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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatgtatctaacactatctgttctgttcagacaatatatgtttcagtacctgtcatttatattcatgttactgatagaaccatgatatatactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGAAAATCATCCCCAACAGGGATTGAAGTGACAGCCAGGGATCCACTCATCC

Basic information

species Zea mays
transcript GRMZM5G808737_T03
intron # 1
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|211066096|gb|FL065386.1|FL065386
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211068839|gb|FL065399.1|FL065399
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|148971778|gb|EE022513.2|EE022513
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211068834|gb|FL065394.1|FL065394
EST:     GGAAGACTCCGGA-GCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|148947961|gb|EC893460.2|EC893460
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|50339378|gb|CO534504.1|CO534504
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211068832|gb|FL065392.1|FL065392
EST:     GGAAGACTCCGGA-GCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211066097|gb|FL065387.1|FL065387
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211068836|gb|FL065396.1|FL065396
EST:     GGAAGACTCCGGA-GCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211068831|gb|FL065391.1|FL065391
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211066098|gb|FL065388.1|FL065388
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211068840|gb|FL065400.1|FL065400
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211068841|gb|FL065401.1|FL065401
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211068842|gb|FL065402.1|FL065402
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211068837|gb|FL065397.1|FL065397
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|9733110|gb|BE511862.1|BE511862
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211068830|gb|FL065390.1|FL065390
EST:     GGAAGACTCCGGA-GCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGATGCTTATGGG
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAG-TGCTTATGGG
EST: gi|74235722|gb|DT643636.1|DT643636
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211068838|gb|FL065398.1|FL065398
EST:     GGAAGACTCCGGA-GCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211068833|gb|FL065393.1|FL065393
EST:     GGAAGACTCCGGA-GCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211068835|gb|FL065395.1|FL065395
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
EST: gi|211066095|gb|FL065385.1|FL065385
EST:     GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCG                         ATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA
genomic: GGAAGACTCCGGAGGCCACGGGCGTTACATTCTCCTGCCGTATTTTTGCGgtaattgcgc ... tactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtacctgtcatttatattcatgttactgatagaaccatgatatatactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGAAAATCATCCCCAACAGGGATTGAAGTGACAGCCAGGGATCCACTCATCC
                        tactgat  putative branch site (score: 2)
          atttatattcatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatgtatctaacactatctgttctgttcagacaatatatgtttcagtacctgtcatttatattcatgttactgatagaaccatgatatatactgggtagATCCCTGGCTAACCAAACAAATGGTGGAGACATGGATTAGTGCTTATGGGAAAATCATCCCCAACAGGGATTGAAGTGACAGCCAGGGATCCACTCATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
-catgtat
- - - - - aacacta
- - - - - - - - - -tgttctg
- - - - - - - - - - - - - - - - - - - -tgtttca
- - - - - - - - - - - - - - - - - - - - - - - gtacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgat