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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCCATTTAGGCTACTGGCTGCTGAATATGGTGCTGATATTACTTATGGAGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATGgtattgtagttcaattgatatttggcatctgatgtggtctattggtcctacaactgtctccactgcatcagtgttttagtttactcatccaagtatccaa...

Basic information

species Zea mays
transcript GRMZM2G468693_T06
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G468693_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g44890.2 (Oryza sativa), 5'ss of exon 2
TTGCCATTTAGGCTACTGGCTGCTGAATATGGTGCTGATATTACTTATGGAGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATGgtattgtagttcaattgatatttggcatctgat-gtggtctattggtcctacaactgtctccactgcatcagtgttttagtttactcatccaagtatccaa---
 |||| ||||||||||||||||||||||||||||||||||| ||||| ||||||||||| || ||||| || || ||||||||||| |||||||||||||||||||||||||||||| | |||||||| | ||  || |||        | ||||||| |  || |      | || |     | |     ||| |        
CTGCCGTTTAGGCTACTGGCTGCTGAATATGGTGCTGATATCACTTACGGAGAAGAAATAATAGATCATAAGTTTTTGAAGTGTGAACGTGTTACAAATGgtattgtagttcaattggtgtttggcattttattatgatctcgca----tgcaactgtattaacagttaagttcttctcagaaaatttgttaagcagttggcat
















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|211460993|gb|FL255146.1|FL255146
EST:     AGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATG                         AATCTCTTGGGACTACTGATTTTGTGGAGAAAGGGACTGACAGTGTAGTTT
genomic: AGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATGgtattgtagt ... tgtttaccagAATCTCTTGGGACTACTGATTTTGTGGAGAAAGGGACTGACAGTGTAGTTT
EST: gi|76922868|gb|DV169214.1|DV169214
EST:     AGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATG                         AATCTCTTGGGACTACTGATTTTGTGGAGAAAGGGACTGACAGTGTAGTTT
genomic: AGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATGgtattgtagt ... tgtttaccagAATCTCTTGGGACTACTGATTTTGTGGAGAAAGGGACTGACAGTGTAGTTT
EST: gi|76015755|gb|DT942925.1|DT942925
EST:     AGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATG                         AATCTCTTGGGACTACTGATTTTGTGGAGAAAGGGACTGACAGTGTAGTTT
genomic: AGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATGgtattgtagt ... tgtttaccagAATCTCTTGGGACTACTGATTTTGTGGAGAAAGGGACTGACAGTGTAGTTT
EST: gi|74237927|gb|DT645841.1|DT645841
EST:     AGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATG                         AATCTCTTGGGACTACTGATTTTGTGGAGAAAGGGACTGACAGTGTAGTTT
genomic: AGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATGgtattgtagt ... tgtttaccagAATCTCTTGGGACTACTGATTTTGTGGAGAAAGGGACTGACAGTGTAGTTT
EST: gi|5915492|gb|AW053133.1|AW053133
EST:     AGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATG                         AATCTCTTGGGACTACTGATTTTGTGGAGAAAGGGACTGACAGTGTAGTTT
genomic: AGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATGgtattgtagt ... tgtttaccagAATCTCTTGGGACTACTGATTTTGTGGAGAAAGGGACTGACAGTGTAGTTT
EST: gi|89762291|gb|DY689959.1|DY689959
EST:     AGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATG                         AATCTCTTGGGACTACTGATTTTGTGGAGAAAGGGACTGACAGTGTAGTTT
genomic: AGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATGgtattgtagt ... tgtttaccagAATCTCTTGGGACTACTGATTTTGTGGAGAAAGGGACTGACAGTGTAGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCCATTTAGGCTACTGGCTGCTGAATATGGTGCTGATATTACTTATGGAGAAGAAATTATTGATCACAAATTCTTGAAGTGTGAGCGTGTTACAAATGgtattgtagttcaattgatatttggcatctgatgtggtctattggtcctacaactgtctccactgcatcagtgttttagtttactcatccaagtatccaa

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG