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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_Os03g45770.1
intron # 11
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|58695202|gb|CK083889.1|CK083889
EST:     TTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGATGATCAG                         TGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTA
genomic: TTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGATGATCAGgtactgtttc ... tcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTA
EST: gi|2443167|gb|C74938.1|C74938
EST:     TTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGATGATCAG                         TGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTA
genomic: TTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGATGATCAGgtactgtttc ... tcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTA
EST: gi|218491801|gb|FG954125.1|FG954125
EST:     TTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGATGATCAG                         TGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTA
genomic: TTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGATGATCAGgtactgtttc ... tcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgcatagcaaattcggtctgtctgaatttactgaattttgtgtcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG
                                           tgtccttt  CT-rich tract
                           aatttactgaatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttaacatttgcaactttcaagcatgcattatcagaattgttgtcatgcatagcaaattcggtctgtctgaatttactgaattttgtgtcctttgcagTGTGAGGACATCTATATCAATGCAGTTCTTCCCGCGCTTTTTCTTGCTGTATTTCTTGGTTTTCCACATTTACTTCTTCTCGTACACATATG

- - - -catttgc
- - - - - - - - - - - agcatgc
- - - - - - - - - - - - - - - - - - - attgttg
- - - - - - - - - - - - - - - - - - - - - - -tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - -agcaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttactga