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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcagtgttcatcagctttgtgaaatcagtttacatcattcttcggatctcaatagtcaacgtgtagtgacaataaaataattttggtttttaatccagAAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG

Basic information

species Zea mays
transcript GRMZM2G114758_T04
intron # 2
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|78118561|gb|DV536945.1|DV536945
EST:     TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG                         AAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG
genomic: TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGgtacacgttt ... tttaatccagAAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG
EST: gi|4753352|gb|AI657257.1|AI657257
EST:     TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG                         AAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG
genomic: TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGgtacacgttt ... tttaatccagAAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG
EST: gi|20301530|gb|BQ164473.1|BQ164473
EST:     TG-TGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG                         AAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG
genomic: TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGgtacacgttt ... tttaatccagAAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG
EST: gi|71304851|gb|DR788540.1|DR788540
EST:     TGATGATGATGGCCTTGGGACATCACTTCCAAGGC---AAG                         AAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG
genomic: TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGgtacacgttt ... tttaatccagAAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG
EST: gi|91048770|gb|EB159188.1|EB159188
EST:     TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG                         AAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG
genomic: TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGgtacacgttt ... tttaatccagAAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG
EST: gi|26456351|gb|CA827934.1|CA827934
EST:     TG-TGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAG                         AAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG
genomic: TGATGATGATGGCCTTGGGACATCACTTCCAAGGCAAGAAGgtacacgttt ... tttaatccagAAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatctcaatagtcaacgtgtagtgacaataaaataattttggtttttaatccagAAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG
                                            ttttaat  putative branch site (score: 3)
                                           ttttt  CT-rich tract
                       tgacaataaaataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcagtgttcatcagctttgtgaaatcagtttacatcattcttcggatctcaatagtcaacgtgtagtgacaataaaataattttggtttttaatccagAAGGCACAGAAGACGAACTCAAAGGTTCAAGAATTCAGCTTGCAATGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT