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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgttgtttcattcagtgggactggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT

Basic information

species Zea mays
transcript GRMZM2G126453_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 24
gtaaatgttgtttcattcagtgggactggattacccagttgt-ataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT
                                        || | | || ||   ||||  | ||||    |  ||   ||   ||||| || |           ||| || | ||  |||       ||| | | |  |  ||||||||||| ||||| || || ||||| ||||| || || ||||| |||||||| |||||||| |||||| |||   | | | |||||||||| || |||
----------------------------------------gtgacagctataaccttgt--gttggggttgggataatgaaaaattgctgtttg-----------ttgatttc-taaccatttggtcgttaattactactgtagGTTAATGGTTAACTTACCTGACGCATCGAATAGAGAAAAGATTCTGAAAGTAATATTGGCAAAGGAAGAGTTGGCTCCAGGTATTGATATGGATTCTCTT
















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|211384433|gb|FL031621.1|FL031621
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         -TTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|32921157|gb|CF025969.1|CF025969
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|58029637|gb|CX725064.1|CX725064
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAA-TTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|32920203|gb|CF025015.1|CF025015
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|211048841|gb|FL187601.1|FL187601
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|211048838|gb|FL187598.1|FL187598
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCA-                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|32921345|gb|CF026157.1|CF026157
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|211048837|gb|FL187597.1|FL187597
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
EST: gi|32920665|gb|CF025477.1|CF025477
EST:     AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAG                         GTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT
genomic: AATAGGCCTTTTGACCTCGACGAGGCTGTGATTAGGAGGTTCCCCCGCAGgtaaatgttg ... attgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT
                                    atcttac  putative branch site (score: 3)
                                              ttgtttc  putative PPT
          aatagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgttgtttcattcagtgggactggattacccagttgtataactgtagttttgttcggtgggccatgattatctaatcgttgcttttgggtagcaatagtttggttccatattcatcaccatcttactcattgtttcagGTTAATGGTAAACTTGCCCGATGCATCAAATAGGGAGAAAATTCTAAAAGTAATTTTGGCAAAAGAAGAGCTGGGATCTGATGTTGATATGGACTCGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT