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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGCACGTCGCTGCACCTCGCCGCTCGCAGCGGGAGCCTGGATTGCACCCGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcaccacatctctgtctctgcagatcttatttcagtgtactctactctacatgccaaagattacatgtggtgggtgtgggtctgagaaaacacgcg...

Basic information

species Zea mays
transcript GRMZM2G069162_T03
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069162_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g02130.1 (Oryza sativa), 5'ss of exon 6
GTAGCACGTCGCTGCACCTCGCCGCTCGCAGCGGGAGCCTGGATTGCACCCGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcaccacatctctgtctctgcagatcttatttcagtgtactctactctacatgccaaag-attacatgtggtgggtgtgggtctgagaaaacacgcg--
| ||||||||||| ||  | || ||||| ||||||| | ||||||||| | |||||||||| ||||||||||| ||||| ||||  |||||||| || ||||||| || | |||| |  | || ||| | || | |  | | |         | |     | |   ||       | | |||  ||     |   || | |  
GAAGCACGTCGCTTCATTTGGCTGCTCGTAGCGGGAACTTGGATTGCATCAGGAAGCTGCTTGCCTGGGGAGCTGATCGGCTCCAAAGGGATTCGGCTGGgtgagaactagatctttcccccttcagtttttgtcttggcgcatatagaagaaaacattgatgtgctatcaagcatagttgttagt---gaagttcaggtgtt
















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|149010154|gb|EE041967.2|EE041967
EST:     CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGG                         GAGGATCCTTTACGCCGTGGCGCTGA
genomic: CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTTACGCCGTGGCGCTGA
EST: gi|93016129|gb|EB641649.1|EB641649
EST:     CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGG                         GAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
genomic: CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
EST: gi|71313857|gb|DR793525.1|DR793525
EST:     CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGAT-CAGCAAG                         GAGGATCCCTT
genomic: CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTT
EST: gi|76913183|gb|DV165033.1|DV165033
EST:     CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGG                         GAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGGCG-
genomic: CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCG-CGG
EST: gi|71320952|gb|DR797192.1|DR797192
EST:     CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGAT-CAGCAGG                         GAGGATCCCTTA
genomic: CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTTA
EST: gi|50328517|gb|CO523643.1|CO523643
EST:     CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGG                         GAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
genomic: CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
EST: gi|71768259|gb|DR966196.1|DR966196
EST:     CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCGGGAGGGAT-CAGCAGG                         GAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
genomic: CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
EST: gi|78080357|gb|DV508769.1|DV508769
EST:     CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGG                         GAGGATCCCTTACGCCGTGGCGCTGAAGCGCACCCACGAGGCGTGCGCGGC
genomic: CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
EST: gi|76013282|gb|DT940452.1|DT940452
EST:     CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGG                         GAGGATCCCTT
genomic: CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTT
EST: gi|67014789|gb|CO443538.1|CO443538
EST:     GGAAGCTGCTCGCCTGGGGAGCGGATCGTCTNCGGGAGG-ATTCAGCAGG                         GAGGATCCCTTACGCCGTGGCGCTGAAGCGCA-CCACGAAGCGTGCGCTGC
genomic: GGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGG-AGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
EST: gi|148951595|gb|EC897330.2|EC897330
EST:     CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGG                         GAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
genomic: CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
EST: gi|101399477|gb|EB821611.1|EB821611
EST:     CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGG                         GAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
genomic: CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
EST: gi|93281560|gb|EB673824.1|EB673824
EST:     CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGG                         GAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
genomic: CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
EST: gi|71304552|gb|DR788396.1|DR788396
EST:     CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGG                         GAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC
genomic: CGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcacca ... gtgttggcagGAGGATCCCTTACGCCGTGGCGCTGAAGCGCAACCACGAGGCGTGCGCGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGCACGTCGCTGCACCTCGCCGCTCGCAGCGGGAGCCTGGATTGCACCCGGAAGCTGCTCGCCTGGGGAGCGGATCGTCTCCGGAGGGATTCAGCAGGgtgagcaccacatctctgtctctgcagatcttatttcagtgtactctactctacatgccaaagattacatgtggtgggtgtgggtctgagaaaacacgcg

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaaca