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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCGTCCGCGCCCCAGCTCGCCGCGCTGGTGCTTGAGGCCACCTCCCACCCGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcactgcccttggcgtgcgccctgctacgttactccgggacccgctgccggactaggttttgggtttcattatctgtttgtcttcgcgtcgattaggtggtgtgtggcgcgatctgacgcgggtttgtttgtttatcggcgcag

Basic information

species Zea mays
transcript GRMZM2G171745_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171745_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 1
TTCGTCCGCGCCCCAGCTCGCCGCGCTGGTGCTTGAGGCCACCTCCCACCCGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcactgcccttggcgtgcgccctgc-tacgttactccgggacccgctgccggactaggttttgggtttcattatctgtttgtcttcgcgtcgattaggtggtgtgtggcgcgatctgacgcgggtttgtttgtttatcggcgcag
 ||||| ||||| ||||| || ||||| ||||| ||||||||||||||||||||||||||||||||||||||||||||| ||||||| ||||||||||||||    |     |||  | |   ||| | || | ||   | ||| |  |||| ||  |  |||| || ||||||        |     ||   | ||       || | |      |||||| | |   ||| |||  |  |         
CTCGTCGGCGCCGCAGCTGGCGGCGCTCGTGCTCGAGGCCACCTCCCACCCGGCCCTCTTCGCCTTCTCCGAGCTCCTCTCCCTCCCCGCCCTCTCCAAGgtataagggac-cccccgcctctcgctccgcctgcgccccgccgcg--ccgc-gcgtgtttagggttagggttttgggggtggaccacctctcc-tcccccctctgattt------cgatctaatgtcagttcgttgatgcag--------
















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|13178371|gb|BG349629.1|BG349629
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211178527|gb|FK980685.1|FK980685
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|78118434|gb|DV536820.1|DV536820
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211178524|gb|FK980682.1|FK980682
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211180924|gb|FK980686.1|FK980686
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|86472725|gb|DY239095.1|DY239095
EST:     CGGCCCTCTTCGCCTTCTCAGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCAGGGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCCCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211178519|gb|FK980677.1|FK980677
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211180926|gb|FK980688.1|FK980688
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|71427328|gb|DR808378.1|DR808378
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|148943925|gb|EC889005.2|EC889005
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|148972927|gb|EE023942.2|EE023942
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|78081417|gb|DV509829.1|DV509829
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|74242379|gb|DT650293.1|DT650293
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211178522|gb|FK980680.1|FK980680
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|149089443|gb|EE178684.2|EE178684
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211178525|gb|FK980683.1|FK980683
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|76931006|gb|DV172592.1|DV172592
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|5268890|gb|AI770854.1|AI770854
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211180929|gb|FK980691.1|FK980691
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211178518|gb|FK980676.1|FK980676
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|29129753|gb|CB380457.1|CB380457
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211180931|gb|FK980693.1|FK980693
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|78112153|gb|DV530549.1|DV530549
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|50339563|gb|CO534689.1|CO534689
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCGCGGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|67021495|gb|CO450244.1|CO450244
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAG                         CTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcac ... atcggcgcagCTCACTGGCACGCAGTACGCGTCGTCACTGGACTTGCTCCGGCTCTTCGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCGTCCGCGCCCCAGCTCGCCGCGCTGGTGCTTGAGGCCACCTCCCACCCGGCCCTCTTCGCCTTCTCCGAGCTCCTCACCCTCCCGGCCCTCTCCAAGgttcgcgcactgcccttggcgtgcgccctgctacgttactccgggacccgctgccggactaggttttgggtttcattatctgtttgtcttcgcgtcgattaggtggtgtgtggcgcgatctgacgcgggtttgtttgtttatcggcgcag

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