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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtctttctccggaaggtcttgagccactatcataccaggcccagaaagcgactcactttccctgtttcaagatcattacaaggcaaacgatat...

Basic information

species Zea mays
transcript GRMZM5G821024_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G821024_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g06170.2 (Oryza sativa), 5'ss of exon 3
AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtctttctccggaaggtcttgagccactatcataccaggcccagaaagcgactcactt--tccctgtttcaagatcattacaaggcaaacgatat
|||||||| |||||  ||||  |||||||||| ||||| || |||||| ||||| |||||||||||||||||||||| |||||||||| ||  | ||  | | |||| ||||  | |  | | ||   ||||||| |||     | |       | | ||||    ||||||     || |    | 
AGGGACACGTCTGGCCTAACTGCTGAGAACAGAGAGCTCAAACTCCGGTTGCAGTCCATGGAAGAACAAGCTAAACTTCGAGATGgtatgtcctattctttcagaagctcttccgtctttgttat-taaggcccacaaataatgttatcaagctcttctttctttgtcattaaggcccagatataa-

upper sequence: GRMZM5G821024_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g06170.1 (Oryza sativa), 5'ss of exon 2
---------------AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtctttctccggaaggtcttgagccactatcataccaggcccagaaagcgactcact--ttccctgtttcaagatcattacaaggcaaacgatat
               |||||||| |||||  ||||  |||||||||| ||||| || |||||| ||||| |||||||||||||||||||||| |||||||||| ||  | ||  | | |||| ||||  | |  | | ||   ||||||| |||     | |       | | ||||    ||||||     || |    | 
TTTACTTATGGTCAGAGGGACACGTCTGGCCTAACTGCTGAGAACAGAGAGCTCAAACTCCGGTTGCAGTCCATGGAAGAACAAGCTAAACTTCGAGATGgtatgtcctattctttcagaagctcttccgtctttgttat-taaggcccacaaataatgttatcaagctcttctttctttgtcattaaggcccagatataa-
















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|78084546|gb|DV512939.1|DV512939
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|71763914|gb|DR961851.1|DR961851
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|76921490|gb|DV168603.1|DV168603
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|76289896|gb|DV029464.1|DV029464
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|76291030|gb|DV030598.1|DV030598
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTTTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|74233755|gb|DT641669.1|DT641669
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|74235022|gb|DT642936.1|DT642936
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTTTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|71443974|gb|DR825024.1|DR825024
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTTTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|71427971|gb|DR809021.1|DR809021
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTTTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|89250945|gb|DY622731.1|DY622731
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|78121824|gb|DV540208.1|DV540208
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|50330894|gb|CO526020.1|CO526020
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTTTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|110519434|gb|EE023832.1|EE023832
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|88755380|gb|DY539521.1|DY539521
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGTTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|93282762|gb|EB675026.1|EB675026
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACCAGCTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCG
EST: gi|71760728|gb|DR958665.1|DR958665
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTTTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|60339341|gb|DN206314.1|DN206314
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|50327404|gb|CO522530.1|CO522530
EST:     GCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|101396399|gb|EB820126.1|EB820126
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
EST: gi|86469183|gb|DY235553.1|DY235553
EST:     GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATG                         CTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG
genomic: GCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtc ... gatgatgcagCTCTAAATGACGCCCTGAGAGAAGAAGTCCAGCGGCTTAAGATAGCCACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAGCTCCGGCTGCAGGCCATGGAAGAACAAGCTAAACTCCGAGATGgtacgtagtctttctccggaaggtcttgagccactatcataccaggcccagaaagcgactcactttccctgtttcaagatcattacaaggcaaacgatat

- - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggcaaa