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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtattgggaataaccgaacaaggcctgagtaggaagcatgcccaggagcaccttaaccttttcataaactggattcacaggccgattgctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAAACAAGCTGGCCCTGCAGAAGTTGATTCCTGAAGTCATCGGCAACGCCCT

Basic information

species Zea mays
transcript GRMZM2G412899_T05
intron # 14
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|110961485|gb|EE181537.1|EE181537
EST:     GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAG                         GTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
genomic: GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAGgtgtgtacca ... ctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
EST: gi|78119069|gb|DV537453.1|DV537453
EST:     GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAG                         GTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
genomic: GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAGgtgtgtacca ... ctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
EST: gi|71760454|gb|DR958391.1|DR958391
EST:     GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAG                         GTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
genomic: GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAGgtgtgtacca ... ctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
EST: gi|71321128|gb|DR797263.1|DR797263
EST:     GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCCCAATAAAG                         GTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
genomic: GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAGgtgtgtacca ... ctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
EST: gi|78110186|gb|DV528601.1|DV528601
EST:     GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAG                         GTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
genomic: GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAGgtgtgtacca ... ctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
EST: gi|71759302|gb|DR957239.1|DR957239
EST:     GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAG                         GTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
genomic: GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAGgtgtgtacca ... ctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
EST: gi|148974491|gb|EE025274.2|EE025274
EST:     GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAG                         GTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
genomic: GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAGgtgtgtacca ... ctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
EST: gi|101396769|gb|EB820310.1|EB820310
EST:     GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAG                         GTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
genomic: GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAGgtgtgtacca ... ctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
EST: gi|211453092|gb|FL443675.1|FL443675
EST:     GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCMCAATAAAG                         GTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
genomic: GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAGgtgtgtacca ... ctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
EST: gi|76015719|gb|DT942889.1|DT942889
EST:     GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAG                         GTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
genomic: GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAGgtgtgtacca ... ctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
EST: gi|211329247|gb|FL462804.1|FL462804
EST:     GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAG                         GTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
genomic: GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAGgtgtgtacca ... ctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
EST: gi|50326105|gb|CO521231.1|CO521231
EST:     GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAG                         GTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
genomic: GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAGgtgtgtacca ... ctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
EST: gi|74240465|gb|DT648379.1|DT648379
EST:     GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAG                         GTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA
genomic: GGAAAGACTTTACAAGAGATAGAGGTTTCACTCCTGCAACCACAATAAAGgtgtgtacca ... ctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggagcaccttaaccttttcataaactggattcacaggccgattgctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAAACAAGCTGGCCCTGCAGAAGTTGATTCCTGAAGTCATCGGCAACGCCCT
       ccttaac  putative branch site (score: 3)
               ttttcataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtattgggaataaccgaacaaggcctgagtaggaagcatgcccaggagcaccttaaccttttcataaactggattcacaggccgattgctcattgcagGTACATATTTGACGTGGCTGGAACCTTGGGCAGGCTGTTTGCTGAACAGAAACAAGCTGGCCCTGCAGAAGTTGATTCCTGAAGTCATCGGCAACGCCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
-tgtattg
- - - - - - - - - - - aggcctg
- - - - - - - - - - - - - - - - - - agcatgc
- - - - - - - - - - - - - - - - - - - - - - caggagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaggc