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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattcctttccagcgttctatttttcattttctatgcgttgcttaaaagggtaattacatggtcatctactaatacccttgtttttcttgcagCTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAG

Basic information

species Zea mays
transcript GRMZM2G060842_T01
intron # 4
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|76280845|gb|DV020413.1|DV020413
EST:     AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCA                         CTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
genomic: AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCAgtatgattcc ... tttcttgcagCTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
EST: gi|50327397|gb|CO522523.1|CO522523
EST:     AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCA                         CTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
genomic: AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCAgtatgattcc ... tttcttgcagCTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
EST: gi|76280844|gb|DV020412.1|DV020412
EST:     AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCA                         CTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
genomic: AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCAgtatgattcc ... tttcttgcagCTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
EST: gi|91875732|gb|EB405689.1|EB405689
EST:     AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCA                         CTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
genomic: AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCAgtatgattcc ... tttcttgcagCTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
EST: gi|76912690|gb|DV164849.1|DV164849
EST:     AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCA                         CTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
genomic: AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCAgtatgattcc ... tttcttgcagCTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
EST: gi|101386086|gb|EB815086.1|EB815086
EST:     AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCA                         CTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
genomic: AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCAgtatgattcc ... tttcttgcagCTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
EST: gi|50323043|gb|CO518169.1|CO518169
EST:     AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCA                         CTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
genomic: AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCAgtatgattcc ... tttcttgcagCTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
EST: gi|50326968|gb|CO522094.1|CO522094
EST:     AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCA                         CTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT
genomic: AGAACGAGAGCAACAAAAGGAAGGAGCTGAATCTTTTGAAATATGAAGCAgtatgattcc ... tttcttgcagCTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcttaaaagggtaattacatggtcatctactaatacccttgtttttcttgcagCTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAG
                             tactaat  putative branch site (score: 1)
                                   tacccttgtttttctt  CT-rich tract
             taattacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgattcctttccagcgttctatttttcattttctatgcgttgcttaaaagggtaattacatggtcatctactaatacccttgtttttcttgcagCTCAAGGATGAATTGCTGCTCTTGACCGCAGGAACTGGAGCAGCATGTAGTTTATATTGTCTCCTGGTTTTCTCTCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG