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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACATACTAGGTCAACTGGCAGCTGCTGTGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctcttttataacttattgtgttatttgcagttcatcttaaatattccttttgtcttgacctatgtgtttccagataatttgctcatgtttgcat...

Basic information

species Zea mays
transcript GRMZM2G035417_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035417_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g15360.1 (Oryza sativa), 5'ss of exon 11
GAACATACTAGGTCAACTGGCAGCTGCTGTGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctcttttataacttattgtgttatttgcagttcatcttaaat-attccttttg---tcttgacctatgtgtttccagataatt-tgctcatgtttgcat
 ||||||||||||||||| ||||| ||| |||||||  | || |||||||| ||||||||||||||||| || |||||||||  | |  ||||||   |||| ||   |||  | |  |    || |   | ||| ||   | || ||   |  ||||||| ||  |    || ||||      
AAACATACTAGGTCAACTAGCAGCCGCTATGCCACAGGCACTTACAGTTACTCCAGAGGAACGGGAGGCCATTCAGCGGgtatgtttgctttatatgctattttggattttctaatgaaagacaattcgctgcttctgaaattttcacacctcagtttccaaatgttgacacttatgtc-----
















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|29130583|gb|CB381287.1|CB381287
EST:     TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|89763928|gb|DY690916.1|DY690916
EST:     TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|18173452|gb|BM348840.1|BM348840
EST:     GACAGTTACCCCAGAGGAACGGTAGACTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: GACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|5468863|gb|AI834654.1|AI834654
EST:     TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|28984929|gb|BQ539309.2|BQ539309
EST:     TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|5152838|gb|AI759136.1|AI759136
EST:     TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|211316184|gb|FL331849.1|FL331849
EST:     TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|16921346|gb|BM075107.1|BM075107
EST:     TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|16377325|gb|BI991866.1|BI991866
EST:     TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|211092608|gb|FL283417.1|FL283417
EST:     GCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: GCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|12969776|gb|BG266651.1|BG266651
EST:     TGCCACAAGCGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAGCCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|7227769|gb|AW566410.1|AW566410
EST:     TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|10450875|gb|BE924799.1|BE924799
EST:     AGGAACGGGAGGCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: AGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|91875123|gb|EB405080.1|EB405080
EST:     TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
EST: gi|7216944|gb|AW563051.1|AW563051
EST:     TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGG                         CTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA
genomic: TGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctct ... tcctgaacagCTCGAGGGAATGGGGTTCAACCGTGAGCTTGTGCTAGAAGTTTTCTTTGCA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACATACTAGGTCAACTGGCAGCTGCTGTGCCACAAACGCTGACAGTTACCCCAGAGGAACGGGAGGCTATCCAGCGGgtacatctcttttataacttattgtgttatttgcagttcatcttaaatattccttttgtcttgacctatgtgtttccagataatttgctcatgtttgcat

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