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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCTAGGGCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactttaactagccctatttttagtatttggtctcaaatattgactataatacatgctttcttctccag

Basic information

species Zea mays
transcript GRMZM5G807639_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807639_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 2
ACTCTAGGGCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactttaactagccctatttttagtatttg--gtctcaaatattgactataatacat-gctttcttctccag
|||||||| ||  | |||||| || |||||| ||| |||||||||||||||||||||||||| |  || |  ||   |||| || | | || |  || || |   ||| || |||||  | | |   || | |||
ACTCTAGGCCTCATCAGGAGTTATTCACATGCCAGGAACTACAGCAGTCAACTTTCAGgttattgattgacata-ttctatattaattgttagttgtttctagctttggctctaatatgtaggtacttttttcag
















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|32862756|gb|CF002438.1|CF002438
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211494399|gb|FL426463.1|FL426463
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
EST: gi|211042919|gb|FL416910.1|FL416910
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
EST: gi|211275057|gb|FL384329.1|FL384329
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCATTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
EST: gi|211011070|gb|FL374939.1|FL374939
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGTTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211518170|gb|FL380292.1|FL380292
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211126388|gb|FL388997.1|FL388997
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
EST: gi|211418591|gb|FL407188.1|FL407188
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211235901|gb|FL373720.1|FL373720
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
EST: gi|67031724|gb|CO460473.1|CO460473
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211490936|gb|FL402016.1|FL402016
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211094733|gb|FL379398.1|FL379398
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
EST: gi|211317708|gb|FL417584.1|FL417584
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCYCAAATCTGACAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
EST: gi|211437186|gb|FL418966.1|FL418966
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|30306817|gb|CD001490.1|CD001490
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|37420219|gb|CF647798.1|CF647798
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211479894|gb|FL423794.1|FL423794
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211137577|gb|FL389523.1|FL389523
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
EST: gi|211157939|gb|FL380349.1|FL380349
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|31349005|gb|CD433362.1|CD433362
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211288450|gb|FL410952.1|FL410952
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
EST: gi|211142865|gb|FL377125.1|FL377125
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
EST: gi|211530093|gb|FL390761.1|FL390761
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211305586|gb|FL419218.1|FL419218
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211150258|gb|FL395029.1|FL395029
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211050734|gb|FL374465.1|FL374465
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAN                         CTTTGATTCCAGCTACTTCTCANTGCTCAAATCTGACAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
EST: gi|93017175|gb|EB642695.1|EB642695
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211347968|gb|FL368837.1|FL368837
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211431976|gb|FL418926.1|FL418926
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
EST: gi|211539307|gb|FL400264.1|FL400264
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211002857|gb|FL384096.1|FL384096
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211511665|gb|FL408091.1|FL408091
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAG
EST: gi|211441962|gb|FL416333.1|FL416333
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|28187901|gb|CB179511.1|CB179511
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG
EST: gi|211063833|gb|FL423073.1|FL423073
EST:     GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAG                         CTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGACAAGAAG
genomic: GCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactt ... tcttctccagCTTTGATTCCAGCTACTTCTCAATGCTCAAATCTGAC---AAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTCTAGGGCTACTAAGGAGTCATACACATGTCAGAAACTACAGCAGTCAACTTTCAGgttaatactttaactagccctatttttagtatttggtctcaaatattgactataatacatgctttcttctccag

- - - - - - - AAGGAG