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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttcattatatgaagcattgatttttaattctatcttaaagttctgcttcagaagaggattgtagagtatatattcattatgagttcttttttgcagGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAG

Basic information

species Zea mays
transcript GRMZM2G061745_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 7
----ttttttcattatatgaagcattgatttttaattctatc-ttaaagttctgcttcagaagaggattgtagagtatatattcattatgagttcttttttgcagGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAG
    ||     |  | ||  |    | |||   | |||| |   | ||    |  | | || |  | |  ||   | | ||||  |||  |        |  |||||||| |||||||| || || ||| | || ||||| ||||| ||||||||||||||||
taacttgccaaacaaaatttaaatataattcaaagttctgttgctgaaacaattttactgatgcagttaataacctgtttattttttaaaaaaa-----tcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCCTTTGCAG
















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|211382592|gb|FK956034.1|FK956034
EST:     TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAATTGAGCTAATTTAAAGC
genomic: TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAGgctagtctct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATT-AAAGC
EST: gi|211382593|gb|FK956035.1|FK956035
EST:     TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAGgctagtctct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|211382591|gb|FK956033.1|FK956033
EST:     TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAG                         GATCTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAGgctagtctct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|211385218|gb|FK956039.1|FK956039
EST:     TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAGgctagtctct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|149014660|gb|EE044326.2|EE044326
EST:     AATTGACGGGAAGCTCCCCACTGA-TCACGAAATTTTGTACCATTTGCAG                         GATGTCTTTAATCCTCCTTC-AAATTT
genomic: AATTGACGGGAAGCTCCC-ACTGAATCACGAAATTTTGTACCATTTGCAGgctagtctct ... ttttttgcagGATGTCTTTAATC-TCCTTCCAAATTT
EST: gi|30705314|gb|CD058743.1|CD058743
EST:     TTGACGGNGAAGCTCCCACTNGAATCACGANAATTTTGTACCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCC
genomic: TTGACGG-GAAGCTCCCACT-GAATCACGA-AATTTTGTACCATTTGCAGgctagtctct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|67017978|gb|CO446727.1|CO446727
EST:     TAATTGACGGGAAGCTCCCACTGA-TCACGAAATTT-GTACCATTTGCAG                         GATGTCTTNTA-TCTCCTTCCNAATTTGAACGTNAATGAGCTAATTAA
genomic: TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAGgctagtctct ... ttttttgcagGATGTCTT-TAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAA
EST: gi|148960678|gb|EE011309.2|EE011309
EST:     TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAG                         GATGTCTTTAAT
genomic: TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAGgctagtctct ... ttttttgcagGATGTCTTTAAT
EST: gi|211385220|gb|FK956041.1|FK956041
EST:     TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAGgctagtctct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|211385221|gb|FK956042.1|FK956042
EST:     TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAGgctagtctct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCC
EST: gi|211385222|gb|FK956043.1|FK956043
EST:     TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGT
genomic: TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAGgctagtctct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATTTGAACGT
EST: gi|211385224|gb|FK956045.1|FK956045
EST:     TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAG                         GATGTCTTTAATCTCCTTCCAAATCTGAACGTAAATGAGCTAATTAAAGCC
genomic: TAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAGgctagtctct ... ttttttgcagGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgcttcagaagaggattgtagagtatatattcattatgagttcttttttgcagGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAG
                                          ttcttttttgc  CT-rich tract
                       agtatatattcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttcattatatgaagcattgatttttaattctatcttaaagttctgcttcagaagaggattgtagagtatatattcattatgagttcttttttgcagGATGTCTTTAATCTCCTTCCAAATTTGAACGTAAATGAGCTAATTAAAGCCTTTGCAG

- -tttcatt
- - - - - - -tgaagca