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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttacttttctttctgggaatcaaattaactgctgttatggtttgtggtcctgggttccttataaatgttctcaccatttggcag

Basic information

species Zea mays
transcript GRMZM2G133029_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133029_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g56930.2 (Oryza sativa), 5'ss of exon 6
ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactt-ttctttctgggaatcaaattaactgctgttatggtttgtggtcctgggttccttataaatgttctcaccatttggcag-
||| ||||||||||||||||||||||||| ||||| |||||||| || | |||||||||| | ||||||||||||||  ||| || |||| | |||  |||||| | |||  | |  ||     |      || |||| | || || || |  ||   |   
ATAACTGCTGCAGTCTCTCCATCTGTGCGCTCTCTTGTCAGCAAGGGGAACCAATGCTTTGTAACTTCCAGCAGgttagcttcttgtttcagtgaaggaaattagcagctcatgttcttcagtatgtcaaattacttacagatattttcgcttttcaaccag
















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|14203670|gb|BG837347.1|BG837347
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|32928510|gb|CF033322.1|CF033322
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACGTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|32919740|gb|CF024552.1|CF024552
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACGTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|84976772|gb|DW475194.1|DW475194
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|211449625|gb|FL035069.1|FL035069
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACGTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTTATGGGTGGTGTTG
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTT-ATGGGTGGTGTTG
EST: gi|74234970|gb|DT642884.1|DT642884
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|148940876|gb|EC885709.2|EC885709
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|32928535|gb|CF033347.1|CF033347
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACGTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|19350596|gb|BM895128.1|BM895128
EST:     TCACGTCCAGCAG                         CGTTGACTCATCGTTTCCAGCCGTAGCCCTTTATTTTATGGGTGGTGTTGC
genomic: TCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|32929051|gb|CF033863.1|CF033863
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACGTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|74234969|gb|DT642883.1|DT642883
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|211449627|gb|FL035071.1|FL035071
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|113702354|gb|EE679858.1|EE679858
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|32931524|gb|CF036336.1|CF036336
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACGTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|33100162|gb|CF060122.1|CF060122
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACGTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|33095406|gb|CF055400.1|CF055400
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACGTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGCGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|148983004|gb|EE028899.2|EE028899
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
EST: gi|33099546|gb|CF059506.1|CF059506
EST:     GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACGTCCAGCAG                         CGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC
genomic: GTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttactttt ... catttggcagCGTTGACTCATCGTTTCCAACCGTAACCCTTTATTTTATGGGTGGTGTTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAGCTGCTGCAGTCTCTCCATCTGTGCGTTCTCTAGTCAGCAAAGGAAGCCAATGCTTTATCACTTCCAGCAGgtttacttttctttctgggaatcaaattaactgctgttatggtttgtggtcctgggttccttataaatgttctcaccatttggcag

- - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - -  AAGGAA