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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAATAATTGAGTACATCCCATTGCTGGCGAGTCAGTTAGGTGTTGGGTTTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatcactagacttatgtcaaaacagtaacgctgtggggctactcaagcatctttcctttccatcttgtatcctcgagtgcatataggacattgtgatgtattgactaatggtttagattaactaaccaaaatttggatttcag

Basic information

species Zea mays
transcript GRMZM2G122135_T04
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122135_T04 (Zea mays), 5'ss of exon 9
lower sequence: AT3G25800.1 (Arabidopsis thaliana), 5'ss of exon 8
TGCAATAATTGAGTACATCCCATTGCTGGCGAGTCAGTTAGGTGTTGGGTTTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatcactagacttatgtcaaaacagtaacgctgtggggctactcaagcatctttcctttccatcttgtatcctcgagtgcatataggacattgtgatgtattgactaatggtttagattaactaaccaaaatttggatttcag
||| ||||| ||||| ||||| ||| |||| ||||||||||||||||| || ||||| || ||||| || || || ||||||||||||||  |||| |||||   | |  ||     |   |   |   | || | |  |    |||    || ||||   | |  |  |||  |  |    |   | |      || |  | | ||  |  ||| | |  ||||                       
TGCTATAATCGAGTATATCCCTTTGTTGGCAAGTCAGTTAGGTGTTGGCTTCTTTGACGATAAGCTTGGTGCTCTTTGCATGCAATGGTTACAAGACAAGgtatttctttctctctcttacttttactgggaatgatcagattatacc---gcttcttatttatagaaattgattttttt--ttttttttttttttttttttttttttgcggatgctctc-attag----------------------

upper sequence: GRMZM2G122135_T04 (Zea mays), 5'ss of exon 9
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 5'ss of exon 9
TGCAATAATTGAGTACATCCCATTGCTGGCGAGTCAGTTAGGTGTTGGGTTTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatcactagacttatgtcaaaacagtaacgctgtggggctactcaagcatctttcctttccatcttgtatcctcgagtgcatataggacattgtgatgtattgactaatggtttagattaactaaccaaaatttggatttcag
 || ||||| ||||| || || ||| |||| ||||| |||||||| || || |||||||| ||||| || || || ||||||||||||||  |||| ||||| | |    ||  || |   |  || ||   |        |   | | ||       ||  | |    |   ||  |  | |   ||||     |                                                    
GGCTATAATCGAGTATATTCCCTTGTTGGCCAGTCAATTAGGTGTAGGCTTCTTTGATGAGAAGCTTGGTGCTCTTTGCATGCAATGGTTACAAGACAAGgtccctcattctctaccttcattgaatcatcca--------gataaataaatttgtcgtctctactgcttgaaattttgaaataattataaattgtcag-------------------------------------------------

upper sequence: GRMZM2G122135_T04 (Zea mays), 5'ss of exon 9
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 5'ss of exon 9
TGCAATAATTGAGTACATCCCATTGCTGGCGAGTCAGTTAGGTGTTGGGTTTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatcactagacttatgtcaaaacagtaacgctgtggggctactcaagcatctttcctttccatcttgtatcctcgagtgcatataggacattgtgatgtattgactaatggtttagattaactaaccaaaatttggatttcag
||||||||| |||||  | ||| || |||| || ||||||||| | || ||||| ||||||||||| || || || |||||||||||| || |||| ||||||    |        | ||||    | |         |     |  |   | |  | |     |  |  |    | ||                                                                     
TGCAATAATAGAGTATGTTCCACTGTTGGCCAGCCAGTTAGGTATAGGATTTTTCGATGACAAGCTCGGAGCCCTTTGCATGCAATGGCTGCAAGACAAGgtttaccttgaatctttgatgtttgcataaatttctcattcacttgttattgtagatattgacactgttctcctccttcag-------------------------------------------------------------------

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|33092634|gb|CF052628.1|CF052628
EST:     TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGAACCATGCGGAA
genomic: TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|31356310|gb|CD440667.1|CD440667
EST:     TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCTATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|17930061|gb|BM267021.1|BM267021
EST:     GCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: GCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|16919855|gb|BM074388.1|BM074388
EST:     GCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: GCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|40336631|gb|CK370701.1|CK370701
EST:     TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|116828872|gb|EC861659.1|EC861659
EST:     TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|32914759|gb|CF019571.1|CF019571
EST:     NNNNNGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: TTTT-GATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|60343317|gb|DN210290.1|DN210290
EST:     TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|60352636|gb|DN219609.1|DN219609
EST:     TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|18167158|gb|BM336997.1|BM336997
EST:     CACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: CACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|211206781|gb|FL154157.1|FL154157
EST:     TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|16926507|gb|BM079570.1|BM079570
EST:     GATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GGCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: GATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|78119292|gb|DV537676.1|DV537676
EST:     TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|5525452|gb|AI861345.1|AI861345
EST:     CTCTGCATGCAATGGTTGGAAGAT-AG                         GTCTTCTCAATCAGAGATGCTGCTGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: CTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|33101424|gb|CF061384.1|CF061384
EST:     TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|32845037|gb|CD984718.1|CD984718
EST:     TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|37393714|gb|CF634122.1|CF634122
EST:     TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|17931830|gb|BM268790.1|BM268790
EST:     CATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: CATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA
EST: gi|78022431|gb|DV490818.1|DV490818
EST:     TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAG                         GTCTTCTCAATCAGAGATGCTGCTGCCAACAACTTGAAGCGCCTTGCGGAA
genomic: TTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatca ... tggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAATAATTGAGTACATCCCATTGCTGGCGAGTCAGTTAGGTGTTGGGTTTTTTGATGACAAGCTGGGGGCACTCTGCATGCAATGGTTGGAAGATAAGgttcgtatcactagacttatgtcaaaacagtaacgctgtggggctactcaagcatctttcctttccatcttgtatcctcgagtgcatataggacattgtgatgtattgactaatggtttagattaactaaccaaaatttggatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA