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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatcctagcacgttaggggctatatatatctgctaggcatggaacataattctgctactaatattttttttacccaaatcttcttgtgttgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCCCTTGCGAGACCATGCTTATTTCCATTGCAAAATCATCAAGCTCTGCATC

Basic information

species Zea mays
transcript GRMZM2G106213_T01
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|60337923|gb|DN204896.1|DN204896
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|31356186|gb|CD440543.1|CD440543
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGCGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|6538829|gb|AW224968.1|AW224968
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGCGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|31357016|gb|CD441373.1|CD441373
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGCGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|32929383|gb|CF034195.1|CF034195
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|211487577|gb|FL154404.1|FL154404
EST:     ATTCCTAGTGGAACAATCATATAAAGGTCAGCCAACACCATGTATATRAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGCGCATCAAGTTCTCTCATCC
genomic: ATTCCTAGTGGAACAATCATATAAAG-TCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|6918703|gb|AW400233.1|AW400233
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGCGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|213183198|gb|FM188476.1|FM188476
EST:     GGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
genomic: GGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|32934685|gb|CF039497.1|CF039497
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|32933844|gb|CF038656.1|CF038656
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|71301127|gb|DR786596.1|DR786596
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|32846616|gb|CD986297.1|CD986297
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|6918472|gb|AW400002.1|AW400002
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGCGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|110511027|gb|EE019293.1|EE019293
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACCCCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTTTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|148950460|gb|EC896030.2|EC896030
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|78180055|gb|DV550428.1|DV550428
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGCGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|60352415|gb|DN219388.1|DN219388
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|37381963|gb|CF627890.1|CF627890
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGCGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|32929486|gb|CF034298.1|CF034298
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGTGCATC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATC
EST: gi|211241905|gb|FL451944.1|FL451944
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGCGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|12046285|gb|BF728424.1|BF728424
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGCGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC
EST: gi|211186265|gb|FL114940.1|FL114940
EST:     AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAG                         GTTGGGTTGCATCATATGGTGATCGCCAATGCGCATCAAGTTCTCTCATCC
genomic: AATTCCTAGTGGAACAATCATATAAAGTCAGCCAACACCATGTATATAAGgtcatatctc ... tgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataattctgctactaatattttttttacccaaatcttcttgtgttgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCCCTTGCGAGACCATGCTTATTTCCATTGCAAAATCATCAAGCTCTGCATC
              taatattttttttacc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatcctagcacgttaggggctatatatatctgctaggcatggaacataattctgctactaatattttttttacccaaatcttcttgtgttgacctgcagGTTGGGTTGCATCATATGGTGATCGCCAATGTGCATCAAGTTCTCTCATCCCTTGCGAGACCATGCTTATTTCCATTGCAAAATCATCAAGCTCTGCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT