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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTACGCCGTTGGCACCTAGGAAGACTTTGCAGCCTGAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttttctgtgtgctaagattttgttgagcatctcatccctttttatgctatttcatagctatgcagctaatatttttaactttcggtatataac...

Basic information

species Zea mays
transcript GRMZM2G163912_T03
intron # 3
splice site 5'
intron type U12 (go to U12 genes for details)

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|211431804|gb|FL298785.1|FL298785
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|31350916|gb|CD435273.1|CD435273
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|148969207|gb|EE019955.2|EE019955
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|211431802|gb|FL298783.1|FL298783
EST:     GAGCAAGCATTTNACMCTCTGGAAGA-GACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|149026634|gb|EE046054.2|EE046054
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|32833725|gb|CD973403.1|CD973403
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|211431805|gb|FL298786.1|FL298786
EST:     GAGCAAGCATTTCACCCTCTGGAAGA-GACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|89757168|gb|DY686883.1|DY686883
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|211431800|gb|FL298781.1|FL298781
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|211431801|gb|FL298782.1|FL298782
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|148940178|gb|EC884940.2|EC884940
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|211431803|gb|FL298784.1|FL298784
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|32910548|gb|CF015360.1|CF015360
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|87156202|gb|DY400991.1|DY400991
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         AACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|148993804|gb|EE033889.2|EE033889
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|22521109|gb|BU079920.1|BU079920
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         AACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|149001239|gb|EE038515.2|EE038515
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|26558978|gb|CA831213.1|CA831213
EST:     GAGCAAGCATCTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         AACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|148944987|gb|EC890160.2|EC890160
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|149099628|gb|EE185673.2|EE185673
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|87156913|gb|DY401702.1|DY401702
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         AACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|32867073|gb|CF006755.1|CF006755
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|22473217|gb|BU037697.1|BU037697
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         AACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
EST: gi|50333496|gb|CO528622.1|CO528622
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         GACTACAACATCATCAAGAG
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAG
EST: gi|22520704|gb|BU079515.1|BU079515
EST:     GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTC                         AACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC
genomic: GAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttt ... ctgtgtaaagGACTACAACATCATCAAGAGCTGGCAGAACTAAGACAACTGTTCCTGTTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTACGCCGTTGGCACCTAGGAAGACTTTGCAGCCTGAGCAAGCATTTCACCCTCTGGAAGAGGACTCTTGTTCTGTGACTTCCTCgtatcctttttctgtgtgctaagattttgttgagcatctcatccctttttatgctatttcatagctatgcagctaatatttttaactttcggtatataac

- - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA