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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctattctttggtgcaatacattttatctgctcatagtcatatgtagtgcttcgttgttcttgtggctaaattggatttaaacttctttttcagCCACACCTGGAAGGCGGTGATAAAG

Basic information

species Zea mays
transcript GRMZM2G114220_T01
intron # 3
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|211392505|gb|FL156794.1|FL156794
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211389874|gb|FL156779.1|FL156779
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211389876|gb|FL156781.1|FL156781
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAG-CGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211389878|gb|FL156783.1|FL156783
EST:     ACTCGTTTGAGCAAACATACCGTTGGTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392499|gb|FL156788.1|FL156788
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392496|gb|FL156785.1|FL156785
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211389879|gb|FL156784.1|FL156784
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAG-CGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|50338446|gb|CO533572.1|CO533572
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392507|gb|FL156796.1|FL156796
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392498|gb|FL156787.1|FL156787
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAG-CGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|76909136|gb|DV163240.1|DV163240
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|6637070|gb|AW261342.1|AW261342
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGCGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|71417924|gb|DR804257.1|DR804257
EST:     ACTCGTCTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392504|gb|FL156793.1|FL156793
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392503|gb|FL156792.1|FL156792
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|91049005|gb|EB159423.1|EB159423
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|32859779|gb|CD999460.1|CD999460
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|32862738|gb|CF002420.1|CF002420
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211395124|gb|FL156801.1|FL156801
EST:     ACTCGTTTGAGCAAACATACCGTTGGTATGCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392510|gb|FL156799.1|FL156799
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211395123|gb|FL156800.1|FL156800
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211392502|gb|FL156791.1|FL156791
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|211389877|gb|FL156782.1|FL156782
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAG-CGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|91873355|gb|EB403312.1|EB403312
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|14242735|gb|BG840580.2|BG840580
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|213183590|gb|FM196389.1|FM196389
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG
EST: gi|93015584|gb|EB641104.1|EB641104
EST:     ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAG                         CCACACCTGGAAGGCGGTGATAAAG
genomic: ACTCGTTTGAGCAAACATACCGTTGTTATCCAGCATCGTTTTTTGATAAGgtatgctatt ... tctttttcagCCACACCTGGAAGGCGGTGATAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgtagtgcttcgttgttcttgtggctaaattggatttaaacttctttttcagCCACACCTGGAAGGCGGTGATAAAG
                         ggctaaa  putative branch site (score: 3)
                                           cttctttttc  putative PPT
                                    atttaaacttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctattctttggtgcaatacattttatctgctcatagtcatatgtagtgcttcgttgttcttgtggctaaattggatttaaacttctttttcagCCACACCTGGAAGGCGGTGATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG