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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttgtttatctttccttaatatggtatactaatcgtgctggcagaggcatactgtgctctttatggccttacctcaccttttgcttgttgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAGAAGACGAAACAGAAACTGGAATGGGCTGAAAAGCAGCGCGAAGCGAATC

Basic information

species Zea mays
transcript GRMZM2G031825_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031825_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g21460.1 (Oryza sativa), 3'ss of exon 5
gttttgtttatctttccttaatatggtatactaatcgtgct----ggcagaggcatactgtgctctttatggccttacctcaccttttgcttgttgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAGAAGACGAAACAGAAACTGGAATGGGCTGAAAAGCAGCGCGAAGCGAATC
    | | ||  | | ||||  |||||||  |  | ||  |       | |   | |  ||       ||    |   || ||   |    |  ||| || |||||||||||||||||||| |||||||| |||||  | |||||||| || || ||   ||| |||||||| ||||||||| |||||||||| ||||| || |
----tatgtacttctacttatcatggtatggttcttgtcattcaaaagaaaaaaaaaaggtaacagccatactttattcttactagtcttattatgacttacagTACACTGTGAAGAACCTGAAATTCATACTGACGGTCGAGCCAGATAACGAAAAAGTGAAGCAGAAACTAGAATGGGCTCAAAAGCAGCGTGAAGCAAACC
















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|32799175|gb|CD951411.1|CD951411
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|84976888|gb|DW475310.1|DW475310
EST:     GGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: GGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|60357818|gb|DN224791.1|DN224791
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|32930224|gb|CF035036.1|CF035036
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|71773157|gb|DR971070.1|DR971070
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|60343728|gb|DN210701.1|DN210701
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|67033911|gb|CO462660.1|CO462660
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|7138069|gb|AW499414.1|AW499414
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACCCTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|60345729|gb|DN212702.1|DN212702
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|211460283|gb|FL454155.1|FL454155
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|74233977|gb|DT641891.1|DT641891
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|211048852|gb|FL416946.1|FL416946
EST:     TCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|76285780|gb|DV025348.1|DV025348
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|32800109|gb|CD952345.1|CD952345
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|86466772|gb|DY233142.1|DY233142
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|13516080|gb|BG518356.1|BG518356
EST:     TACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATTGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGA
genomic: TACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCA-TGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGA
EST: gi|28982871|gb|BQ538319.2|BQ538319
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|60346352|gb|DN213325.1|DN213325
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|71429897|gb|DR810947.1|DR810947
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
EST: gi|32826625|gb|CD966303.1|CD966303
EST:     TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAG                         TACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG
genomic: TTACACTGGGTTCGCTGCCAAAGTCAACCCGAGTTTACTGTGGGCATGAGgtacaatctc ... tgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggcatactgtgctctttatggccttacctcaccttttgcttgttgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAGAAGACGAAACAGAAACTGGAATGGGCTGAAAAGCAGCGCGAAGCGAATC
                           acctcac  putative branch site (score: 3)
              tctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgtttatctttccttaatatggtatactaatcgtgctggcagaggcatactgtgctctttatggccttacctcaccttttgcttgttgagttgcagTACACTGTGAAGAACCTAAAATTCATGCTGACACTGGAGCCAGAGAATGAGAAGACGAAACAGAAACTGGAATGGGCTGAAAAGCAGCGCGAAGCGAATC

-ttttgtt
- - - - - - - - - - - - - - - - - - -tgctggc
- - - - - - - - - - - - - - - - - - - - - - - -ggcatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgctc