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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttccaggctgaaagtcagtggagttctcagttctcaccaacattcagaaaactgttggctcgctgacaagtccaactgtgtttttcttggactacagATGAAGCGAGCTCGAAGGCGTATGTGCAAGAGATGACTGATGAGGGATGCTAGTGACATTGATGAACTTGTTACGGGCGTGCTGGCGACCGTCATCGAAC

Basic information

species Zea mays
transcript GRMZM2G069970_T02
intron # 1
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|78086197|gb|DV514590.1|DV514590
EST:     CGCTGAATCCCAATCCGAGCCCGCCAATTGGGCGCCCCGCCCACGCCAAG                         ATGAAGCGAGCTCGAAGGCGTATGTGCAAGAGATGACTGATGAGGGATGCT
genomic: CGCTGAATCCCAATCCGAGCCCGCCAATTGGGCGCCCCGCCCACGCCAAGgtgcgacttt ... tggactacagATGAAGCGAGCTCGAAGGCGTATGTGCAAGAGATGACTGATGAGGGATGCT
EST: gi|211178849|gb|FL219806.1|FL219806
EST:     CACTGAATCCCAATCCGAGCCCGCCAATTGGGCGCCCCACCCACGCCAAG                         ATGAAGCGAGCTCGAAGGCGTATGTGCAAGAGATGACTGATGAGGGATGCT
genomic: CGCTGAATCCCAATCCGAGCCCGCCAATTGGGCGCCCCGCCCACGCCAAGgtgcgacttt ... tggactacagATGAAGCGAGCTCGAAGGCGTATGTGCAAGAGATGACTGATGAGGGATGCT
EST: gi|148970773|gb|EE021521.2|EE021521
EST:     CGCTGAATCCCAATCCGAGCCCGCCAATTGGGCGCCCCGCCCACGCCAAG                         ATGAAGCGAGCTCGAAGGCGTATGTGCAAGAGATGACTGATGAGGGATGCT
genomic: CGCTGAATCCCAATCCGAGCCCGCCAATTGGGCGCCCCGCCCACGCCAAGgtgcgacttt ... tggactacagATGAAGCGAGCTCGAAGGCGTATGTGCAAGAGATGACTGATGAGGGATGCT
EST: gi|149085363|gb|EE174870.2|EE174870
EST:     CGCTGAATCCCAATCCGAGCCCGCCAATTGGGCGCCCCGCCCACGCCAAG                         ATGAAGCGAGCTCGAAGGCGTATGTGCAAGAGATGACTGATGAGGGATGCT
genomic: CGCTGAATCCCAATCCGAGCCCGCCAATTGGGCGCCCCGCCCACGCCAAGgtgcgacttt ... tggactacagATGAAGCGAGCTCGAAGGCGTATGTGCAAGAGATGACTGATGAGGGATGCT
EST: gi|93283061|gb|EB675325.1|EB675325
EST:     CGCTGAATCCCAATCCGAGCCCGCCAATTGGGCGCCCCGCCCACGCCAAG                         ATGAAGCGAGCTCGAAGGCGTATGTGCAAGAGATGACTGATGAGGGATGCT
genomic: CGCTGAATCCCAATCCGAGCCCGCCAATTGGGCGCCCCGCCCACGCCAAGgtgcgacttt ... tggactacagATGAAGCGAGCTCGAAGGCGTATGTGCAAGAGATGACTGATGAGGGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagaaaactgttggctcgctgacaagtccaactgtgtttttcttggactacagATGAAGCGAGCTCGAAGGCGTATGTGCAAGAGATGACTGATGAGGGATGCTAGTGACATTGATGAACTTGTTACGGGCGTGCTGGCGACCGTCATCGAAC
                  cgctgac  putative branch site (score: 3)
                                    tgtttttctt  putative PPT
                                      tttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttccaggctgaaagtcagtggagttctcagttctcaccaacattcagaaaactgttggctcgctgacaagtccaactgtgtttttcttggactacagATGAAGCGAGCTCGAAGGCGTATGTGCAAGAGATGACTGATGAGGGATGCTAGTGACATTGATGAACTTGTTACGGGCGTGCTGGCGACCGTCATCGAAC

tgcttcc
- - - - -gctgaaa
- - - - - - - - - - - - - - - - - - -caccaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgaca