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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC

Basic information

species Oryza sativa
transcript LOC_Os01g27020.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 3
-----atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
     ||  || ||     | ||    ||| |||| ||||| | |||  | ||   | ||  |  | | | | |||   |   |||| || |||    |   ||||| |||||||||||||||||||||||||||||||| ||||| || |||||||| ||||| ||||| ||  ||||||| || ||||||||||||||||| |
cttggatgaatagtgcgctttttagtctgccatatttgcttaatttgaatgcaactactttgtctctactgt-taaaactgggatgtacactat----ttgccagGTGGAACAGTTGCACAAGATTTTCAAGCTATGTGGTTCCCCTTCTGAGGAGTACTGGAAGAAGTCTAAATTGCCACACGCAACAATATTCAAACCTCAAC

upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------------------------atttattgtttttatcttgtgttgctatatatgctttagttgctta--cataaaattgat-tgccattttctaattttaatatgtgcaatatgaactgat-cagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
                                                                                   |    | |||| |  |   | ||     |   ||  | | |||     | |||||  |        || || || ||  ||  |||   | |  || |  |||| || ||| | |||||||| ||||| |||||||| || || || || || |||||||||||||| ||| |||| |||||||| || || || || || |
gtaatctatgatggatacattatatagggtctatagttgcatcttttaagggcataatgtgtattcagtttactagtctaaggtgcaagattttgttgtccatggcctctcaattttctgctacttgattgtgaaatttgtgctttggattttacttctataattagcatccttatgtgttgtagGTGGAGCAGCTACACAAGATATTCAAACTATGTGGTTCTCCTTCTGATGAATATTGGAAAAAGTCAAAGTTGCCTCATGCTACCATTTTTAAGCCCCAAC

upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------------------atttattgtttttatcttgtgttgctatatatgctttagttgctta--cataaaatt---gattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
                                                                                            |  |  |||||  | | |  | |||    |   ||  | | |||     | |||||   | ||   |||||     | ||||  |     | |         ||||||| ||| | |||||||| ||||| |||||||| || || || || || |||||||||||||| ||| ||||||||||||| || || || || || |
gtaatctctatgatggatacactatatagggcttaatgtctatagttgcatcttttaagggcttaatgtgtattcagtttactagtctaaggtgcaaggttttgttgtcg-atggcttctcaattttctgctacttgattgtgaaatttgtgcttcagattttactgctataattagcatcctttatgtgttatagGTAGAGCAGCTACACAAGATATTCAAACTATGTGGTTCTCCTTCTGACGAATATTGGAAAAAGTCAAAGTTGCCACATGCTACCATTTTTAAGCCCCAAC

upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 3
atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgat-tgccattttctaattttaatatgtgcaa--tatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
 |||      | ||  |||  ||   | ||||  |  | |||| |  ||   ||   | |   |      ||||  | | | |  ||    | |   |   |||| ||||| ||||||||||| | ||| |||||||| || || ||||| ||||||||||| ||||| ||| ||||  |||||||    || ||||| |   
-tttgcatggtatagtttgaatt-taagatata-tcaaattgcatttatttgatgattataagaaaacacaattagattttttctaagtcttcactcgcatagGTGGAACAATTGCACAAGATATACAAACTATGTGGTTCACCTTCAGATGAGTATTGGAAGAAGTCAAAGTTGCCTAATGCTACCTCGTTTAAACCACGAG

upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S89_168V6.1 (Physcomitrella patens), 3'ss of exon 4
atttattgtttttatcttgtgttgctatatatgcttta-gttgctta---cataaaattga--ttgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
 ||||         | | ||       | || | |||     ||  |     |    ||||    |  |||       |||   |  | |  | |||  |    |||| ||||| ||||||||||| || ||| | || || ||||| || |||||||||||||| ||||| ||  |||| ||||| || |||||||| ||||| |
-tttacctccggcgtttggtaacagattgtagggtttgtagggcccaagttgtggggttgaggccgtaattggaggggtttggcacattct-tgtgatgt----agGTGGAACAATTGCACAAGATCTTTAAGTTGTGCGGTTCCCCATCCGAGGAGTATTGGAAGAAGTCGAAATTGCCGCATGCGACGATATTCAAGCCTCAAC

upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S271_84V6.1 (Physcomitrella patens), 3'ss of exon 3
atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaac---tgat--cagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
     | |     |   |||| ||    ||  |     | ||  |     ||  |||    | |  |  | |     |   ||    |||      || |  ||||| |||||| ||||||||||||||||| | || || || || || |||||||||||||| ||||| |||||||| || || || |||||||| |||||||
--cagtcgcggcgagtgtgtggtgagtgatggggggggggtgtgtg---gaatgtgaggcgcgtgctgaagtggggttggttgtggcatgggtgtgtggtggcagGTGGAACAGCTGCACAAGATTTTCAAGTTGTGCGGTTCGCCGTCGGAGGAGTATTGGAAGAAGTCGAAGCTGCCGCACGCGACGATATTCAAGCCTCAGC

upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S428_20V6.1 (Physcomitrella patens), 3'ss of exon 3
----atttattgtttttatcttgtgttgctatatatgc-tttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
       | |||   |         |||   || |||| ||| | |  | | ||   ||| | |   |         |||  || | | ||||||   ||  ||||| |||||  | || ||||| |||||| |||| || || || || |||||||||||||||||||| ||  |||| || ||||| |||||||| ||||| |
ttttccctcttgcggtggctacagattggagtagatgcgtttgggttgtaagatggtatttaat-ttagagaacgggtttggtacg-ggaatatgg--tgg-cagGTGGAACAACTTCATAAGATCTTCAAGTTATGCGGTTCTCCGTCCGAGGAGTATTGGAAAAAGTCAAAATTGCCGCACGCTACGATATTCAAGCCTCAAC

upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ35595 (Selaginella moellendorffii), 3'ss of exon 2
atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
                           |||   | || |||  ||   | |   || ||   |    ||   |||  | |      |||  |  || ||||| || || || ||||||||||| |||||||||||||| || || || |||||||||||||| ||||| || || || ||||| || || || || ||||
--------------------------gtatgctcgttggtt-tttgttttacgatgtttagtaacgcctgcctttcttct------tattgatcgaacagGTGGAGCAATTACACAAGATTTTTAAGCTATGTGGCTCGCCATCGGAAGAGTATTGGAAAAAATCCAAACTTCCTCACGCTACGATTTTTAAGCCGCAGC

upper sequence: LOC_Os01g27020.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ24328 (Selaginella moellendorffii), 3'ss of exon 4
atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
                           |||   | || |||  |||  | |   || ||   |    ||   |||  |         ||  |  || ||||| || || || ||||||||||| |||||||||||||| || || || |||||||||||||| ||||| || || || ||||| || || || || ||||
--------------------------gtatgctccttggtt-tttattttacgatgtttagtaacgcctgcctttctt---------attgatcgaacagGTGGAGCAATTACACAAGATTTTTAAGCTATGTGGCTCGCCATCGGAAGAGTATTGGAAAAAATCCAAACTTCCTCACGCTACGATTTTTAAGCCGCAGC

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|58597309|gb|CK007837.1|CK007837
EST:     TTCTGGCAGAGCTCTTGCATGGGAAGCCCATCATGCCTGGGCGTACTGAG                         GTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAG
genomic: TTCTGGCAGAGCTCTTGCATGGGAAGCCCATCATGCCTGGGCGTACTGAGgtgagtcata ... aactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAG
EST: gi|58659085|gb|CK047765.1|CK047765
EST:     TTCTGGCAGAGCTCTTGCATGGGAAGCGCATCATGCCTGGGCGTACTGAG                         GTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAG
genomic: TTCTGGCAGAGCTCTTGCATGGGAAGCCCATCATGCCTGGGCGTACTGAGgtgagtcata ... aactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAG
EST: gi|88726999|gb|CI750654.1|CI750654
EST:     TTCTGGCAGAGCTCTTGCATGGGAAGCCCATCATGCCTGGGCGTACTGAG                         GTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAG
genomic: TTCTGGCAGAGCTCTTGCATGGGAAGCCCATCATGCCTGGGCGTACTGAGgtgagtcata ... aactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC
                 attttctaattttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttattgtttttatcttgtgttgctatatatgctttagttgcttacataaaattgattgccattttctaattttaatatgtgcaatatgaactgatcagGTAGAACAGTTGCACAAGATTTTCAAGCTATGTGGCTCCCCCTCAGAGGAGTATTGGAAAAAGTCCAAGCTGCCACATGCTACAATATTCAAACCTCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC