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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGGGATGGTGTCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAATgtaaaatccacaattcaatatttctagttaatgttatattctatattttctcactgccaagtctgttctccatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g39310.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39310.3 (Oryza sativa), 5'ss of exon 9
lower sequence: AC196426.3_FGT007 (Zea mays), 5'ss of exon 8
ATATGGGATGGTGTCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAATgtaaaatccacaattcaatatttct--agttaatgttatattctatatttt-ctcactgccaagtctgttctc-catgcag
|||||||||| ||| || |||||||||||||| || ||||||||| | |||||||||||| ||||||||  ||  | | ||  |||||       ||||| ||| ||  | ||  || |  |   | |   || || ||| |||
ATATGGGATGCTGTTCCGAAACCCCATGCCCATAAAGAAACTCCAATTAGTGAATTTTTCGATgtaaaaatcatgacttaacctttcttcgacacatgttttatactgaagttcgctaaaagttcatttaattttcacatccag

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA08G20610.1 (Glycine max), 5'ss of exon 9
ATATGGGATGGTGTCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAATgtaaaatccacaattc---aatatttctagt-----taatgttatattctatattttctcactgccaagtctgttctccatgcag----------------------
|||||||||  ||| |||||||| || |||||||||||||| ||| | |||||||||||||||||||  ||  || | |    ||||| ||| |     | ||||| |  | ||       |   |   |||| | |  |  |||                         
ATATGGGATTCTGTTCCTAAACCACAGGCCCACAAGGAAACCCCATTAAGTGAATTTTTCAATgtaagttcttcattcctttgatattgctaatcttactgatgttcttgtatagcaagattttatatgaagtttatagtaaatgtttattcttggtaacaaatgaccag

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA07G01230.1 (Glycine max), 5'ss of exon 9
ATATGGGATGGTGTCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAATgtaaaatccacaattc---aatatttctagt-----taatgttatattctatattttctcactgccaagtctgttctccatgcag----------------------
||||||||   ||| |||||||| || |||||||||||||| ||| | |||||||||||||||||||  ||  || | |    ||||| ||| |     | ||||| |  | ||       |   |   |||| | |  |   ||                         
ATATGGGACTCTGTTCCTAAACCACAGGCCCACAAGGAAACCCCATTAAGTGAATTTTTCAATgtaagttcttcattcctttgatattgctaatcttactgatgttcttgtttagcaagattttatatgaagtttatagtaattgtttattcttggtaataaatggccag

upper sequence: LOC_Os01g39310.3 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 5'ss of exon 9
ATATGGGATGGTGTCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAATgtaaaat-ccacaatt-----caatattt-ctagttaatgttatattctatattttctcactgccaagtctgttctccatgcag---------------------------
||||||||   ||| ||||| || || || || ||||||||||| |||||||||||||| ||||||| ||   ||||||     ||| ||   ||    |||||    |||||| |||    |        | |    |  |||                              
ATATGGGACTCTGTTCCTAAGCCACAAGCACATAAGGAAACTCCGCTGAGTGAATTTTTTAATgtaagatgttacaattttaggcaagataagcttaggaatgtccatttctatttttcacgaggatttgcttttggatttatgtttggcttactatatctattaaatggtcag

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|29675672|gb|CB671947.1|CB671947
EST:     TCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAAT                         GTCGAAGTTGTGGCCCTATCTAGTTATGAGGAAAAGGAGGAGTTATTCANA
genomic: TCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAATgtaaaatcca ... ctccatgcagGTCGAAGTTGTGGCCCTATCTAGTTATGAGGAAAAGGAGGAGTTATTCAAA
EST: gi|29671821|gb|CB668096.1|CB668096
EST:     TCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAAT                         GTCGAAGTTGTGGCCCTATCTAGTTATGAGGAAAAGGAGGAGTTATTCAAA
genomic: TCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAATgtaaaatcca ... ctccatgcagGTCGAAGTTGTGGCCCTATCTAGTTATGAGGAAAAGGAGGAGTTATTCAAA
EST: gi|29664221|gb|CB660496.1|CB660496
EST:     TCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAAT                         GTCGAAGTTGTGGCCCTATCTAGTTATGAGGAAAAGGAGGAGTTATTTCAA
genomic: TCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAATgtaaaatcca ... ctccatgcagGTCGAAGTTGTGGCCCTATCTAGTTATGAGGAAAAGGAGGAGTTATT-CAA
EST: gi|29632288|gb|CB637297.1|CB637297
EST:     TCCCTAAACCCCATGCCCACAAAGAAACTCCACTGAGTGAATGTTTCAAT                         GTCGAAGTTGTGGCCCTATCTAGTTATGAGGA
genomic: TCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAATgtaaaatcca ... ctccatgcagGTCGAAGTTGTGGCCCTATCTAGTTATGAGGA
EST: gi|88364128|gb|CI610472.1|CI610472
EST:     TCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAAT                         GTCGAAGTTGTGGCCCTATCTAGTTATGAGGAAAAGGAGGAGTTATTCAAA
genomic: TCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAATgtaaaatcca ... ctccatgcagGTCGAAGTTGTGGCCCTATCTAGTTATGAGGAAAAGGAGGAGTTATTCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGGGATGGTGTCCCTAAACCCCATGCCCACAAGGAAACTCCACTGAGTGAATTTTTCAATgtaaaatccacaattcaatatttctagttaatgttatattctatattttctcactgccaagtctgttctccatgcag

- - - - - - - - - - - - - - - -  AAGGAA