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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_Os02g10070.1
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 50 (upstream exon), 69 (downstream exon)
Score: 39

GTTCTGGGAGCCTACCTATGAAGATTGCTTAAATTTGATAGCTCGCCTTCCAGCAGTGGCTTCATATGTTTACCGGAGgtagcttttt ... ttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGCAGCAAATTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtaaaaattttcaactgcaatagcaataatgccgttttctggttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGCAGCAAATTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTTGAG
                                     ttttctggttctct  CT-rich tract
     aaaaattttcaact  TA-rich tract