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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacagtagtgcgcgcggccgtcgtcctcgcggcggcatgggcgaatcggtcggtcgtcatgcgagcgctcgggcgcccttcactgactcgggtgcccttcttctatcttgtctgtcccagCACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCGCCGCACTCGTGCAGGATGCTCGTCCTCAAGCCCAGGATCCAGATCCAGT

Basic information

species Zea mays
transcript GRMZM2G095126_T02
intron # 11
splice site 3'
intron type U2

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|110489816|gb|EE013039.1|EE013039
EST:     ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTG                         CACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
genomic: ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTGgtacgtacag ... tctgtcccagCACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
EST: gi|71323535|gb|DR798428.1|DR798428
EST:     ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTG                         CACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTTGACGTCGCG
genomic: ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTGgtacgtacag ... tctgtcccagCACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
EST: gi|161580098|gb|EY955473.1|EY955473
EST:     CGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTG                         CACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
genomic: CGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTGgtacgtacag ... tctgtcccagCACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
EST: gi|88753305|gb|DY537446.1|DY537446
EST:     ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTG                         CACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
genomic: ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTGgtacgtacag ... tctgtcccagCACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
EST: gi|94473544|gb|EB702502.1|EB702502
EST:     ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTG                         CACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTTGACGTCGCG
genomic: ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTGgtacgtacag ... tctgtcccagCACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
EST: gi|148929477|gb|EC875592.2|EC875592
EST:     ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTG                         CACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTTGACGTCGCG
genomic: ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTGgtacgtacag ... tctgtcccagCACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
EST: gi|5740192|gb|AI947882.1|AI947882
EST:     ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTG                         CACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
genomic: ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTGgtacgtacag ... tctgtcccagCACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
EST: gi|149080680|gb|EE169738.2|EE169738
EST:     ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTG                         CACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
genomic: ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTGgtacgtacag ... tctgtcccagCACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
EST: gi|71767715|gb|DR965652.1|DR965652
EST:     ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTG                         CACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG
genomic: ACATCGGCCTCCCCGCCGGCACGCCCGTCGAGGCCAGGGACCTGTGGCTGgtacgtacag ... tctgtcccagCACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctcgggcgcccttcactgactcgggtgcccttcttctatcttgtctgtcccagCACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCGCCGCACTCGTGCAGGATGCTCGTCCTCAAGCCCAGGATCCAGATCCAGT
               cactgac  putative branch site (score: 2)
                             cccttcttctatcttg  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtacagtagtgcgcgcggccgtcgtcctcgcggcggcatgggcgaatcggtcggtcgtcatgcgagcgctcgggcgcccttcactgactcgggtgcccttcttctatcttgtctgtcccagCACGAGACGTTGGACGCCACGTTCACGGACAAGATGAGCTTCGACGTCGCGCCGCACTCGTGCAGGATGCTCGTCCTCAAGCCCAGGATCCAGATCCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG