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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGAAGAGCACAATTGGTTGGAGCGTTGGCAATATATTACTTGATCTCACAGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgcatttgtccttcgattttactcccatggttttgtattgcaccagactgttttcctcactgaacaaattgtgatgcag

Basic information

species Zea mays
transcript GRMZM2G015869_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015869_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g18110.1 (Oryza sativa), 5'ss of exon 6
CGGAAGAGCACAATTGGTTGGAGCGTTGGCAATATATTACTTGATCTCACAGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgcatttgtccttcgattttactccc--atggttttgtattgcaccagactgttttcctcactgaacaaattgtgatgcag
 ||||||| ||||||||||||||  |||||||||| ||||||||||| |||||||||||||| || ||| | |||||||||||||| || |||||||||||||||||||||| |||||| |||  || |     ||   | |  | |    ||||   |||| || |||||||| |||||| |||||
AGGAAGAGTACAATTGGTTGGAGTATTGGCAATATTTTACTTGATCTTACAGGAGGGGTGCTAAACTTTGGCCAGATGGGTGTGCAATCAATAGATCAACgtaagctgcattggtcctttgatcatagtgtatgatatatattaagtatgtcagatatttttactgactgaacatattgtgttgcag
















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|60338746|gb|DN205719.1|DN205719
EST:     AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAAC                         ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
EST: gi|78092412|gb|DV520786.1|DV520786
EST:     AGGAGGGGTGCTGAATTTTTGTCAGAGGGGTGTGCAGTCTATAGATCAAC                         ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
EST: gi|166698057|gb|EG194972.1|EG194972
EST:     CTGAA-TTTTGTCAGATGGGTGTGCAGTCTATAGATCAAC                         ATAACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: CTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagAT-ACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
EST: gi|78084914|gb|DV513307.1|DV513307
EST:     AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAAC                         ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
EST: gi|5932718|gb|AW057079.1|AW057079
EST:     GAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAAC                         ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: GAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
EST: gi|50323027|gb|CO518153.1|CO518153
EST:     AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAAC                         ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
EST: gi|78081909|gb|DV510321.1|DV510321
EST:     AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAAC                         ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
EST: gi|211091569|gb|FL457271.1|FL457271
EST:     AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAAC                         ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
EST: gi|50329143|gb|CO524269.1|CO524269
EST:     AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAAC                         ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
EST: gi|14244729|gb|BG842667.2|BG842667
EST:     TTTTTGTCAGATGGGTGTGCAGTCTATAGATCAAC                         ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: TTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
EST: gi|14208276|gb|BG841954.1|BG841954
EST:     ATGGGTGTGCAGTCTATAGAT-AAC                         ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: ATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
EST: gi|5919428|gb|AW054525.1|AW054525
EST:     GAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAAC                         ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: GAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
EST: gi|78084875|gb|DV513268.1|DV513268
EST:     AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAAC                         ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
EST: gi|213191208|gb|FM187518.1|FM187518
EST:     AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAAC                         ATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG
genomic: AGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgca ... tgtgatgcagATACTTTGGTGAATTTCTATGGAAACATTGGGAAAACCCTTCTTTCATTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGAAGAGCACAATTGGTTGGAGCGTTGGCAATATATTACTTGATCTCACAGGAGGGGTGCTGAATTTTTGTCAGATGGGTGTGCAGTCTATAGATCAACgtaagctgcatttgtccttcgattttactcccatggttttgtattgcaccagactgttttcctcactgaacaaattgtgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA