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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGCCCGATAAAGCAAAACCCTGGGAGCTGATGGAAGTCCTAAATGCTCAGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatccaacttgttcttgcgtagtttgcacttctcttcatgtaatcgttcagaaggctaacaacatttatatacag

Basic information

species Oryza sativa
transcript LOC_Os01g15020.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 18
AAGGCCCGATAAAGCAAAACCCTGGGAGCTGATGGAAGTCCTAAATGCTCAGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatccaacttgttcttgcgtagtttgcacttctcttcatgtaatcgttcagaaggctaacaacatttatatacag
|| ||| |||||||||||||| ||||| || |||||||| |||||| | |||||||||| |||||| ||||||||||||||||||||||||||||| |||||| |       || |  |   |||  || |||      ||||| ||| || ||   |  | ||| | ||| | |||||
AAAGCCTGATAAAGCAAAACCTTGGGAACTAATGGAAGTTCTAAATCCCCAGCAATGCCATGTAGCAACAATGCCAGAAACTCCAGACCAAGCCAGAAAGgttgg------tttttcttgatgtatgtttcacacggtatcatggaat-gtgcaagggtttcacatcttttgtgtacag

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G416836_T01 (Zea mays), 5'ss of exon 16
AAGGCCCGATAAAGCAAAACCCTGGGAGCTGATGGAAGTCCTAAATGCTCAGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatccaacttgttct-tgcgtagtttgcacttctcttcatgtaatcgttcagaag----gctaacaacatttatatacag----------------
|| | | |||||||||||| | | ||| || ||||| || |||||| | || |||||||||||||| ||||||||||||||||| || || || || ||||||||      |||| | |  |  |         || | || |   || |   ||| ||    ||| |  | ||| ||| | |                 
AAAGTCTGATAAAGCAAAAGCTTCGGAACTAATGGAGGTTCTAAATCCCCAACAATGCCGTGTAGCAACAATGCCAGAAACTCCCGATCAGGCTAGAAAGgtttggattttcttgatgtacgtttcacacttgttttttttaaacgaaccaggcaggagagctgctgattatattaataaagaagtggttcagatcggac
















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|58595855|gb|CK006383.1|CK006383
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|58679784|gb|CK068471.1|CK068471
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|58661141|gb|CK049821.1|CK049821
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|29625565|gb|CB630576.1|CB630576
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|58606459|gb|CK034492.1|CK034492
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|58601227|gb|CK011755.1|CK011755
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACGAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|29626131|gb|CB631142.1|CB631142
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|29619450|gb|CB624462.1|CB624462
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|29630393|gb|CB635402.1|CB635402
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
EST: gi|29625310|gb|CB630321.1|CB630321
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCT
EST: gi|33675602|gb|CF303841.1|CF303841
EST:     AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAG                         GTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT
genomic: AGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatcca ... ttatatacagGTTGTCAGACTTCTGTACACAAATTCTGGTGTTGGCTTGCTAGCACTTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGCCCGATAAAGCAAAACCCTGGGAGCTGATGGAAGTCCTAAATGCTCAGCAATGCCGTGTAGCTACAATGCCAGAAACTCCAGACCAAGCCAGCAAGgtttgatccaacttgttcttgcgtagtttgcacttctcttcatgtaatcgttcagaaggctaacaacatttatatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG