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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTTCTGCAGCAGGTCAAGGGGCTGCTGCGGCTGGACTTCGCCGTCGCAGCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttctctcttttgctttgacctgtcatgtttcagcgtggtagaagttcaagcgcatctaattttgtctcggtctctcggaggagtatagtggtat...

Basic information

species Zea mays
transcript GRMZM2G146206_T05
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146206_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g62420.2 (Oryza sativa), 5'ss of exon 3
TTTTTCTGCAGCAGGTCAAGGGGCTGCTGCGGCTGGACTTCGCCGTCGCAGCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttctctcttttgctttgacctgtcatgtttcagcgtggtagaagttcaagcgcatctaattt-tgtctcggtc--tctcggaggagtatagtggtat
| || |||| |||||| |||||  |||| |||| ||||||| ||||||| |||||||| ||||||||||||||||||||||||||||| |||||||||||||   | || |||     ||    ||||   ||||||            |||       |  | |||  ||  |   |     | ||  ||  |    ||  |
TGTTCCTGCCGCAGGTGAAGGGTTTGCTCCGGCCGGACTTCTCCGTCGCCGCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtc-ctcccccactcc--cctgctctgtttcccttccccttttgttttgagagagatgattagtgatttatttggcattgggtgaacaactcggcct
















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|34391231|gb|CF384459.1|CF384459
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|149095398|gb|EE181040.2|EE181040
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|37361179|gb|CF602468.1|CF602468
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|150037302|gb|DY843516.1|DY843516
EST:     GCGCAG-ACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|61118911|gb|DN559872.1|DN559872
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|6021382|gb|AW066310.1|AW066310
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|211332034|gb|FL380493.1|FL380493
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|76928137|gb|DV171503.1|DV171503
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|38568995|gb|CF974880.1|CF974880
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|74242319|gb|DT650233.1|DT650233
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|148995363|gb|EE034577.2|EE034577
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|31351356|gb|CD435713.1|CD435713
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|32915342|gb|CF020154.1|CF020154
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|37361339|gb|CF602628.1|CF602628
EST:     GCGCANAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|211504304|gb|FL391671.1|FL391671
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|31354853|gb|CD439210.1|CD439210
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|32851161|gb|CD990842.1|CD990842
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|211405784|gb|FL400096.1|FL400096
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|38229553|gb|CF919866.1|CF919866
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|211387019|gb|FL373417.1|FL373417
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|110517584|gb|EE022171.1|EE022171
EST:     CTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: CTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|71757929|gb|DR955866.1|DR955866
EST:     CTGCTGGGTGCGCAAGGGCGGCGCC-TCACCCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: CTGCTGGGTGCGCAAGGGCGGCGCCTTCA-CCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|28566674|gb|CB278322.1|CB278322
EST:     GCGCAGAACTGCTGGGTGCACAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|28576049|gb|CB281941.1|CB281941
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|32909130|gb|CF013942.1|CF013942
EST:     CCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: CCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|71436570|gb|DR817620.1|DR817620
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|211247588|gb|FL403551.1|FL403551
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|33770896|gb|CF273190.1|CF273190
EST:     GCGCANAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|211416108|gb|FL411159.1|FL411159
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|30160504|gb|CB924233.1|CB924233
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|67015285|gb|CO444034.1|CO444034
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|149097486|gb|EE183358.2|EE183358
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|71330645|gb|DR802096.1|DR802096
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
EST: gi|149005099|gb|EE039628.2|EE039628
EST:     GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAG                         TGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC
genomic: GCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttct ... cttgtttcagTGCTGAGATGCTGGTAAACCTGCAGGTGCCCTGGGTCATTTTGGGACATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTTCTGCAGCAGGTCAAGGGGCTGCTGCGGCTGGACTTCGCCGTCGCAGCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttctctcttttgctttgacctgtcatgtttcagcgtggtagaagttcaagcgcatctaattttgtctcggtctctcggaggagtatagtggtat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA