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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcaccgcgccctctgctgcggctacgggagctagctcgtgaattcaactcttttttcatatttttttaattcatttagctgcctttttctgtgttgtttctgcggcagAGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGTGGACCGGCTCGCAGGCGCTGCTGTTACCTTGGGTGGAG

Basic information

species Zea mays
transcript GRMZM2G095727_T04
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|67028242|gb|CO456991.1|CO456991
EST:     GAACTCTCGCGGCCTCATCTCCTCCTCGTCATCGTAACACCCACGCTTAG                         AGTTCGTGAGGGTCGCCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAG
genomic: GAACTCTCGCGGCCTCAACTCCTCCTCGTCATCGTAACACCCACGCTTAGgtgcgcaccg ... tctgcggcagAGTTCGTGAGGGTCG-CCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAG
EST: gi|78086698|gb|DV515091.1|DV515091
EST:     GAACTCTCGCGGCCTCAACTCCTCCTCGTCATCGTAACACCCACGCTTAG                         AGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGT
genomic: GAACTCTCGCGGCCTCAACTCCTCCTCGTCATCGTAACACCCACGCTTAGgtgcgcaccg ... tctgcggcagAGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGT
EST: gi|71432179|gb|DR813229.1|DR813229
EST:     GAACTCTCGCGGCCTCAACTCCTCCTCGTCATCGTAACACCCACGCTTAG                         AGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGT
genomic: GAACTCTCGCGGCCTCAACTCCTCCTCGTCATCGTAACACCCACGCTTAGgtgcgcaccg ... tctgcggcagAGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGT
EST: gi|31441071|gb|CD510502.1|CD510502
EST:     GAACTCTCGCGGCCTCAACTCCTCCTCGTCATCGTAACACCCACGCTTAG                         AGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGT
genomic: GAACTCTCGCGGCCTCAACTCCTCCTCGTCATCGTAACACCCACGCTTAGgtgcgcaccg ... tctgcggcagAGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGT
EST: gi|89252032|gb|DY623818.1|DY623818
EST:     GAACTCTCGCGGCCTCAACTCCTCCTCGTCATCGTAACACCCACGCTTAG                         AGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGT
genomic: GAACTCTCGCGGCCTCAACTCCTCCTCGTCATCGTAACACCCACGCTTAGgtgcgcaccg ... tctgcggcagAGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGT
EST: gi|94478976|gb|EB707934.1|EB707934
EST:     GAACTCTCGCGGCCTCAACTCCTCCTCGTCATCGTAACACCCACGCTTAG                         AGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGT
genomic: GAACTCTCGCGGCCTCAACTCCTCCTCGTCATCGTAACACCCACGCTTAGgtgcgcaccg ... tctgcggcagAGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGT
EST: gi|211378749|gb|FL130659.1|FL130659
EST:     GAACTCTCGCGGCCTCAACTCCTCCTCGTCATCGTAACACCCACGCTTAG                         AGTTCGTGAGGGTCGCCCCCGGGGGATCTCGAGACGTCCGTTTCCAAGAGT
genomic: GAACTCTCGCGGCCTCAACTCCTCCTCGTCATCGTAACACCCACGCTTAGgtgcgcaccg ... tctgcggcagAGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatatttttttaattcatttagctgcctttttctgtgttgtttctgcggcagAGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGTGGACCGGCTCGCAGGCGCTGCTGTTACCTTGGGTGGAG
          ttttaat  putative branch site (score: 3)
                                        ttgtttct  putative PPT
     tatttttttaattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgcaccgcgccctctgctgcggctacgggagctagctcgtgaattcaactcttttttcatatttttttaattcatttagctgcctttttctgtgttgtttctgcggcagAGTTCGTGAGGGTCGCCCCCAGGGGATCTCGAGACGTCCGTTTCCAAGAGTGGACCGGCTCGCAGGCGCTGCTGTTACCTTGGGTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG