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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACTTCAAATGGATCGTCAGGCGCCACAGAAGATTAAAAAACCTACTGAGAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttccatagttgctttatttgaattctacatcaatttgtggttgactttgaagatttacattccctttgtggcaattatag

Basic information

species Oryza sativa
transcript LOC_Os02g47220.3
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47220.2 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 17
AAACTTCAAATGGATCGTCAGGCGCCACAGAAGATTAAAAAACCTACTGAGAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttcc-----atagttgctttatttgaattct-acatcaatttgtggttgactttgaagatttacattccctttgtggcaattatag
|||||| |  ||||||||||| |  | || |||  ||  || || || |||| ||  ||||||||||| || ||||| ||||| ||  ||||||||||||||||||||||     |  ||||| ||     | | ||  ||  || | |   |||| |||  |||  |   || ||||||    |||| |||
AAACTTAATTTGGATCGTCAGCCATCCCAAAAGGGTATGAAGCCAACCGAGACTAGCAATAAACTAACTACGAATCGGGTACCAGCTCGGAATAGCCCAGgcaagtttcctatatagggttgcattgcccaactccttgcacgaaatgggttttgattttttagaactttttttcctttg---gaattgtag
















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|89168902|gb|CI020983.1|CI020983
EST:     GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAG                         GTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
genomic: GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttcc ... gcaattatagGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
EST: gi|88841164|gb|CI080618.1|CI080618
EST:     GAATAGCCCAG                         GTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
genomic: GAATAGCCCAGgcaagtttcc ... gcaattatagGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
EST: gi|38481521|gb|CF965610.1|CF965610
EST:     GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAG                         GTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
genomic: GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttcc ... gcaattatagGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
EST: gi|88288597|gb|CI663386.1|CI663386
EST:     GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAG                         GTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
genomic: GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttcc ... gcaattatagGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
EST: gi|58683626|gb|CK072313.1|CK072313
EST:     GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAG                         GTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
genomic: GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttcc ... gcaattatagGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
EST: gi|88571807|gb|CI663180.1|CI663180
EST:     GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAG                         GTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
genomic: GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttcc ... gcaattatagGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
EST: gi|117220171|gb|CT852510.1|CT852510
EST:     GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAG                         GTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
genomic: GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttcc ... gcaattatagGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
EST: gi|58673432|gb|CK062118.1|CK062118
EST:     GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAG                         GTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
genomic: GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttcc ... gcaattatagGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
EST: gi|29625052|gb|CB630063.1|CB630063
EST:     GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAG                         GTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
genomic: GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttcc ... gcaattatagGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
EST: gi|163918501|gb|EG711431.1|EG711431
EST:     GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAG                         GTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
genomic: GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttcc ... gcaattatagGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
EST: gi|88327669|gb|CI657403.1|CI657403
EST:     GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAG                         GTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA
genomic: GAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttcc ... gcaattatagGTCACCCTGTATTAAGGCATTCACGCAGTTTACCTGAAACTGGCCGGGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACTTCAAATGGATCGTCAGGCGCCACAGAAGATTAAAAAACCTACTGAGAGTAATAATAAACTAACCACTAATCGAGTACCTGCAAGGAATAGCCCAGgcaagtttccatagttgctttatttgaattctacatcaatttgtggttgactttgaagatttacattccctttgtggcaattatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA