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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatcccaaacaagtcgaaatctttcataattttttccaatccacatgggattggaataaccgaacaaggcataaaggagatcttattactctttcacagGAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGGAAACAAAAAGGCGTCAAAGATGCTTCCTCACATAGTTGTTGTTGCATCG

Basic information

species Zea mays
transcript GRMZM2G149994_T02
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|211510550|gb|FL129059.1|FL129059
EST:     GTGATATTCATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAG                         GAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG
genomic: GTGATATTTATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAGgcaagttttg ... tctttcacagGAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG
EST: gi|211510555|gb|FL129064.1|FL129064
EST:     GTGATATTCATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAG                         GAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG
genomic: GTGATATTTATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAGgcaagttttg ... tctttcacagGAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG
EST: gi|211510558|gb|FL129067.1|FL129067
EST:     GTGATATTCATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAG                         GAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG
genomic: GTGATATTTATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAGgcaagttttg ... tctttcacagGAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG
EST: gi|211510556|gb|FL129065.1|FL129065
EST:     GTGATATTCATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAG                         GAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG
genomic: GTGATATTTATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAGgcaagttttg ... tctttcacagGAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG
EST: gi|211512912|gb|FL129068.1|FL129068
EST:     GTGATATTCATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAG                         GAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG
genomic: GTGATATTTATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAGgcaagttttg ... tctttcacagGAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG
EST: gi|71445517|gb|DR826567.1|DR826567
EST:     GTGATATTTATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAA                         GAGAGAGAATG
genomic: GTGATATTTATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAGgcaagttttg ... tctttcacagGAGAGAGAATG
EST: gi|211512914|gb|FL129070.1|FL129070
EST:     GTGATATTCATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAG                         GAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG
genomic: GTGATATTTATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAGgcaagttttg ... tctttcacagGAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG
EST: gi|211510557|gb|FL129066.1|FL129066
EST:     GTGATATTCATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAG                         GAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG
genomic: GTGATATTTATTGACGAACTTGATGCCATATGTCCACGCCGCAATAGTAGgcaagttttg ... tctttcacagGAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgggattggaataaccgaacaaggcataaaggagatcttattactctttcacagGAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGGAAACAAAAAGGCGTCAAAGATGCTTCCTCACATAGTTGTTGTTGCATCG
         gaataac  putative branch site (score: 2)
                                    tcttattactctttc  putative PPT
                                   atcttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatcccaaacaagtcgaaatctttcataattttttccaatccacatgggattggaataaccgaacaaggcataaaggagatcttattactctttcacagGAGAGAGAATGAGTCCCGCATTGTTGGCCAACTTCTTACTCTCATGGATGGAAACAAAAAGGCGTCAAAGATGCTTCCTCACATAGTTGTTGTTGCATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG