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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCAAGTGGAAGCGTGGAAGCCAATCGTAGACGGCGTTCATGCCAAAGGAGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACAgtatgtttactatatctgatataagcatgttccctagctatataattatctgtgtagacatgtagttatttgcaagcaggagaacctttaaattggattt...

Basic information

species Oryza sativa
transcript 13113.m00235
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: 13113.m00235 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G087192_T02 (Zea mays), 5'ss of exon 3
GAGCAAGTGGAAGCGTGGAAGCCAATCGTAGACGGCGTTCATGCCAAAGGAGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACAgtatgtttactatatctgatataagcatgttcccta-gctatataattatctgtgtagacatgtagttatttgcaagcaggagaacctttaaattggattt-------
|||||||| ||||| |||||||| ||||||||||| |||||    |||||||| ||||||||||||||||||||||||||||| |||||||| |||  |||||||||||| |  ||| |   |     |||| | | |||||| | ||| | |        | |||| |   ||  ||| |||||  ||  | |  || ||       
GAGCAAGTCGAAGCATGGAAGCCGATCGTAGACGGGGTTCACCAGAAAGGAGGGATATTTTTCTGTCAGATTTGGCACGTAGGGAGAGTCTCCAATTCCAgtatgtttaccacctctaacgcagatcggttctcaaagctataaatttaacggca-----gtctagtca---gcttgcaagagaaaattggattcagagttatccatg
















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|29665521|gb|CB661796.1|CB661796
EST:     AGGAATATTTTTCTGTCAGATTTGGCACGTACGAAGAGTCTCTAATAACA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
genomic: AGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACAgtatgtttac ... cactatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
EST: gi|319908506|gb|HS977634.1|HS977634
EST:     AGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACA                         CTTTTCAGCCTANTGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
genomic: AGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACAgtatgtttac ... cactatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
EST: gi|58694336|gb|CK083023.1|CK083023
EST:     GGAATATTTTTCTTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
genomic: GGAATATTTTTC-TGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACAgtatgtttac ... cactatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
EST: gi|29621672|gb|CB626683.1|CB626683
EST:     AGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
genomic: AGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACAgtatgtttac ... cactatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
EST: gi|29683991|gb|CB680266.1|CB680266
EST:     AGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
genomic: AGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACAgtatgtttac ... cactatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
EST: gi|29685578|gb|CB681853.1|CB681853
EST:     AGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
genomic: AGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACAgtatgtttac ... cactatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
EST: gi|29669631|gb|CB665906.1|CB665906
EST:     AGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
genomic: AGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACAgtatgtttac ... cactatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
EST: gi|29621017|gb|CB626028.1|CB626028
EST:     AGGAATATTTTTCTGTCAGATTTGGCACGTACGAAGAGTCTCTAATAACA                         CTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA
genomic: AGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACAgtatgtttac ... cactatgcagCTTTTCAGCCTAATGGGCAGGCTCCAATTTCGAGCACCAATAAGTCACTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCAAGTGGAAGCGTGGAAGCCAATCGTAGACGGCGTTCATGCCAAAGGAGGAATATTTTTCTGTCAGATTTGGCACGTAGGAAGAGTCTCTAATAACAgtatgtttactatatctgatataagcatgttccctagctatataattatctgtgtagacatgtagttatttgcaagcaggagaacctttaaattggattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA