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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttaacatttgcaactttcaagcatgcattatcagaattgttgtcatgcatagcaaattcggtctgtctgaatttactgaattttgtgtcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG

Basic information

species Oryza sativa
transcript LOC_Os03g45770.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 2
catttaacatttgcaactttcaagcatgcat-tatcagaattgttgtcatgcatagcaaa---ttcggtctgtctgaattta----ctgaattttgtgtc----ctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG
            ||   |  || | |||||| |||||||| || | |  || |   | ||   |||   ||        |||    || |   ||   ||    |||| ||||||| ||||||| ||||| ||||||||||| || ||||| |||||||||||||| ||||||||||| || ||||||||||| || || ||||
------------gcgggtagcatgaatgcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATG

upper sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G814310_T02 (Zea mays), 3'ss of exon 2
catttaacatttgcaactttcaagcatgcat-tatcagaattgttgtcatgcatagcaaa---ttcggtctgtctgaattta----ctgaattttgtgtc----ctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG--------
            ||   |  || | |||||| |||||||| || | |  || |   | ||   |||   ||        |||    || |   ||   ||    |||| ||||||| ||||||| ||||| ||||||||||| || ||||| |||||||||||||| ||||||||||| || ||||||||||| || || ||||        
------------gcgggtagcatgaatgcatctatcagaaatgatcttgtgtaggacgaaattttcaagctaatcattcttaaatacttatccttaaatctttgcttttcagTGTGCGGACATCCATATCGATGCAGTTCTTTCCACGCTTCTTCTTGCTGTATTTTTTGGTTTTCCATATCTACTTCTTCTCATATACCTATGGTATGTGT

upper sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 11
---catttaacatttgcaac--tttcaagcatgcattatcagaattgttgtcatgcatagcaaattcggtctgtctgaatttactgaattttgtgtcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG
   | ||||| || || | |  | || |  || |||| |||      ||   | |  |      | | |  | |   |||  |   | | |  |||   |||||||||  | ||| | ||||||||| ||||||| || ||||| || |||||||||||| |||| |||||||| || |||||||| ||  | ||||
gttcttttaatatctggaccagtatctattatacattttcatgcacatttgtagggttgt--ggtccagcgtatgataataca---agtgtattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTATG

upper sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA15G05080.1 (Glycine max), 3'ss of exon 11
-catttaacatttgcaac--tttcaagcatgcattatcagaattgttgtcatgcatagcaaattcggtctgtctgaatttactgaattttgtgtcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG
 | ||||| || || | |  | ||    |  |||| |||      |  |  ||         | | |  | |   |||  | ||  ||   |||   |||||||||  | ||| | ||||||||| ||||||| || ||||| || |||||||||||| |||| |||||||| || |||||||| ||  | || |
tcttttaatatctggaccagtatctgttacacattttcatgcacat--ttgtggggttgtggtccagcgtatgataatg-agtgtgttcattgtaacttgcagTGTCCGAACACCAATATCAATGAAGTTCTTTCCTCGCTTCTTTTTGCTGTATTTCCTGGTCTTCCACATATATTTCTTCTCTTATGCTTACG

upper sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G60995.1 (Arabidopsis thaliana), 3'ss of exon 12
--------------------------------catttaacatttgcaactttcaagcatgcattatcagaattgttgtcatgcatagcaaattcggtctgtctga------atttactgaattttgtgtcct-----ttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG
                                 ||||    | || | || |   ||  |   ||     | ||      |  |       ||    ||||   |      | | ||  | | || |   |      ||||||||| |||||| | ||||| ||| ||||||||||||| || ||||||||||| |||||||| ||||| ||||| |||||||| ||  ||||||
gttttggtctcctcttttgcctcagtcacctgtatttccactatgaagctcttttgctcgtgataatctcactgccaagttaaagttttttttgtagctgttcaatggaataataacaaactcttatcctccatatattgcagTGTCAGGACACCAATATCGATGAAGTTCTTCCCGCGTTTCTTCTTGCTGTACTTCTTGGTGTTCCATATTTATTTCTTCTCATATGCATATG

upper sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S96_202V6.1 (Physcomitrella patens), 3'ss of exon 12
catttaacatttgcaactttcaagcatgcattatc-agaattgttgtcatgcatag-caaattcggtc-tgtctgaatttactgaattttgtgtcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG
 | ||    | || ||       |  |   | ||   ||||| |   | | | | | |  ||   |||  |   | |     || | ||    |  ||||||| ||||||||  |  |||| ||||||||||| || ||||| || || || |||||| ||| ||||||||||||||||||||| || || || |
gaatttttttctgtaagcggtt-gtttatttcatttggaattataagcttcctttgacggatattgtcacgcgagcaccctttgtacttgccat--tttgcagCGTGAGGACGCCCCTATCGATGCAGTTCTTTCCTCGCTTCTTTTTTCTCTATTTCATGGCTTTCCACATTTACTTCTTCTCTTATACCTACG

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|2443167|gb|C74938.1|C74938
EST:     TTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGATGATCAG                         TGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTA
genomic: TTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGATGATCAGgtactgtttc ... tcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTA




















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: 52 (upstream exon), 74 (downstream exon)
Score: 18

TTGGGATCCTCTTTTTTCTATTTGAGTTCTATGATGATCAGTTGCTTGCATTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGATGATCAGgtactgtttc ... tcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgcatagcaaattcggtctgtctgaatttactgaattttgtgtcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG
                                           tgtccttt  CT-rich tract
                           aatttactgaatttt  TA-rich tract