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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaaacattttctcatactattgctaaatttgtcattttccgtgattatcagaattaaacttcatgtttatatttcttagcatgtaagcacatg...

Basic information

species Zea mays
transcript GRMZM2G147726_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147726_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g15040.1 (Oryza sativa), 5'ss of exon 6
GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaaacattt-----tctcata--ctattgctaaatttgtcattttccgtgattatcagaattaaacttcatgtttatatttcttagcatgtaagcacatg
|||||||| || |||||||||||||||||||| ||||| ||||| |||||||||  ||||  ||     |||||||  || ||| ||| |||||    ||   |   | ||| |  ||  || |     || |||| |  ||||||         
GAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaaaccattctgggtctcatacactgttgttaattttgtgtgcttaaattggtttcaaacgta--ctccggtgctacatttttctgcatgtggtt-----

upper sequence: GRMZM2G147726_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g15040.2 (Oryza sativa), 5'ss of exon 6
----------------------------------------------------GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaaacattt-----tctcatac--tattgctaaatttgtcattttccgtgattatcagaattaaacttcatgtttatatttcttagcatgtaagcacatg
                                                    |||||||| || |||||||||||||||||||| ||||| ||||| |||||||||  ||||  ||     ||||||||  | ||| ||| |||||    ||   |   | ||| |  ||  || |     || |||| |  ||||||         
TTGATTTCATTTAGGTGCATTTGCTTATTGGCTGCTTGCCTTCAACTGGCAGGAGGATGAGCTAAAAGGTGCAGTTGTCCTTGTATATGCGAATAAACAGgtaaaaccaaaccattctgggtctcatacactgttgttaattttgtgtgcttaaattggtttcaaacgta--ctccggtgctacatttttctgcatgtggtt-----
















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|211217104|gb|FL383487.1|FL383487
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         G-T------G---CACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|18181584|gb|BM382794.1|BM382794
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|60396369|gb|DN229238.1|DN229238
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|32945768|gb|CF050587.1|CF050587
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|5456152|gb|AI833842.1|AI833842
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|211104194|gb|FL471169.1|FL471169
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|31611779|gb|CD568401.1|CD568401
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCTAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|149086485|gb|EE176030.2|EE176030
EST:     TGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: TGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|60346093|gb|DN213066.1|DN213066
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|29946538|gb|CB816199.1|CB816199
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|6994080|gb|AW453294.1|AW453294
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|44901570|gb|CK828115.1|CK828115
EST:     CTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: CTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|71426509|gb|DR807559.1|DR807559
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAGTAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|14203130|gb|BG836807.1|BG836807
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATG-TGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|211068733|gb|FL060710.1|FL060710
EST:     GAGGATGAACTTAAAGGTGGAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|60399097|gb|DN231911.1|DN231911
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|32906937|gb|CF011750.1|CF011750
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTCGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|211301270|gb|FL181609.1|FL181609
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|71775316|gb|DR973194.1|DR973194
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|29544164|gb|CB604544.1|CB604544
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCCCTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|78110076|gb|DV528491.1|DV528491
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|18175608|gb|BM350861.1|BM350861
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|21809994|gb|BQ668312.1|BQ668312
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
EST: gi|33092385|gb|CF052379.1|CF052379
EST:     GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAG                         GATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA
genomic: GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaa ... tttcatgcagGATCTTCCAGGTGCACTCGATGATGCTGCCATTACAGAGTCATTAGAACTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGATGAACTTAAAGGTGCAGTTGTCCTTGTGTATGCAAATAAGCAGgtaaaaagaaacattttctcatactattgctaaatttgtcattttccgtgattatcagaattaaacttcatgtttatatttcttagcatgtaagcacatg

 AGGATG