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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTCTCGACCCCGCCGCCAGTACCACCTCGCCGCCGCAGCCCTCGTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctcagccccttgcgcaagttccctttttattcctgcattcctgattattcgataaggagttcaggactagtcgaaacgtaaaagcaaaatgtt...

Basic information

species Zea mays
transcript GRMZM2G032944_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032944_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g23169.1 (Oryza sativa), 5'ss of exon 1
CTTTCTCGACC-CCGCCGCCAGTACCACCTCGCCGCCGCAGCCCTCGTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgca-tctcagccccttgcgcaagttccctttttattcctgcattcctgattattcgataaggagttcaggactagtcgaaacgtaaaagcaaaatgtt
 |  | |||||  || | ||      ||  ||||||||| |||  | |||||||||||||  |||||||||||||||||  | | ||| || || || |||||| || |||| || |    | |   | ||||    |   |||   || |  || ||   |  ||| | |   | | ||    |  ||  |     ||  |
-TCCCACGACCGTCGGCACCCCGGAGACGCCGCCGCCGCCGCCGCCCTCGGAGGCCTGGACGAGCTTCCACCGTCGCCACACATGCGGCAAGTTTTTCAAGgtttcaatctccgctctcctccctgttaccctgcgcagatctgtcgtc-tactttttttttccggactgcgcaaatcgttaggaattaggatttctattgt
















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|37417157|gb|CF646231.1|CF646231
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|31355055|gb|CD439412.1|CD439412
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|211385269|gb|FL300401.1|FL300401
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|76914812|gb|DV165698.1|DV165698
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|149085005|gb|EE174515.2|EE174515
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|211385273|gb|FL300405.1|FL300405
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGC
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGC
EST: gi|91047980|gb|EB158398.1|EB158398
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|211385271|gb|FL300403.1|FL300403
EST:     ARGCCTGGAGAAGCTTCCACCGTCGCCATGTGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAA
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAA
EST: gi|76014696|gb|DT941866.1|DT941866
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|71448268|gb|DR829318.1|DR829318
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|89761751|gb|DY689640.1|DY689640
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|78124012|gb|DV542396.1|DV542396
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|211385274|gb|FL300406.1|FL300406
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGG
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGG
EST: gi|93284543|gb|EB676807.1|EB676807
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|93284224|gb|EB676488.1|EB676488
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|211385267|gb|FL300399.1|FL300399
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|211385272|gb|FL300404.1|FL300404
EST:     GGCCTGGAGAAGCTTCCACCGTCGCCATGCGTTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTT
genomic: GGCCTGGAGAAGCTTCCACCGTCGCCATGCGT-CCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTT
EST: gi|71765663|gb|DR963600.1|DR963600
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|211385270|gb|FL300402.1|FL300402
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTT-GTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|78116629|gb|DV535016.1|DV535016
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|211387892|gb|FL300408.1|FL300408
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
EST: gi|71438631|gb|DR819681.1|DR819681
EST:     AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAG                         GAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT
genomic: AGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctc ... acttttacagGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTCTCGACCCCGCCGCCAGTACCACCTCGCCGCCGCAGCCCTCGTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTTTAAGgttgcatctcagccccttgcgcaagttccctttttattcctgcattcctgattattcgataaggagttcaggactagtcgaaacgtaaaagcaaaatgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagcaaaa