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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtgttccgtattccacatccttactattttggtcagcatcgtggttatctgaaagcatgtatatttggtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGAACCAGAAAGGAGAGACAGGGTTGAGTCTCGAGATGGTAGAAGAGATTAT

Basic information

species Zea mays
transcript GRMZM2G069916_T05
intron # 12
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|60351428|gb|DN218401.1|DN218401
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|9952074|gb|BE638657.1|BE638657
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|148929409|gb|EC875422.2|EC875422
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|83278840|gb|DV942848.1|DV942848
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|32833686|gb|CD973364.1|CD973364
EST:     AAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCATCGGCCGGTCGTCCAGGGATAGAGA
genomic: AAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|149000972|gb|EE038212.2|EE038212
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|148973851|gb|EE024992.2|EE024992
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|60343955|gb|DN210928.1|DN210928
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|89761162|gb|DY689288.1|DY689288
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|88756296|gb|DY540437.1|DY540437
EST:     AGGAGCAGGGAAATAAAAGGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: AGGAGCAGAGAAATAAAA-GGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|211376324|gb|FL375223.1|FL375223
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|32838976|gb|CD978657.1|CD978657
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|71330189|gb|DR801853.1|DR801853
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|88757903|gb|DY542044.1|DY542044
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|83278696|gb|DV942704.1|DV942704
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|60400106|gb|DN232913.1|DN232913
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|8665973|gb|BE186789.1|BE186789
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|60399919|gb|DN232727.1|DN232727
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
EST: gi|148952946|gb|EE152419.2|EE152419
EST:     CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACG                         ATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA
genomic: CAGGAGCAGAGAAATAAAAGGAGACCGGGCAAAGCTGAAGATGATAGACGgtatggtgtt ... gtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actattttggtcagcatcgtggttatctgaaagcatgtatatttggtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGAACCAGAAAGGAGAGACAGGGTTGAGTCTCGAGATGGTAGAAGAGATTAT
 tccttac  putative branch site (score: 2)
                                              tgttttt  putative PPT
                                  atgtatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtgttccgtattccacatccttactattttggtcagcatcgtggttatctgaaagcatgtatatttggtgtttttagATCAAGAGAGCACAGCAAGGATCGCAACGGCCGGTCGTCCAGGGATAGAGAACCAGAAAGGAGAGACAGGGTTGAGTCTCGAGATGGTAGAAGAGATTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA