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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATCTTGAGCTAATTGCTTACACTGTCTGGAATGCACTTGAGTATTCTTATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttgggttgaacttatgttgatttcactctctgaatgctttaggcatgtgctgagtctagcactggttaagctttcttttgaaactagtatcttatcttctgcag

Basic information

species Zea mays
transcript GRMZM2G000749_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000749_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 5'ss of exon 11
CAATCTTGAGCTAATTGCTTACACTGTCTGGAATGCACTTGAGTATTCTTATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgtt-gggttgaacttatgttgatttcac----tctctgaatgcttt--aggcatgtgctgagtctagcactggttaagctttcttttgaaactagtatc----ttatcttctgcag------------------
 ||||| || | | | |    ||   | |||||||||  ||| | |||||||||||| ||| | | |||||| ||||||||||||||||| ||||| ||||| ||||  |||||| ||| |||  ||||||     | | ||  ||||||  |||   |||  |||   | ||| |  |  | |||||| ||   | | |||     ||  | | |                      
AAATCTGGACCAAGTCGTAGGCATCATATGGAATGCAACTGAATCTTCTTATGCCTTTGAAAGCAGAGCTGAACAACTAAAGAAGGAACGTCTGGAGCAGgtatgtttaggttgatcttctgtgtatttcatatcttatttgtttgcttttgaggatggtggggagaggatcacagaatgcgatttcttatgtgccaattattagcattgacgtttaagcacctttggttgtatccag
















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|21987416|gb|BQ778944.1|BQ778944
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|211021453|gb|FL457596.1|FL457596
EST:     ATGCCTTTGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAG
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAG
EST: gi|211264027|gb|FL283565.1|FL283565
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|60341236|gb|DN208209.1|DN208209
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|88756696|gb|DY540837.1|DY540837
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|211534613|gb|FL443294.1|FL443294
EST:     TGCCTTTGAAGGAATAGGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: TGCCTTCGAAGGAATA-GCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|211264028|gb|FL283566.1|FL283566
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|67040818|gb|CO467073.1|CO467073
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|22543109|gb|BU093547.1|BU093547
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
EST: gi|211264029|gb|FL283567.1|FL283567
EST:     ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAG                         GTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT
genomic: ATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttggg ... tcttctgcagGTGGCACTGAAAAGTGGTCAGACCAGTGATGAAGTGACTCCTTTGGATGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATCTTGAGCTAATTGCTTACACTGTCTGGAATGCACTTGAGTATTCTTATGCCTTCGAAGGAATAGCTGAGCAACTAAAGAAGGAACGGCTGGAACAGgtttgttgggttgaacttatgttgatttcactctctgaatgctttaggcatgtgctgagtctagcactggttaagctttcttttgaaactagtatcttatcttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA