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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcaatctctaccgtccgtttcgctgcttctttcttgccaatggttcaactcactccaataatgtcattctgtttttgttagCAGAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGGAGTTAAAATCCTTGACCGATTCAATCGGTCATACCAGGGAACCCAT

Basic information

species Zea mays
transcript GRMZM2G363460_T06
intron # 5
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|20300876|gb|BQ163819.1|BQ163819
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATG-A-                         -AGAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCA
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... tttttgttagCAGAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCA
EST: gi|148946560|gb|EC885619.2|EC885619
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGTATGAAG                         -A-AAA-GAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCA
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... tttttgttagCAGAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCA
EST: gi|31354170|gb|CD438527.1|CD438527
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATG-A-                         -AGAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCA
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... tttttgttagCAGAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCA
EST: gi|149085990|gb|EE175517.2|EE175517
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAG                         -A-AAA-GAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCA
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... tttttgttagCAGAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCA
EST: gi|148941345|gb|EC886254.2|EC886254
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAG                         -A-AAA-GAAGATACTAGTGACGTTGACANCA-GCTCTAGATTCCCAAGCC
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... tttttgttagCAGAAAAGAAGATACTAGTGACGTTGACA-CAAGCTCTAGATTCCCAAGCC
EST: gi|31355282|gb|CD439639.1|CD439639
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAG                         CAGAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCA
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... tttttgttagCAGAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCA
EST: gi|76913179|gb|DV165031.1|DV165031
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAG                         -A-AAA-GAAGATACTAGTGACGTTGACACAAGCTCTAGATTCTCAAGCCA
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... tttttgttagCAGAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttcttgccaatggttcaactcactccaataatgtcattctgtttttgttagCAGAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGGAGTTAAAATCCTTGACCGATTCAATCGGTCATACCAGGGAACCCAT
                    aactcac  putative branch site (score: 2)
                                        ttctgttttt  putative PPT
                                             tttttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcaatctctaccgtccgtttcgctgcttctttcttgccaatggttcaactcactccaataatgtcattctgtttttgttagCAGAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGGAGTTAAAATCCTTGACCGATTCAATCGGTCATACCAGGGAACCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG