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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTGGACTAGAATGGGGAAAGCTATATGAGATAGAAGCCGCGTACCTGCCTCAGGTCACAGACGAGTTGGACACCCAGAACTTTGAGAAGTTTGAGGAGgtaataaatgcatggtgctgtcgtttacaaagaaacgtgctttaatttctcactcactcaccggatacttattatctgtgtgcgtggtgttttaatttgtttggcag

Basic information

species Zea mays
transcript GRMZM2G088245_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
CAGTGGACTAGAATGGGGAAAGCTATATGAGATAGAAGCCGCGTACCTGCCTCAGGTCACAGACGAGTTGGACACCCAGAACTTTGAGAAGTTTGAGGAGgtaataaatgcatggtgctgtcgtttacaaagaaacgtgctttaatttctcactcactcaccggatacttattatctgtgtgcgtggtgttttaatttgtttggcag
 |||||| |||||||||  ||  ||||||| |||||||| || || |  ||||| ||||| || ||||| || || ||||| |||||||||||||| ||||| |    |    | | || | |     || |||    | || |||   |   | |   |    || | |||  | ||| |  |  |                    
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggt---cgtttcttttggcctaaaggaattcagtttcaataagttggt-ataaatgttattcctatggtgtgttt-tgcag--------------------
















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|93015890|gb|EB641410.1|EB641410
EST:     CTCAGGTCACAGACGAGTTGGACACCCAGAACTTTGAGAAGTTTGAGGAG                         TCCTCGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGA
genomic: CTCAGGTCACAGACGAGTTGGACACCCAGAACTTTGAGAAGTTTGAGGAGgtaataaatg ... tgtttggcagTCCTCGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGA
EST: gi|9954068|gb|BE640651.1|BE640651
EST:     CACCCAGAACTTTGAGAAGTTTGAGGAG                         TCCTCGGACGGTAGTAGCGTTCAGGGTTCAGCGAAGACGGGCCCTTGGAGA
genomic: CACCCAGAACTTTGAGAAGTTTGAGGAGgtaataaatg ... tgtttggcagTCCTCGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGA
EST: gi|6952724|gb|AW424792.1|AW424792
EST:     CCAGAACTTTGAGAAGTTTGAGGAG                         TCCTCGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGA
genomic: CCAGAACTTTGAGAAGTTTGAGGAGgtaataaatg ... tgtttggcagTCCTCGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGA
EST: gi|78180424|gb|DV550797.1|DV550797
EST:     CTCAGGTCACAGACGAGTTGGACACCCAGAACTTTGAGAAGTTTGAGGAG                         TCCTCGGACGGTAGTAGCGTTCAGGGTTCAGCGAAGACGGGCCCTTGGAGA
genomic: CTCAGGTCACAGACGAGTTGGACACCCAGAACTTTGAGAAGTTTGAGGAGgtaataaatg ... tgtttggcagTCCTCGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGA
EST: gi|12047061|gb|BF729200.1|BF729200
EST:     CTTTGAGAAGTTTGAGGAG                         TCCTCGGACGGTAGTAGCGTTCAGGGTTCAGCGAAGACGGGCCCTTGGAGA
genomic: CTTTGAGAAGTTTGAGGAGgtaataaatg ... tgtttggcagTCCTCGGACGGTAGTAGCGTTCAGGGTTCAGCAAAGGCGGGCCCTTGGAGA
EST: gi|71298682|gb|DR785316.1|DR785316
EST:     CTCAGGTCACAGACGAGTTGGACACCCAGAACTTTGAGAAGTTTGAGGAG                         TCCTCGGACGGTAGTAGCGTTCAGGGTTC
genomic: CTCAGGTCACAGACGAGTTGGACACCCAGAACTTTGAGAAGTTTGAGGAGgtaataaatg ... tgtttggcagTCCTCGGACGGTAGTAGCGTTCAGGGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTGGACTAGAATGGGGAAAGCTATATGAGATAGAAGCCGCGTACCTGCCTCAGGTCACAGACGAGTTGGACACCCAGAACTTTGAGAAGTTTGAGGAGgtaataaatgcatggtgctgtcgtttacaaagaaacgtgctttaatttctcactcactcaccggatacttattatctgtgtgcgtggtgttttaatttgtttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG