAGgtacgttaat ... ctgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacgtaatgtgtatggattcacttgttagtaacccatctcattaactgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG
                         ttagtaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttaatttttttttgctcttaaagtttgaaattctatgaattatcctcacttaatgtgaaaagcagatatttggagacgtaatgtgtatggattcacttgttagtaacccatctcattaactgtttgcagAGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA