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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgaacagagtttgttttcttatgtatgtcttatctgcaacctaacactccaatctttcttgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG

Basic information

species Zea mays
transcript GRMZM2G003692_T05
intron # 4
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|67023347|gb|CO452096.1|CO452096
EST:     GGCTCTANAANAAA-TGAGGGAA-GTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: GGCTCTAGAAGAAAGTGA-GGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|50324032|gb|CO519158.1|CO519158
EST:     TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|71320805|gb|DR797121.1|DR797121
EST:     TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|91877563|gb|EB407520.1|EB407520
EST:     TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|37387558|gb|CF630976.1|CF630976
EST:     GAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: GAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|5343223|gb|AI795408.1|AI795408
EST:     AGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: AGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|91872747|gb|EB402704.1|EB402704
EST:     TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|6095476|gb|AW120143.1|AW120143
EST:     GAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: GAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|93015973|gb|EB641493.1|EB641493
EST:     TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|71758502|gb|DR956439.1|DR956439
EST:     TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|71768646|gb|DR966583.1|DR966583
EST:     TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: TCAAATTGCAGAAACGGAGGGCTCTAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|32864069|gb|CF003751.1|CF003751
EST:     TAGAAGAAAGTGAGGAAGGTCTTAAG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: TAGAAGAAAGTGAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
EST: gi|6194694|gb|AW146798.1|AW146798
EST:     GAGGAAGGTCTTANG                         GCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA
genomic: GAGGAAGGTCTTAAGgtacatgaac ... tgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttatgtatgtcttatctgcaacctaacactccaatctttcttgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG
                        acctaac  putative branch site (score: 2)
                                ctccaatctttctt  CT-rich tract
     tatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgaacagagtttgttttcttatgtatgtcttatctgcaacctaacactccaatctttcttgctagatagGCTACATTGAATGTCAATGTCTTCGGAACTATTACTTTAACTCGCCTTCTAGCACCTTACATGCTTGATAGAGAGATGGGCCATTTTGTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG