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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACCATCCATTCAGATTTCAAGTCTGGTCTAGAAGGCCTTCTGAAGGAGAAGCCCACCAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGCGgtgattttcttttaccattgctcatttgttgttaacaaccccttgcacctattgtacgcaatgattatgcccatggtgttcccagttccttacagttttggtatctcactgaactttgagtaaacacaattttgaaatgatag

Basic information

species Zea mays
transcript GRMZM2G381933_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381933_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g15490.3 (Oryza sativa), 5'ss of exon 4
AACCATCCATTCAGATTTCAAGTCTGGTCTAGAAGGCCTTCTGAAGGAGAAGCCCACCAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGCGgtgattttcttttaccattgctcatttgttgttaacaaccccttgcacctattgtacgcaatgattatgcccatggtgttcccagttccttacagttttggtatctcactgaactt-tgagtaaacacaattttgaaatgatag
||| ||||  || ||||| |||||||| |||||||||||  |||| |||| ||| || ||||||||||| ||||| || |||||||| ||||||||||| || |||||||| | || ||| | | ||| | || | | | |  |  || | || |   ||||  | |||||||| |   |  || ||  | |      | |  || |  | ||| | | | | |  ||| ||| |  || ||||
AACTATCCGCTCGGATTTTAAGTCTGGCCTAGAAGGCCTATTGAAAGAGAGGCCTACTAAAGCAATTTTTATTGGTACTAGAATTGGCGATCCAAATGCAgtaattttcttgttcccttgtttagttgctcttcaaatctcgatagacttgttatgtccaatcctcatgcccatagacctttcacttattgatgtccctagactcccgataaacctattacttactacagttt-gggattatag
















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|211136285|gb|FL006477.1|FL006477
EST:     AGCCCACGAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGCG                         GTTGGTCAAGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATG
genomic: AGCCCACCAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGCGgtgattttct ... gaaatgatagGTTGGTCAAGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATG
EST: gi|211136284|gb|FL006476.1|FL006476
EST:     GCCCACGAAAGCA-TTTTCATTGGCACAAGAATTGTTGATCCAAATGCCG                         GTGGGTCA-GAACAGTTCTCTCCTA
genomic: GCCCACCAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGC-Ggtgattttct ... gaaatgatagGTTGGTCAAGAACAGTTCTCTCCTA
EST: gi|33770862|gb|CF273156.1|CF273156
EST:     AGCCCACCAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGCG                         GTTGGTCAAGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATG
genomic: AGCCCACCAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGCGgtgattttct ... gaaatgatagGTTGGTCAAGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATG
EST: gi|74242522|gb|DT650436.1|DT650436
EST:     AGCCCACCAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGCG                         GTTGGTCAGGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATG
genomic: AGCCCACCAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGCGgtgattttct ... gaaatgatagGTTGGTCAAGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATG
EST: gi|31353159|gb|CD437516.1|CD437516
EST:     AGCCCACCAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGCG                         GTTGGTCAAGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATG
genomic: AGCCCACCAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGCGgtgattttct ... gaaatgatagGTTGGTCAAGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATG
EST: gi|32932020|gb|CF036832.1|CF036832
EST:     AGCCCACCAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGCG                         GTTGGTCAAGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATG
genomic: AGCCCACCAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGCGgtgattttct ... gaaatgatagGTTGGTCAAGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACCATCCATTCAGATTTCAAGTCTGGTCTAGAAGGCCTTCTGAAGGAGAAGCCCACCAAAGCAATTTTCATTGGCACAAGAATTGGTGATCCAAATGCGgtgattttcttttaccattgctcatttgttgttaacaaccccttgcacctattgtacgcaatgattatgcccatggtgttcccagttccttacagttttggtatctcactgaactttgagtaaacacaattttgaaatgatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA