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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatgagacatattagcatactaacaaagtaacaagtcccttgtatagaaggacttctgcccacatctgcagttaacattacttttatctttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTGGATTACAAAAGGGAGTGTGGCCGGGATAGTGTGCTGCAATCACACACCT

Basic information

species Zea mays
transcript GRMZM2G406603_T01
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|32869619|gb|CF009301.1|CF009301
EST:     ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG                         AGCGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
EST: gi|166466077|gb|EG135583.1|EG135583
EST:     ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG                         AGCGCACCCATCTC
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTC
EST: gi|71327050|gb|DR800172.1|DR800172
EST:     AATCAGCATGTCAATAATGTTAAATACATTGCGTGGGTTCTTGAG                         AGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: AATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
EST: gi|24773338|gb|CA408592.1|CA408592
EST:     ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATCCTTGAG                         AGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
EST: gi|5915436|gb|AW053077.1|AW053077
EST:     ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG                         AGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
EST: gi|211441828|gb|FL296923.1|FL296923
EST:     ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG                         AGCGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
EST: gi|24961561|gb|CA483567.1|CA483567
EST:     ATATAAATCAGCATGTCAATAATGCTAAATACATTGCGCGGATCCTTGAG                         AGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
EST: gi|60356288|gb|DN223261.1|DN223261
EST:     ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG                         AGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagaaggacttctgcccacatctgcagttaacattacttttatctttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTGGATTACAAAAGGGAGTGTGGCCGGGATAGTGTGCTGCAATCACACACCT
                          agttaac  putative branch site (score: 3)
                                     cttttatctttgcttc  putative PPT
                            ttaacattacttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatgagacatattagcatactaacaaagtaacaagtcccttgtatagaaggacttctgcccacatctgcagttaacattacttttatctttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTGGATTACAAAAGGGAGTGTGGCCGGGATAGTGTGCTGCAATCACACACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC