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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTATTTGGATGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatcaatattattaatgtgtatggtgtgccattattatgtcctatatgctagtcaggaattttaaatattatacacctgtttgtatgcactgcct...

Basic information

species Zea mays
transcript GRMZM2G042099_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042099_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g54784.1 (Oryza sativa), 5'ss of exon 8
GTTTATTTGGATGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatcaa-tat-tattaatgtgtatggtgtgccattattatgtcctatatgctagtcaggaattttaaatattatacacctgtttgtatgcactgcct
||||| ||||||||||| |||||||| ||| |||||||||||||||| ||||||||||| |||||||||    ||| |||     | |||    | |||| ||||||||  | ||  ||| || ||  |||     | |      |     || | |    ||
GTTTACTTGGATGTATTCTCAGTAGTTGTTCTTGTACTTGGTGGTGCGCTGGCATGTTATGgtaagcatagcctatgtatactcatctataccataccataattatgtcgca-atattaggcatgatgttttctagtcaattgtttcaacctaag-ataaact
















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|71301931|gb|DR787043.1|DR787043
EST:     TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
EST: gi|91053130|gb|EB163548.1|EB163548
EST:     TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
EST: gi|71313708|gb|DR793441.1|DR793441
EST:     TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
EST: gi|71301929|gb|DR787042.1|DR787042
EST:     TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
EST: gi|149088757|gb|EE177881.2|EE177881
EST:     TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
EST: gi|94478108|gb|EB707066.1|EB707066
EST:     TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
EST: gi|91053129|gb|EB163547.1|EB163547
EST:     TATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: TATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
EST: gi|78179907|gb|DV550280.1|DV550280
EST:     TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
EST: gi|60354545|gb|DN221518.1|DN221518
EST:     TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
EST: gi|78079632|gb|DV508044.1|DV508044
EST:     TTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: TTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
EST: gi|78105386|gb|DV523804.1|DV523804
EST:     TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
EST: gi|91052961|gb|EB163379.1|EB163379
EST:     TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
EST: gi|148962185|gb|EE013000.2|EE013000
EST:     TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: TGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
EST: gi|149089186|gb|EE178375.2|EE178375
EST:     AGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACG                         GTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA
genomic: AGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatca ... ggtcatgtagGTGCAGTGTTATTCTCGAAGATGAGCAAAGTTCGTTCTGAAACTGTATCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTATTTGGATGTATTTTCAGTAGTAGTTATTGTACTTGGTGGTGCTCTGGCATGTTACGgtaagcatcaatattattaatgtgtatggtgtgccattattatgtcctatatgctagtcaggaattttaaatattatacacctgtttgtatgcactgcct

- - - - - - - - - - - - - - - - - - - TGGTGG