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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagactactactttcattattggatcacattgatttagagaagaaactgtaatgcaacatgatttagtctaacattattcttgctatttttcttctaacagAATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTAACCTTCTACAAGTTGACGCATCCCCTTGACAAGTCGTGGCATGTCCTTG

Basic information

species Oryza sativa
transcript LOC_Os09g36190.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G386971_T01 (Zea mays), 3'ss of exon 8
gtgagactactactttcattattggatcacattgatt-tagagaagaaactgtaatgcaa---catgatttagtctaacat--------tattcttgctatttttct-------tctaacagAATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTAACCTTCTACAAGTTGACGCATCCCCTTGACAAGTCGTGGCATGTCCTTG
|||||  | | | | |    | || ||  |||   ||  | ||||   ||    ||| |    | |  || |    | |||        ||||| | ||  | ||||        ||   ||||||||||| |||| ||||||||||||||||| ||||| ||||||||||| |||||||| ||||||||||| || || |||||||| |||||||| ||||
gtgaggattcaattcttgacactgaattgcatgatttacaaagaactgacaaatatgtacattcttagttaaactcatcatatctcacatattcctcctgctgttctgttctgtccttttagAATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTGACCTTCTATAAGTTGACGCACCCACTGGACAAGTCATGGCATGTTCTTG

upper sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G379577_T01 (Zea mays), 3'ss of exon 8
gtgagactactactttcattattggatcacattgatttagagaagaaa-----ctgtaa-----tgcaacatgatttag----------tctaacattattct--tgctatttt---------tcttctaacagAATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTAACCTTCTACAAGTTGACGCATCCCCTTGACAAGTCGTGGCATGTCCTTG
|||||| | | | | |  ||| || ||  ||| |||||| | || |||      || ||     | ||  || |||||           ||| ||||  | ||  |||| || |         | ||||   ||||||||| | | |||||||||||||||||||| ||||| ||||||||||| |||||||||||||||||||| || || |||||||| |||||||| ||||
gtgagaattcaattcttgttactgaattgcat-gatttacaaaaaaaaaggttttggaaatctgtacattattatttaaactcatcatatctcacatagtcctcctgctgttctattctgttctgttctgttagAATGAAGGCAGAGTTCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTGACCTTCTACAAGTTGACGCACCCACTGGACAAGTCATGGCATGTTCTTG

upper sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S21_294V6.1 (Physcomitrella patens), 3'ss of exon 8
gtgagactactactttcattat---tggatcacattgatttagagaagaaactgtaatgcaacatgatttagtctaacattattcttgctatttttcttcta-acagAATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTAACCTTCTACAAGTTGACGCATCCCCTTGACAAGTCGTGGCATGTCCTTG
 |||    |  |  | || |     ||    |||||    |     | |||        |||| ||| || |||| ||    ||     | | ||    | |  ||||||| | || |     | |||||||| || ||  | || |||||  |   ||| |||||||||||| | ||||| ||||||||||| ||||||||  | |
-tgaattcagcatgtccaatgaccatgagcgacattatcatgtctcacaaa-----ggacaacctgaatt-gtctgacggatttacatgtgtcttcgcaccatgcagAATGCAAACAGAACATTGTGGAAGCTGGGAACATTGCCTCCTGGGTTGGCAACATTCTACAAGTTGTCCCATCCACTTGACAAGTCATGGCATGTTTTAG

upper sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ18619 (Selaginella moellendorffii), 3'ss of exon 3
gtgagactactactttcattattggatcacattgatttagagaagaaactgtaatgcaacatgatttagtctaacattattcttgctatttttcttctaacagAATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTAACCTTCTACAAGTTGACGCATCCCCTTGACAAGTCGTGGCATGTCCTTG
                              || | |||||    || |      |    | |  |   |  | |||  |   ||    |||   |||   ||||| || ||| || | || |||||||| || ||||| || ||||||||| | ||||||||||| |||||||||||  | |||||||||||||| ||||| |
---------------------------gtaatggctttaggatcgatatctatcttttgcctcgt---gcttgacaagaggttttgcttttgctttc---cagAACGAGGACAGGCTGCTGTGGAAGCTCGGAACGCTACCCCCTGGCCTCATCACCTTCTACAACTTGACGCATCCATTGGACAAGTCGTGGCACGTCCTGG

upper sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ36191 (Selaginella moellendorffii), 3'ss of exon 3
gtgagactactactttcattattggatcacattgatttagagaagaaactgtaatgcaacatgatttagtctaacattattcttgctatttttcttctaacagAATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTAACCTTCTACAAGTTGACGCATCCCCTTGACAAGTCGTGGCATGTCCTTG
                              || | |||||    || |      |    | |  |   || | |||  |   ||    |||   |||   ||||| || ||| || | || |||||||| || ||||| || ||||||||| | ||||||||||| |||||||||||  | |||||||||||||| ||||| |
---------------------------gtaatggctttaggatcgatatctatcttttgcctcgt---gtttgacaagaggttttgcttttgctttc---cagAACGAGGACAGGCTGCTGTGGAAGCTCGGAACGCTACCCCCTGGCCTCATCACCTTCTACAACTTGACGCATCCATTGGACAAGTCGTGGCACGTCCTGG

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|55436196|gb|CV731236.1|CV731236
EST:     AGTGGAAGAAGAAAGATATCACTGGGATCTACCACAAGTGGCAAAGCATG                         AATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTA
genomic: AGTGGAAGAAGAAAGATATCACTGGGATCTACCACAAGTGGCAAAGCATGgtgagactac ... cttctaacagAATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTA
EST: gi|88847768|gb|CI018459.1|CI018459
EST:     AAGAAAGATATCACTGGGATCTACCACAAGTGGCAAAGCATG                         AATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTA
genomic: AAGAAAGATATCACTGGGATCTACCACAAGTGGCAAAGCATGgtgagactac ... cttctaacagAATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTA
EST: gi|86499556|gb|CI142189.1|CI142189
EST:     GAAGAAAGATATCACTGGGATCTACCACAAGTGGCAAAGCATG                         AATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTA
genomic: GAAGAAAGATATCACTGGGATCTACCACAAGTGGCAAAGCATGgtgagactac ... cttctaacagAATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTA
EST: gi|29628541|gb|CB633552.1|CB633552
EST:     AGTGGAAGAAGAAAGATATCACTGGGATCTACCACAAGTGGCAAAGCATG                         AATGAAGACCGGGTTCTTTGGAAGCTTGGGACACTTCCACCTGGCCTCTTA
genomic: AGTGGAAGAAGAAAGATATCACTGGGATCTACCACAAGTGGCAAAGCATGgtgagactac ... cttctaacagAATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTA

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: 26 (upstream exon), 31 (downstream exon)
Score: 1

TCCAAATGCATGTGGCTGGGCTTATGGAATGAACATCTTTGATCTGAAGGAGTGGAAGAAGAAAGATATCACTGGGATCTACCACAAGTGGCAAAGCATGgtgagactac ... cttctaacagAATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTAACCTTCTACAAGTTGACGCATCCCCTTGACAAGTCGTGGCATGTCCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtaatgcaacatgatttagtctaacattattcttgctatttttcttctaacagAATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTAACCTTCTACAAGTTGACGCATCCCCTTGACAAGTCGTGGCATGTCCTTG
                    gtctaac  putative branch site (score: 1)
                            ttattcttgctatttt  CT-rich tract
                                      tatttttcttctaa  TA-rich tract