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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcaactctcaagtgcatatctctcatgatattgatgaactctccctttgttctcttttatcacagagattatcatcttgttcttattccttgtcattccatttcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAG

Basic information

species Oryza sativa
transcript LOC_Os08g40530.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G132712_T03 (Zea mays), 3'ss of exon 26
gtctcaactctcaagtgcatatctctcatgatattgatgaactctccctttgttctcttttatcacagagattatcatcttgttcttattccttgtcattccatttcttgtg-tagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAG
   | |  | |  ||  ||   |  | ||||     || |  | |  |    ||   ||  ||    ||| ||| | | |     |  | ||||| |  | ||||| ||||  ||||||||||||||||| |||||||||||||| |||||||||||||| |||||||| |||||||||||||||||||||||  ||||||| |||||||| |||
--gtgacatgttcagctcaagacattgatgaggc--attacatattgcaccttttctttgcattgatgagcttaccgtttctaattgctgccttgcctcttcatttgttgtcctagGCCGATATAGGTCTTTCAATGGGCATTTCCGGGACAGAAGTTGCTAAAGAAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAG

upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S8_288V6.1 (Physcomitrella patens), 3'ss of exon 26
gtctcaactctcaagtgcatatctctc-atgatattgatgaactctccctttgttctcttt-tatcacag---agattatcatcttgttcttattcct--tgtcattccatttcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAG
            ||  |  || || |  ||  | |   | |||  |      ||  | | | | ||||||   |  ||    ||  | ||      ||  ||  |    |||     || ||||||| || ||||| |||||||| ||  |||| || ||||| || ||||||||||| ||||| || ||| | |||||||| ||||| || ||||| |||
----------gtaaaaggctacctattgatactttctttcaacggttttggcgtgatgtgtatgtcacagtttaattttctgtcgaggtcacgaggctgatggtacattattggcactgcagGCCGACATTGGTCTTTCAATGGGTATAGCAGGAACGGAAGTCGCGAAAGAAAGTTCGGACATCATTATCCTCGATGACAATTTCACTTCTGTTGTTAAG

upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 22
gtctcaactctcaagtgcatatctctcatgatattgatgaactctccctttgttctcttttatcacagagattatcatcttgttcttattccttgtcattccatttcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAG
                                                           |       | | | |||||| |   |  |||   ||    |  | |  || |  |||| ||||| ||||| |||||||||||   |||||| || || ||||||||||| || |||||||||||  |||||||||||||  |||| ||||| |||
----------------------------------------------------------gtgggtttggcggtaatcatcgtagacgcattttctgatgataaactg-ttat-cagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG

upper sequence: LOC_Os08g40530.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 21
gtctcaactctcaagtgcatatctctcatgatattgatgaactctccctttgttctcttttatcacagagattatcatcttgttcttattccttgtcattccatttcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAG
                                                           |       | | | |||||| |  ||  |||   ||    |  | |  || |  |||| ||||| ||||| |||||||||||   |||||| || || ||||||||||| || |||||||||||  |||||||||||||  |||| ||||| |||
----------------------------------------------------------gtgggtttggcggtaatcatcgtagtcgcattttctgatgataaactg-ttat-cagGCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAG

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|29665351|gb|CB661626.1|CB661626
EST:     TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAG                         GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAA
genomic: TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAGgtctcaactc ... tcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAA
EST: gi|88591696|gb|CI709748.1|CI709748
EST:     TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAG                         GCCGATATAGGTCTCTCAATGGGCATTTCA
genomic: TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAGgtctcaactc ... tcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCA
EST: gi|33678328|gb|CF306567.1|CF306567
EST:     TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAG                         GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAA
genomic: TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAGgtctcaactc ... tcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAA
EST: gi|33678453|gb|CF306692.1|CF306692
EST:     TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAG                         GCCGATATAGGTCTCTCAATGGGCATT
genomic: TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAGgtctcaactc ... tcttgtgtagGCCGATATAGGTCTCTCAATGGGCATT
EST: gi|29681421|gb|CB677696.1|CB677696
EST:     TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAG                         GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAA
genomic: TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAGgtctcaactc ... tcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAA
EST: gi|88328484|gb|CI676694.1|CI676694
EST:     TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAG                         GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAA
genomic: TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAGgtctcaactc ... tcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAA
EST: gi|88589477|gb|CI707360.1|CI707360
EST:     TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAG                         GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAA
genomic: TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAGgtctcaactc ... tcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAA
EST: gi|88589322|gb|CI707190.1|CI707190
EST:     TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAG                         GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAA
genomic: TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAGgtctcaactc ... tcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAA
EST: gi|88388660|gb|CI683447.1|CI683447
EST:     TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAG                         GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAG
genomic: TTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAGgtctcaactc ... tcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcacagagattatcatcttgttcttattccttgtcattccatttcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAG
                      ttcttattccttgtca  CT-rich tract
          attatcat  TA-rich tract