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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtcgggtatgcattactgcacctgtcttatttcctgtgcgcatgcttaacacagtgattggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAGCAGCTTTTGTTGAATGTTTGTACTATGTGTGTAGTTGCCTGCTCCATCA

Basic information

species Zea mays
transcript GRMZM2G416069_T02
intron # 9
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|18659884|gb|BM500573.1|BM500573
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGGAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATANGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|60353637|gb|DN220610.1|DN220610
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|60399460|gb|DN232272.1|DN232272
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|5713812|gb|AI943797.1|AI943797
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGGAG                         TTGCTCGAGGACTCTCACCTTCGACATGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|32856812|gb|CD996493.1|CD996493
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|67019300|gb|CO448049.1|CO448049
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGGAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|211099838|gb|FL388151.1|FL388151
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|33092424|gb|CF052418.1|CF052418
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|9953703|gb|BE640286.1|BE640286
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|60396930|gb|DN229749.1|DN229749
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|32857536|gb|CD997217.1|CD997217
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCG-GGTACNT-TCACCTTCGACCTGAGAAAGTATAGGGAATCGTGA
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGG-AC-TCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGA
EST: gi|32931521|gb|CF036333.1|CF036333
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|32856527|gb|CD996208.1|CD996208
EST:     TATGACAAGGCCGAGACACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|60340169|gb|DN207142.1|DN207142
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|32932198|gb|CF037010.1|CF037010
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCAGCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|32839032|gb|CD978713.1|CD978713
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGGACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|60397605|gb|DN230421.1|DN230421
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|67026121|gb|CO454870.1|CO454870
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGGAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|211416225|gb|FL415027.1|FL415027
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|211089791|gb|FL379369.1|FL379369
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGA
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGA
EST: gi|211099837|gb|FL388150.1|FL388150
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|74034784|gb|DT535275.1|DT535275
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCCTTCGACCCTGAGAAAGTATAGGGGAATCGTG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACC-TTCGACC-TGAGAAAGTATAGGG-AATCGTG
EST: gi|5895740|gb|AW036986.1|AW036986
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGGAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|32838704|gb|CD978385.1|CD978385
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|6742487|gb|AW313302.1|AW313302
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|32932580|gb|CF037392.1|CF037392
EST:     AAGGCCGAGGCGCTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: AAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|211438053|gb|FL453415.1|FL453415
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|211072011|gb|FL419961.1|FL419961
EST:     TATGACAAGGCCGAGGCACTTGTTGGKGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTYTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAG
EST: gi|166438907|gb|EG193297.1|EG193297
EST:     TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAG                         TTGCTCGAGGACTCTCACCTTCGACCTAAGAA
genomic: TATGACAAGGCCGAGGCACTTGTTGGTGTTTATAGGGACTCAGAACGAAGgtaggtcggg ... ggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgcacctgtcttatttcctgtgcgcatgcttaacacagtgattggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAGCAGCTTTTGTTGAATGTTTGTACTATGTGTGTAGTTGCCTGCTCCATCA
                             gcttaac  putative branch site (score: 3)
          tcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtcgggtatgcattactgcacctgtcttatttcctgtgcgcatgcttaacacagtgattggatgtgcagTTGCTCGAGGACTCTCACCTTCGACCTGAGAAAGTATAGGGAATCGTGAAGCAGCTTTTGTTGAATGTTTGTACTATGTGTGTAGTTGCCTGCTCCATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT