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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataatataaaattaaaatgtggtcaagcgcatgcaagatgtactttgtgcagtctgacgatataaaaatctgtcattttattttgatttcttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCCGCACAGTATAGCAAACTGCGAAGCCTGCAACTACTAGAGTTTGGTCTGT

Basic information

species Zea mays
transcript GRMZM5G896082_T03
intron # 10
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|78114033|gb|DV532422.1|DV532422
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|50329133|gb|CO524259.1|CO524259
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|78112820|gb|DV531214.1|DV531214
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|6952732|gb|AW424800.1|AW424800
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGCTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|91053496|gb|EB163914.1|EB163914
EST:     CAAAATTTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTTTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|78107801|gb|DV526219.1|DV526219
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|71325792|gb|DR799575.1|DR799575
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|148949266|gb|EC894709.2|EC894709
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|16379762|gb|BI993135.1|BI993135
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|149084782|gb|EE174281.2|EE174281
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|110522813|gb|EE026997.1|EE026997
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|12046214|gb|BF728353.1|BF728353
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAAAATAAAGGTGGCTGGCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|13515906|gb|BG518182.1|BG518182
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|7135775|gb|AW498259.1|AW498259
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAAAATAAAGGTGGCTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|32926038|gb|CF030850.1|CF030850
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGCTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|78121212|gb|DV539596.1|DV539596
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|33467814|gb|CF244863.1|CF244863
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|32925306|gb|CF030118.1|CF030118
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGCTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|71756718|gb|DR954655.1|DR954655
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTTTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
EST: gi|76908968|gb|DV163158.1|DV163158
EST:     CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAG                         GAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC
genomic: CAAAATCTCGGGTGATCACACTTCCAGAAGCATCAAATGCATAAACATAGgtacgagtct ... ttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcagtctgacgatataaaaatctgtcattttattttgatttcttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCCGCACAGTATAGCAAACTGCGAAGCCTGCAACTACTAGAGTTTGGTCTGT
                              ttttattttgatttct  CT-rich tract
              atataaaaatctgtca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataatataaaattaaaatgtggtcaagcgcatgcaagatgtactttgtgcagtctgacgatataaaaatctgtcattttattttgatttcttcttttcagGAACAGGGAGCTCCAGAGCTTGTGAATTCTATAGAATAAAGGTGGTTGTCCGCACAGTATAGCAAACTGCGAAGCCTGCAACTACTAGAGTTTGGTCTGT

- - - - - - - - - - - - - -cgcatgc
- - - - - - - - - - - - - - - - - - gatgtac
- - - - - - - - - - - - - - - - - - - - - - -tgtgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaa