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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttctacaactactacaattcctgcctacttgaacaataggcttatgggcttattataaattgataattctttatgtgataataactcttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGGACTACTGGTTCTCGTG

Basic information

species Zea mays
transcript GRMZM2G069174_T02
intron # 6
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|94479305|gb|EB708263.1|EB708263
EST:     ATGGCTTTGTAGAATTTGAGGATGGCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTGGAAGAGAAAAGG
genomic: ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|93282822|gb|EB675086.1|EB675086
EST:     ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
genomic: ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|22715613|gb|BU197864.1|BU197864
EST:     ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
genomic: ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|74246261|gb|DT654175.1|DT654175
EST:     ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
genomic: ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|76015058|gb|DT942228.1|DT942228
EST:     ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
genomic: ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|21809923|gb|BQ668241.1|BQ668241
EST:     GAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
genomic: GAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|37425821|gb|CF650659.1|CF650659
EST:     ATGGCTTTGTAGACTTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATCCTTTGTCGAAGAGAAAAGG
genomic: ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|23357551|gb|BU645200.1|BU645200
EST:     ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
genomic: ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|101391401|gb|EB817635.1|EB817635
EST:     ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
genomic: ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|32838442|gb|CD978120.1|CD978120
EST:     ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
genomic: ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|211347561|gb|FL462321.1|FL462321
EST:     ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
genomic: ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|22521297|gb|BU080108.1|BU080108
EST:     TTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
genomic: TTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|87157178|gb|DY401967.1|DY401967
EST:     ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
genomic: ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|71763868|gb|DR961805.1|DR961805
EST:     ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
genomic: ATGGCTTTGTAGAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
EST: gi|84969571|gb|DW468004.1|DW468004
EST:     TGGC-TTGTAGGAATTGGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAG                         GCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG
genomic: TGGCTTTGTA-GAATTTGAGGATGCCAGTGCAGTTCAAGCTGCAATAGAGgtattaatct ... ttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgggcttattataaattgataattctttatgtgataataactcttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGGACTACTGGTTCTCGTG
                                          ctctt  CT-rich tract
       ttattataaattgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcttctacaactactacaattcctgcctacttgaacaataggcttatgggcttattataaattgataattctttatgtgataataactcttgattgcagGCTTCTCCTGTTACTATTGGTGAGCGGCAATGCTTTGTCGAAGAGAAAAGGACTACTGGTTCTCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA