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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaacatatgatgtgaaacgtacctcaaaatgagtaagaagctatggaaacatgaggattgaccttacagatcctgaaacttatgaaccacaactacagGACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTGCTATACGGTCTCCTACGGTTCGAGCCATCGGAACGCCTGACAGCAGAAG

Basic information

species Zea mays
transcript GRMZM2G094039_T06
intron # 9
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|88748004|gb|DY532145.1|DY532145
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAGgttttagttc ... acaactacagGACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
EST: gi|6031579|gb|AW076481.1|AW076481
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAGgttttagttc ... acaactacagGACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
EST: gi|149082188|gb|EE171368.2|EE171368
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAGgttttagttc ... acaactacagGACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
EST: gi|74234528|gb|DT642442.1|DT642442
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAGgttttagttc ... acaactacagGACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
EST: gi|18167576|gb|BM337416.1|BM337416
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAGgttttagttc ... acaactacagGACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
EST: gi|16925980|gb|BM079048.1|BM079048
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAGgttttagttc ... acaactacagGACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
EST: gi|71432789|gb|DR813839.1|DR813839
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAGgttttagttc ... acaactacagGACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
EST: gi|50333914|gb|CO529040.1|CO529040
EST:     CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAG                         GACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG
genomic: CTGTTTCAAGAGAAAGCATCAGAGCTGTGAGGAAACTGGATCGACTAAAGgttttagttc ... acaactacagGACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaaacatgaggattgaccttacagatcctgaaacttatgaaccacaactacagGACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTGCTATACGGTCTCCTACGGTTCGAGCCATCGGAACGCCTGACAGCAGAAG
                 accttac  putative branch site (score: 3)
                                aaacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actaacatatgatgtgaaacgtacctcaaaatgagtaagaagctatggaaacatgaggattgaccttacagatcctgaaacttatgaaccacaactacagGACTTGGTATCGAGGAACGCTGACCATTCAAAGGTGGCACTGGTGGACTTGCTATACGGTCTCCTACGGTTCGAGCCATCGGAACGCCTGACAGCAGAAG

- - - - atgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatcctg