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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCGTCCGCGCAGCAGCTCGCCGCTCTGGTGCTCGAGGCCACCTCCCACCCGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccccgcccttcggtggcttgctttgttacaccgggacccattgccggactaggattagggtttcattatccgtttgttctcgcgtcgaataggtggtgtgctgctcgatctgacgcgtgtttgtttgtttgtttgtttgtttcccggcacag

Basic information

species Zea mays
transcript GRMZM2G085670_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085670_T07 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 1
TTCGTCCGCGCAGCAGCTCGCCGCTCTGGTGCTCGAGGCCACCTCCCACCCGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtac---gcaccccgcccttcggtggcttgctttgttacaccgggacccattgccggactaggattagggtttcattatccgtttgttctcgcgtcgaataggtggtgtgctgctcgatctgacgcgtgtttgtttgtttgtttgtttgtttcccggcacag
 ||||| |||| |||||| || || || ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| |||||||||| ||||    | ||||| | | ||  | |||     ||   | |||   | |   ||  |  |||| |||||||||        |      ||| | ||       || |       ||||||| | |   ||| |||  |                        
CTCGTCGGCGCCGCAGCTGGCGGCGCTCGTGCTCGAGGCCACCTCCCACCCGGCCCTCTTCGCCTTCTCCGAGCTCCTCTCCCTCCCCGCCCTCTCCAAGgtataagggaccccccgcctc--tcgctccgcctgc-gccccgccgcgccgcgcgtgtttagggttagggttttgggggtggaccac-ctctcctcccccctctgat------ttcgatctaatgtcagttcgttgatgcag--------------------
















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|211281967|gb|FL132368.1|FL132368
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512613|gb|FL228206.1|FL228206
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512616|gb|FL228209.1|FL228209
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512608|gb|FL228201.1|FL228201
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512618|gb|FL228211.1|FL228211
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512617|gb|FL228210.1|FL228210
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211281965|gb|FL132366.1|FL132366
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512610|gb|FL228203.1|FL228203
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211514961|gb|FL228214.1|FL228214
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|211512615|gb|FL228208.1|FL228208
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
EST: gi|76294401|gb|DV033969.1|DV033969
EST:     CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATG                         CTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC
genomic: CGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccc ... cccggcacagCTCGCTGGCACTCAGTACTCGTCTTCACTGGACTTGCTCCGGCTCTTCGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCGTCCGCGCAGCAGCTCGCCGCTCTGGTGCTCGAGGCCACCTCCCACCCGGCCCTCTTCGCCTTCTCCGAGCTCCTCGCCCTCCCGGCCCTCTCCATGgtacgcaccccgcccttcggtggcttgctttgttacaccgggacccattgccggactaggattagggtttcattatccgtttgttctcgcgtcgaataggtggtgtgctgctcgatctgacgcgtgtttgtttgtttgtttgtttgtttcccggcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC