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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagatatggtggattgtatcctcatttgcgtgatcaatagtttctttttcatttcttgattgttgtttatagatttacctttttgctttcgtatgcctcctccggggaaaataacttaagaggcaatttatttttctcaagcaccgtgaactcttacatggttatatctgcaactgtattttgtagGGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAG

Basic information

species Oryza sativa
transcript LOC_Os08g01740.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g01740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G135568_T01 (Zea mays), 3'ss of exon 6
gtatagatatggtggattgtatcctcatttgcgtgatcaatagtttctttttcatttcttgattgttgtttatagatttacctttttgctttcgtatgcctcctccggggaaaataacttaagaggcaatttatttttctcaagcaccgtgaactcttacatggttatatctgcaactgtatt-ttgtagGGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAG
            ||  ||  |     ||   | | ||||||| | ||| | || ||   |  |  | | |||    || |  ||  ||| |   | | ||  ||          |   ||   ||  ||  |  ||||   | | |     ||||  | |          ||    |||| || ||| |||||||||| ||||| ||||||||||||||||| |||||||| || ||||| || || || || ||||| || ||||||||||||||
---------gtatgtgttaaactaatatccacatcatcaata-tatctgtatccttctctact--tcgattacttgttgaa-ttgatgcatctctgtaccctct----------tgcatttgtagctaaaatgcttttactatgtat----aacttatgc---------cctagtgctgtgttcttgcagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGGATGATGCACCTTGTTATGACATCAAG

upper sequence: LOC_Os08g01740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G834205_T01 (Zea mays), 3'ss of exon 6
gtatagatatggtggattgtatcctcatttgcgtgatcaatagtttctttttcatttcttgattgttgtttatagatttacctttttgctttcgtatgcctcctccggggaaaataacttaagaggcaatttatttttctcaagcaccgtgaactcttacatggttatatctgcaactgtattttgtagGGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAG
                                                               | ||| || | |  ||   |||   | |   ||| |||| | | | | |       ||| | ||  |||| | ||   ||    | |   | ||  |   | | | |           | |||||||||||||| ||||| ||||||||||||||||| |||||||| || ||||| || || ||||||||||| || ||||||||||||||
---------------------------------------------------------------ttttgcttgttggatt-tttttgcacctctctat-cctcttgctgtgtag-----ctaaaatgct-tttactctttataa----cttatgccctagc---gctgtgt-----------tcttgtagGGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG
















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|27577615|gb|CB000310.1|CB000310
EST:     TGGAAGTTCTAAAGGACGTGCTTGATTCGATGGATCCTAGACACCCTGAG                         GGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAA
genomic: TGGAAGTTCTAAAGGACGTGCTTGATTCGATGGATCCTAGACACCCTGAGgtatagatat ... tattttgtagGGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAA
EST: gi|58602320|gb|CK012848.1|CK012848
EST:     TGGAAGTTCTAAAGGACGTGCTTGATTCGATGGATCCTAGACACCCTGAG                         GGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAA
genomic: TGGAAGTTCTAAAGGACGTGCTTGATTCGATGGATCCTAGACACCCTGAGgtatagatat ... tattttgtagGGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAA
EST: gi|66924274|gb|CX111122.1|CX111122
EST:     TGGAAGTTCTAAAGGACGTGCTTGATTCGATGGATCCTAGACACCCTGAG                         GGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAA
genomic: TGGAAGTTCTAAAGGACGTGCTTGATTCGATGGATCCTAGACACCCTGAGgtatagatat ... tattttgtagGGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAA

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: 69 (upstream exon), 63 (downstream exon)
Score: 25

TATAATTCGGAAAGCTTCTAGTGTCATGGAAGTTCTAAAGGACGTGCTTGATTCGATGGATCCTAGACACCCTGAGgtatagatat ... tattttgtagGGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctcaagcaccgtgaactcttacatggttatatctgcaactgtattttgtagGGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAG
                   ctcttac  putative branch site (score: 25)
                                             tattttgta  TA-rich tract