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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgaatctgttcaattaaatgagttctgtggcaacacaatgatcgagagaaagcaaaagtcacatcacatcctttctcataggttacttttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAAGATGGGGGATAATGTGATGCTTATAGTTGCTGAAAAAGATGATAAACTA

Basic information

species Zea mays
transcript GRMZM2G158097_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158097_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g36062.1 (Oryza sativa), 3'ss of exon 9
tctgaatctgttca-attaaatgagttctgtggcaa--cacaatgatcgagagaaagcaaaagtcacatcacatcctttc-tcatagg-ttacttttcgc-----tgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAAGATGGGGGATAATGTGATGCTTATAGTTGCTGAAAAAGATGATAAACTA
          |||| |||  ||  |  |||   ||       ||  | |     ||  |    ||  ||   || ||| | | ||||| ||| |||| |      | ||| |||||||||||||||||||||||||| |||||||||| |||||||||||||||||| || || ||||||||||| ||||||||| | || |||||||  
----------ttcacattttatatggcctgatacatatttttatattagtatagaaatatttttcttatgttattcttcccttataggattattttttgtgtgctttcagCTGGGGCAGACCATACTTGACAAGGGAATTCTTTCACCGCTTGGGAGAAAAGATGGGTGACAAGGTGATGCTTATTGTTGCTGAACATGACGATAAACAT
















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|78124181|gb|DV542565.1|DV542565
EST:     ACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: ACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
EST: gi|71766886|gb|DR964823.1|DR964823
EST:     CTTCTATAAATTCTACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: CTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
EST: gi|32841147|gb|CD980828.1|CD980828
EST:     AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
EST: gi|32840869|gb|CD980550.1|CD980550
EST:     AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
EST: gi|13389377|gb|BG462692.1|BG462692
EST:     AGATTTTTTGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
EST: gi|32841581|gb|CD981262.1|CD981262
EST:     AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
EST: gi|32841639|gb|CD981320.1|CD981320
EST:     AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCA                         TTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA
genomic: AGACACTGGGACACCTTCTATAAATTCTACCGTAACACAACTGATAATCAgtttggtttc ... ttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagagaaagcaaaagtcacatcacatcctttctcataggttacttttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAAGATGGGGGATAATGTGATGCTTATAGTTGCTGAAAAAGATGATAAACTA
                                       ttacttttc  CT-rich tract
                                       ttactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgaatctgttcaattaaatgagttctgtggcaacacaatgatcgagagaaagcaaaagtcacatcacatcctttctcataggttacttttcgctgcagTTGGGGCAGACCATACTTGACAAGGGATTTCTTTCACCTCTTGGGAGAAAAGATGGGGGATAATGTGATGCTTATAGTTGCTGAAAAAGATGATAAACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG