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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtcaaaggtttctgcaaatttgtttttcatgcatacatttatagattgttttctggcttagttctctgatgctttttttttttttgcaaactttcttacagTACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGACGACGACGACGACAATGACAAGGTTGGTGATGCTGTGTCTTTGGTTTCCT

Basic information

species Zea mays
transcript GRMZM2G472991_T04
intron # 12
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|26456479|gb|CA828062.1|CA828062
EST:     CTGGTTCCTTGGACAAGGAACTAGCTGCAAGTGGATATTCCAGGAAAGAGCAAGTGGAGATGGACAAG        
genomic: AACTAGCTGCAAGTGGATATACCAGGAAAGAGCAAGTGGAGATGGACAAGgtaggtcaaa ... tttcttacagT
EST: gi|78077807|gb|DV506236.1|DV506236
EST:     AACTAGCTGCAAGTGGATATACCAGGAAAGAGCAAGTGGAGATGGACAAG                         TACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGAC
genomic: AACTAGCTGCAAGTGGATATACCAGGAAAGAGCAAGTGGAGATGGACAAGgtaggtcaaa ... tttcttacagTACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGAC
EST: gi|60337135|gb|DN204108.1|DN204108
EST:     TACCAGGAAAGAGCAAGTGGAGATGGACAAG                         TACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGAC
genomic: TACCAGGAAAGAGCAAGTGGAGATGGACAAGgtaggtcaaa ... tttcttacagTACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGAC
EST: gi|78120951|gb|DV539335.1|DV539335
EST:     AGGAAAGAGCAAGTGGAGATGGACAAG                         TACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGAC
genomic: AGGAAAGAGCAAGTGGAGATGGACAAGgtaggtcaaa ... tttcttacagTACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGAC
EST: gi|91056419|gb|EB166837.1|EB166837
EST:     AACTAGCTGCAAGTGGATATACCAGGAAAGAGCAAGTGGAGATGGACAAG                         TACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGAC
genomic: AACTAGCTGCAAGTGGATATACCAGGAAAGAGCAAGTGGAGATGGACAAGgtaggtcaaa ... tttcttacagTACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGAC
EST: gi|74246122|gb|DT654036.1|DT654036
EST:     AAGAGCAAGTGGAGATGGACAAG                         TACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGAC
genomic: AAGAGCAAGTGGAGATGGACAAGgtaggtcaaa ... tttcttacagTACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGAC
EST: gi|78077806|gb|DV506235.1|DV506235
EST:     AAGTGGATATACCAGGAAAGAGCAAGTGGAGATGGACAAG                         TACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGAC
genomic: AAGTGGATATACCAGGAAAGAGCAAGTGGAGATGGACAAGgtaggtcaaa ... tttcttacagTACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttctggcttagttctctgatgctttttttttttttgcaaactttcttacagTACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGACGACGACGACGACAATGACAAGGTTGGTGATGCTGTGTCTTTGGTTTCCT
                 ctctgat  putative branch site (score: 4)
                                            ctttcttac  putative PPT
                          tttttttttttttgca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtcaaaggtttctgcaaatttgtttttcatgcatacatttatagattgttttctggcttagttctctgatgctttttttttttttgcaaactttcttacagTACATTGAGGAAGATGCTGAAAGACATGATTCCAGCTCAGATGATGATGACGACGACGACGACAATGACAAGGTTGGTGATGCTGTGTCTTTGGTTTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG