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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_Os08g40530.2
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

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), 68 (downstream exon)
Score: 18

TCCAAATGACAAACTTTTGCTTGTCCAAGCTTTGAAAAGAAAGGGTCATGTTGTGGCTGTTACTGGTGATGGCACAAATGATGCTCCTGCATTGCATGAGgtctcaactc ... tcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcacagagattatcatcttgttcttattccttgtcattccatttcttgtgtagGCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAG
                      ttcttattccttgtca  CT-rich tract
          attatcat  TA-rich tract