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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactctttgttttgaagcatcacaatgttctgttcattttccacagctaaaaatatttctggctaaggttgctccattcttttgtcgcaaatgttggtcttttttatttttaaatggtatgggcattgttaatatcactgactgttattgacccctgaggtatttgcag

Basic information

species Zea mays
transcript GRMZM2G320307_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G320307_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g47790.1 (Oryza sativa), 5'ss of exon 2
GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactctttgttttgaagcatcacaatgttctgttcattttccacagctaaaaatatttctggctaaggttgctccattcttttgtcgcaaatgttggtcttttttatttttaaatggtatgggcattgttaatatcactgactgttattgacccctgaggtatttgcag
 ||||||||||||| ||||||||| |||||||||||||||| |||||| |||||| | ||  |||  |        |   ||||| |  |||    | ||   |       |||| |        ||||| ||  || ||     | |  ||      ||||||  | |                                                         
TTTGCTCCTTATGAGCGTCCTGCATTAAGCAAAGGCTATTTGCTCCCACAAGgtaccgacattttcat----gatctttgaatgtgcaattc----tgcatgtcgtttgtcatttat--------ttgcttcaaactgtt----tataattttactccttttatcctcag--------------------------------------------------------
















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:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|13558384|gb|BG549740.1|BG549740
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|211343496|gb|FL158171.1|FL158171
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|148960823|gb|EE011492.2|EE011492
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|74239090|gb|DT647004.1|DT647004
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|76282291|gb|DV021859.1|DV021859
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|211343497|gb|FL158172.1|FL158172
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|76294433|gb|DV034001.1|DV034001
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|6021228|gb|AW066156.1|AW066156
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAA                         GTGCTGCTCGTCTTCCAGGATTT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTT
EST: gi|91052072|gb|EB162490.1|EB162490
EST:     CTCCTTAAGAAAC-TCCTGGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: CTCCTTATGAA-CGTCCTG-CACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|149014462|gb|EE044078.2|EE044078
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|93282877|gb|EB675141.1|EB675141
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|101396936|gb|EB820393.1|EB820393
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|50324177|gb|CO519303.1|CO519303
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|93014386|gb|EB639906.1|EB639906
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|211341114|gb|FL158167.1|FL158167
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|74236111|gb|DT644025.1|DT644025
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|148957305|gb|EC903342.2|EC903342
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|87155794|gb|DY400583.1|DY400583
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|148969919|gb|EE020823.2|EE020823
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|76015963|gb|DT943133.1|DT943133
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|31360581|gb|CD444938.1|CD444938
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|74233733|gb|DT641647.1|DT641647
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|211343502|gb|FL158177.1|FL158177
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTRCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
EST: gi|148949714|gb|EC895192.2|EC895192
EST:     TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAG                         GTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT
genomic: TGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactc ... gtatttgcagGTGCTGCTCGTCTTCCAGGATTTCATACTTGTGTTGGTGCTAATGATGAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCTCCTTATGAACGTCCTGCACTAAGCAAAGGCTATTTACTCCCAGAAGgtaacaactctttgttttgaagcatcacaatgttctgttcattttccacagctaaaaatatttctggctaaggttgctccattcttttgtcgcaaatgttggtcttttttatttttaaatggtatgggcattgttaatatcactgactgttattgacccctgaggtatttgcag

- - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - GCAAAG