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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaaatctggctgcaaattttctgcaaaactttcattttcatacaactcatgtgccagtataagaatctaaagatggcaaatgtttgtgatgtacataacatttacaatgctttcttttgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT

Basic information

species Zea mays
transcript GRMZM2G039889_T06
intron # 7
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|78107919|gb|DV526337.1|DV526337
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|67022594|gb|CO451343.1|CO451343
EST:     CTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|76910226|gb|DV163762.1|DV163762
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|78107918|gb|DV526336.1|DV526336
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|76284975|gb|DV024543.1|DV024543
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|211026941|gb|FL261358.1|FL261358
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTTTCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|50336508|gb|CO531634.1|CO531634
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|30032149|gb|CB834000.1|CB834000
EST:     TCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: TCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|78123847|gb|DV542231.1|DV542231
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|78115266|gb|DV533654.1|DV533654
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|31612380|gb|CD569002.1|CD569002
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|76016911|gb|DT944081.1|DT944081
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|71299499|gb|DR785760.1|DR785760
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|31910879|gb|CD651644.1|CD651644
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|71326312|gb|DR799844.1|DR799844
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|60400549|gb|DN233356.1|DN233356
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|211213178|gb|FL436853.1|FL436853
EST:     TTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTTTCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: TTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
EST: gi|71762950|gb|DR960887.1|DR960887
EST:     CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTG                         GTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT
genomic: CACTGGTTCAAGCTACTCTTCCTTCATCAGCACCCATTGTCCCTGCAGTGgtattaaatc ... tgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggcaaatgtttgtgatgtacataacatttacaatgctttcttttgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT
                    acataac  putative branch site (score: 3)
                                   tgctttctttt  putative PPT
                      ataacatttacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaaatctggctgcaaattttctgcaaaactttcattttcatacaactcatgtgccagtataagaatctaaagatggcaaatgtttgtgatgtacataacatttacaatgctttcttttgtaaaacagGTTGAACCTTTGCCAATGATCTATCCTCAAAGGCCAGGAGAAACTGTTTGTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA