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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctcataacttgataatttgaccacttcattatctttgcaagctactacattattcccaagagattgaattattgaagatatacacaactaattgtttttgttatccgttcagtttatgcag

Basic information

species Oryza sativa
transcript LOC_Os03g57790.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g57790.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 4
GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctcataacttgataatttgaccacttcattatctttgcaagctactacattattcccaagagattgaattattgaagatatacacaactaattgtttttgttatccgttcagtttatgcag
|||||||||||||||| || ||||||||||||||||| ||||||||||| ||   |||||||||||| || ||||||||||||||||| |||||||    |   ||     ||     |||  |||||  |   |   |   || | | | |   || | | | |  || || |      ||| |  || |||                        
GCACGTTCAAGCTGACTCTGCAATTTACAGAAGATTACCCCAACAAACCTCCGACTGTTCGGTTTGTTTCGAGGATGTTTCACCCAAACAgtatgttctct---ttagatgttaaggaactaaattattctcata--ttggcacctgagtacattgacaataagtggtttaatac-----caattctttttttccag--------------------

upper sequence: LOC_Os03g57790.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G120674_T01 (Zea mays), 5'ss of exon 3
GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctcataacttgataatttgaccacttcattatctttgcaagctactacattattcccaagagattgaattattgaagatatacacaactaattgtttttgttatccgttcagtttatgcag
|||||||||||||||| || |||| |||||||||||| ||||||||||| |||  |||||||||||| || ||||||||||| ||||| |||||||    |   ||     ||     |||  |||||| |       |   ||      |  || ||||| |   ||  |||   |  |  || | || |||  |                     
GCACGTTCAAGCTGACTCTGCAATGTACAGAAGATTACCCCAACAAACCTCCAACTGTTCGGTTTGTTTCGAGGATGTTTCATCCAAACAgtatgttctct---ttagatgttaaggaactaaattatcctcatgtattgacac------ctgaatagattta-caat--aagtggtttaataccatttttttcag---------------------
















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|11025772|gb|AU162373.1|AU162373
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|11025772|gb|AU162373.1|AU162373
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|88220568|gb|CI220128.1|CI220128
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|88220568|gb|CI220128.1|CI220128
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|58688873|gb|CK077560.1|CK077560
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|58688873|gb|CK077560.1|CK077560
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|38469192|gb|CF953323.1|CF953323
EST:     GAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: -AACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|38469192|gb|CF953323.1|CF953323
EST:     GAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: -AACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|4716198|gb|AU057314.1|AU057314
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|4716198|gb|AU057314.1|AU057314
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|4716198|gb|AU057314.1|AU057314
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|4716198|gb|AU057314.1|AU057314
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|38468844|gb|CF952975.1|CF952975
EST:     CAACAAACCACCAGTTGTGCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|38468844|gb|CF952975.1|CF952975
EST:     CAACAAACCACCAGTTGTGCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|218505167|gb|FG956727.1|FG956727
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|218505167|gb|FG956727.1|FG956727
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|38469613|gb|CF953744.1|CF953744
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         ATGGAAGTATCTGCTTGGATATCCTACAAAATCAATGGAGCCCTATATATG
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcagATGGAAGTATCTGCTTGGATATCCTACAAAATCAATGGAGCCCTATATATG
EST: gi|58590675|gb|CF988983.1|CF988983
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTGTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|58590675|gb|CF988983.1|CF988983
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTGTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|42592241|gb|CK738727.1|CK738727
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|42592241|gb|CK738727.1|CK738727
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|86489541|gb|CI132174.1|CI132174
EST:     CAACAAACCACGAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|86489541|gb|CI132174.1|CI132174
EST:     CAACAAACCACGAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|218485740|gb|FG958740.1|FG958740
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|218485740|gb|FG958740.1|FG958740
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|27576883|gb|CA999577.1|CA999577
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|27576883|gb|CA999577.1|CA999577
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|38468296|gb|CF952427.1|CF952427
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|38468296|gb|CF952427.1|CF952427
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|38474625|gb|CF958758.1|CF958758
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|38474625|gb|CF958758.1|CF958758
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|38474625|gb|CF958758.1|CF958758
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|38474625|gb|CF958758.1|CF958758
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|86419732|gb|CI054533.1|CI054533
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|86419732|gb|CI054533.1|CI054533
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|38480664|gb|CF964753.1|CF964753
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|38480664|gb|CF964753.1|CF964753
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|87030448|gb|CI252725.1|CI252725
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         ATGGAAGTATCTGCTTGGATATCCTACAAAATCAATGGAGCCCTATATATG
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcagATGGAAGTATCTGCTTGGATATCCTACAAAATCAATGGAGCCCTATATATG
EST: gi|58677295|gb|CK065982.1|CK065982
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|58677295|gb|CK065982.1|CK065982
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|29666285|gb|CB662560.1|CB662560
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|29666285|gb|CB662560.1|CB662560
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATATTTATGCA                  
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCC--A-A---AT--Agtatgtctca ... gtt
EST: gi|33797775|gb|CF324747.1|CF324747
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|33797775|gb|CF324747.1|CF324747
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|33797775|gb|CF324747.1|CF324747
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|33797775|gb|CF324747.1|CF324747
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|218500669|gb|FG957555.1|FG957555
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|218500669|gb|FG957555.1|FG957555
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|218500669|gb|FG957555.1|FG957555
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-
EST: gi|218500669|gb|FG957555.1|FG957555
EST:     CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATA                         T
genomic: CAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctca ... gtttatgcag-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACGTTCAAGCTGACACTACAATTTACAGAAGATTATCCCAACAAACCACCAGTTGTTCGGTTTGTCTCAAGGATGTTTCACCCAAATAgtatgtctcataacttgataatttgaccacttcattatctttgcaagctactacattattcccaagagattgaattattgaagatatacacaactaattgtttttgttatccgttcagtttatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG