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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagaatcagagtactctctagttctctgttctatgtttttttttattcagacacgtgctttgctagctagttacaatttttttcctgtattctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG

Basic information

species Zea mays
transcript GRMZM2G320307_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G320307_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g47790.1 (Oryza sativa), 3'ss of exon 1
--------------tcagaat--cagagtactc--tctagttc--tctgttctat-gtttttttttattcagacacgtgctttgctagctagttacaatttttttcctgtattctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG
               | || |  || | |||||  | |  ||   | | || ||  |     |  || ||| |  | || |   ||   |   |    ||     ||| || | |   ||| ||||||||||||| ||||||||| |||||||||||||||| |||||| |||
gtacgttttcttctcctgatttgcatactactccgtatgatttaatttattgtacagcaaaatcctaatcaaaatcatgttccact---tttctttctttccccccctctactattaacagTTTGCTCCTTATGAGCGTCCTGCATTAAGCAAAGGCTATTTGCTCCCACAAG
















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|78112090|gb|DV530486.1|DV530486
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|13558384|gb|BG549740.1|BG549740
EST:     GGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|211343500|gb|FL158175.1|FL158175
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|211343496|gb|FL158171.1|FL158171
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|148960823|gb|EE011492.2|EE011492
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|74239090|gb|DT647004.1|DT647004
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|76282291|gb|DV021859.1|DV021859
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|211343497|gb|FL158172.1|FL158172
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|76294433|gb|DV034001.1|DV034001
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|6021228|gb|AW066156.1|AW066156
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GNTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|91052072|gb|EB162490.1|EB162490
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTAAGAAAC-TCCTGGCACTAAGCAAAGGCTATTTACTCCCAG
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAA-CGTCCTG-CACTAAGCAAAGGCTATTTACTCCCAG
EST: gi|149014462|gb|EE044078.2|EE044078
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|93282877|gb|EB675141.1|EB675141
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|101396936|gb|EB820393.1|EB820393
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|50324177|gb|CO519303.1|CO519303
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|93014386|gb|EB639906.1|EB639906
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|211341114|gb|FL158167.1|FL158167
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|74236111|gb|DT644025.1|DT644025
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|148957305|gb|EC903342.2|EC903342
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|211343498|gb|FL158173.1|FL158173
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTA
EST: gi|87155794|gb|DY400583.1|DY400583
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|22714917|gb|BU197541.1|BU197541
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCA
EST: gi|148969919|gb|EE020823.2|EE020823
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|76015963|gb|DT943133.1|DT943133
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|31360581|gb|CD444938.1|CD444938
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|74233733|gb|DT641647.1|DT641647
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|211343502|gb|FL158177.1|FL158177
EST:     GCCGCGGTGGGTACTCCCGCGGANAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
EST: gi|148949714|gb|EC895192.2|EC895192
EST:     GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCC                         GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA
genomic: GCCGCGGTGGGTACTCCCGCGGAGAGCTCTGCATCATCTCCGAAGAGGCCgtaagctctg ... ttctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcagacacgtgctttgctagctagttacaatttttttcctgtattctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG
                                tttttttcctgtattc  CT-rich tract
                       tagttacaattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagaatcagagtactctctagttctctgttctatgtttttttttattcagacacgtgctttgctagctagttacaatttttttcctgtattctcgccagGTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - tgttttt
- - - - - - - - - - - - - - - - - - - - - - - - - - cacgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctagc