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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggttttacacgtctacacattgtcagttctagtgacttcaatcagtggttccctgatagtcacgtgttttctgccaatttcatgtgttatagGGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGCCCTCGGGGCGGGGATAAGAGTGAAGCCAGGAAAATCTCTCCCAGTCCTT

Basic information

species Zea mays
transcript GRMZM2G137479_T02
intron # 3
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|89250820|gb|DY622606.1|DY622606
EST:     AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAG                         GGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC
genomic: AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAGgtaaggtttt ... tgtgttatagGGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC
EST: gi|50326187|gb|CO521313.1|CO521313
EST:     AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAG                         GGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC
genomic: AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAGgtaaggtttt ... tgtgttatagGGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC
EST: gi|211312062|gb|FL442680.1|FL442680
EST:     AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAG                         GGGGTTCAAGGCCATTCACCGCAGGTTGTTACCAAATCTCCGCGACAGAGC
genomic: AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAGgtaaggtttt ... tgtgttatagGGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC
EST: gi|149083392|gb|EE172703.2|EE172703
EST:     AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAG                         GGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC
genomic: AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAGgtaaggtttt ... tgtgttatagGGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC
EST: gi|211510021|gb|FL440680.1|FL440680
EST:     AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAG                         GGGGTTCAAAGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC
genomic: AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAGgtaaggtttt ... tgtgttatagGGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC
EST: gi|149084036|gb|EE173431.2|EE173431
EST:     AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAG                         GGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAAAGC
genomic: AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAGgtaaggtttt ... tgtgttatagGGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC
EST: gi|4609860|gb|AI600699.1|AI600699
EST:     AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAG                         GGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC
genomic: AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAGgtaaggtttt ... tgtgttatagGGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC
EST: gi|148965556|gb|EE016384.2|EE016384
EST:     AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAG                         GGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC
genomic: AAATGGAAGCCACCTCGCAATCCCAGGACATAAAGCCCCGAGTTCCTGAGgtaaggtttt ... tgtgttatagGGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatcagtggttccctgatagtcacgtgttttctgccaatttcatgtgttatagGGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGCCCTCGGGGCGGGGATAAGAGTGAAGCCAGGAAAATCTCTCCCAGTCCTT
             ccctgat  putative branch site (score: 4)
                                      aatttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggttttacacgtctacacattgtcagttctagtgacttcaatcagtggttccctgatagtcacgtgttttctgccaatttcatgtgttatagGGGGTTCAAGGCCATTCACCGAAGGTTGTTACTAAATCTCCGCGACAGAGCCCTCGGGGCGGGGATAAGAGTGAAGCCAGGAAAATCTCTCCCAGTCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC