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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctttttatcaattcattcaccatctttacttaccaggcaatctgtaaaaattttcaactgcaatagcaataatgccgttttctggttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGCAGCAAATTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTTGAG

Basic information

species Oryza sativa
transcript LOC_Os02g10070.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 10
------------------------gtagctttttatcaattcatt--------caccatctttacttacc--aggcaa---tctgtaaaaattttcaactgcaatagcaataatgccgttttctggttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGCAGCAAATTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTTGAG
                          |  |||| ||  | | | |        || ||  |  | ||     ||  ||   | | || | |||||  | |  |  |  |||| |  | ||   | ||| | ||||| || |||||||  |||||| | |||| ||||||| || | ||||||||||| |||||||| ||||| |||||||| ||||| || ||||  ||||| |||
gtagcttttgttcagatatatgcttcaatttttaatgcaattactggaggtcgcatcacttgaattttgtgaagttaaagttgtttacagattttagaattaatgattaatatt--ctttcatttgttgtttgaagAATTTTCAAGGATGGGAAATCAATAGAAGCTGATGATTCTCTGGATTATGCGGCAAATTTATCACATATGCTTGGTTTTGACGACCCCAGGATGCTGGAG

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 11
--------------------------------------------------------gtagctttttatcaattcattcac---catctttacttaccaggcaatc-tgtaaaaattttcaactgcaatagcaataatgccgtttt-ctggttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGCAGCAAATTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTTGAG
                                                          |  |||||    |   | |      ||  | |  ||   |  ||      |  |||||||  | |  |||   ||| ||   ||||   | ||| | ||||| || |||||| | |||||| | |||| ||| |||||| |  |||| ||||| |||||||| |||||||||||||| ||||| || || |||||||| |||
gtagcttttgtttagaaatgtttcatttttaatgcacttactggtggtgacatcagtcaattttttcctgaactagttgtgtacagatgtttttttgaaacagctgcattcaaattttagaat-taatg--aattatattgtttcatttgttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGCGGCAAATTTCTCACACATGCTTGGTTTTGACGACCCAAAAATGCTGGAG

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 12
------------------gtagcttt--ttatcaattcattcaccatcttta-cttaccaggcaatctgtaaa-----aattttcaac------tgcaatagc--aataatgccgtttt-ctggttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGCAGCAAATTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTTGAG
                   | ||||   || | ||| || | ||      |  | |  |  | | | ||||||     |||| || ||      |  |||     ||||||    |||   | ||||| ||||| || |||||||| |||||| | |||| | |||| ||| | ||||||||||| |||||||| |||||||||||||| |||||||| || |||||||| |||
gtagcttttgttcagacatttgcttcaatttttaatgcaattactggaggtggcatcactcgaattttgtaaagttaaaattgtctacaaattttagaattattgaataatattatttcatttgttctttgaagAATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGCGGCAAATTTCTCACACATGCTTGGTTTTGATGACCCTAAAATGCTGGAG

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 10
gtagctttttatcaattcattcaccatctttactt------accaggcaatctgtaaaaattttcaactgc----aatagcaat----aatgccgttttctggttctc--tgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGCAGCAAATTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTTGAG
||    |||||  |  |  | ||     ||||  |      || ||  ||| |    | ||||||   |      | |   | |    |||| |   ||||  ||| |  || ||||| | |||||  || |  |  ||  ||   ||| || |  |||||||||  |||||||||||||||||||| || ||||||  |||  | |||   |||
gttaaattttaggatcttttccaatgcttttagcttcctggactagttaattttcttagattttcctttcttcagagtgttatttttcaatgtc-cattctaattcacattgcagGATGTACAAGGATGGTAGCATCATTCCATTAGATGATTCTTTGGATTATGGTGCAAATTTTTCACACATGCTGGGATTTGATAGTCCTCAGATGAAAGAG

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|58695418|gb|CK084105.1|CK084105
EST:     TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG                         GATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGC
genomic: TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAGgtagcttttt ... ttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGC
EST: gi|218505577|gb|FG949556.1|FG949556
EST:     TTAAATTTGATA-CTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG                         GATATTCAAGGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATG
genomic: TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAGgtagcttttt ... ttctctgaagGATATTCAA-GGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATG
EST: gi|29614058|gb|CB619071.1|CB619071
EST:     TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG                         GATATTCAAGGGAAGGGAAAACTATAG
genomic: TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAGgtagcttttt ... ttctctgaagGATATTCAAGGGA-GGGAAAACTATAG
EST: gi|33794400|gb|CF323084.1|CF323084
EST:     TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG                         GATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGC
genomic: TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAGgtagcttttt ... ttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGC
EST: gi|14571277|gb|BI118645.1|BI118645
EST:     TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG                         GATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGC
genomic: TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAGgtagcttttt ... ttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGC
EST: gi|58599089|gb|CK009617.1|CK009617
EST:     TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG                         GATATTCAAGGG
genomic: TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAGgtagcttttt ... ttctctgaagGATATTCAAGGG
EST: gi|33794508|gb|CF323141.1|CF323141
EST:     TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG                         GATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGC
genomic: TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAGgtagcttttt ... ttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGC
EST: gi|58668188|gb|CK056874.1|CK056874
EST:     TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAG                         GATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGC
genomic: TTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAGgtagcttttt ... ttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtaaaaattttcaactgcaatagcaataatgccgttttctggttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGCAGCAAATTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTTGAG
                                     ttttctggttctct  CT-rich tract
     aaaaattttcaact  TA-rich tract