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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctacagatgttactaaatatctccttcggtgcaattggtctgtctgtctgtcactccacctgatgtaatgtattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAACAAGCTTCTCGAAGAAGCTTCCCGAAGGGGAAGCTCCGATAACATCACAG

Basic information

species Zea mays
transcript GRMZM2G166035_T01
intron # 7
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|19057928|gb|BM736595.1|BM736595
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAACCAGCAACC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60399168|gb|DN231982.1|DN231982
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|148962276|gb|EE013101.2|EE013101
EST:     GACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: GACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|87152813|gb|DY397602.1|DY397602
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|6826953|gb|AW330596.1|AW330596
EST:     ATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGGCTG-C-CTAATGAG                         GAAGCTGTTGCCATGGTCA
genomic: ATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGT-TGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCA
EST: gi|211526714|gb|FL481404.1|FL481404
EST:     AATTCCTCATCCTTGCTAGCGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|19855109|gb|BQ060161.1|BQ060161
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|211336615|gb|FL398412.1|FL398412
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60341783|gb|DN208756.1|DN208756
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|5525216|gb|AI861214.1|AI861214
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCNCTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|78023072|gb|DV491459.1|DV491459
EST:     TTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: TTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60394820|gb|DN227689.1|DN227689
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|21329699|gb|BQ485080.1|BQ485080
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60347289|gb|DN214262.1|DN214262
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60344579|gb|DN211552.1|DN211552
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60348720|gb|DN215693.1|DN215693
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|71419053|gb|DR804631.1|DR804631
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|6827326|gb|AW330969.1|AW330969
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|211247655|gb|FL406574.1|FL406574
EST:     AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGCGACGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... tattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcggtgcaattggtctgtctgtctgtcactccacctgatgtaatgtattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAACAAGCTTCTCGAAGAAGCTTCCCGAAGGGGAAGCTCCGATAACATCACAG
                                acctgat  putative branch site (score: 4)
                                     atgtaatgtatttta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctacagatgttactaaatatctccttcggtgcaattggtctgtctgtctgtcactccacctgatgtaatgtattttacagGAAGCTGTTGCCATGGTCAAGCCTATCCAGGACCCCCAGGAAGCAGCAAACAAGCTTCTCGAAGAAGCTTCCCGAAGGGGAAGCTCCGATAACATCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC