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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAGgtatcactaaatttcatctgtattagaacaaattgagatgttctttttttgcttgaatgaagcgttatttggatatacgcatgatggcatgactagtttt...

Basic information

species Zea mays
transcript GRMZM2G361847_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G361847_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g48820.2 (Oryza sativa), 5'ss of exon 5
ACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAGgtatcactaaatttcatctgtattagaacaaattgagatgttctttttttgcttgaatgaagcgttatttggatatacgcatgatggcatgactagtttt------------
||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||||  |||  |    || ||   |     |  ||     | | ||  | ||  | ||  |||| || |||||| |  |  | |||    |   |    ||            
ACAATTCGGCGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAGgtactactgcag---atttgctct----tatgtt----cgcttttgctctgaataaa-aaagccttgtttggaaaagcataggattaattctgtgaacttacctgtgcaaac

upper sequence: GRMZM2G361847_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA20G39050.2 (Glycine max), 5'ss of exon 5
ACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAGgtatcactaaat-ttcatctgtattagaacaaattgagatgttctttttttgcttgaatgaagcgttat-ttggatatacgcatgatgg-catgactagtttt
||  | ||| ||||||| || ||||||||||||||||||||||||||| |||| || || |||  | ||  |  | |  | | ||     ||  |  | ||||     | |   | | |     ||| | ||   | | |  || ||    || ||||     
ACTCTCCGAAGGCTTGCTCAGAATCGTGAGGCAGCAAGAAAAAGTCGGTTGAGAAAGAAAgtaggaatatgtacttacatattttttgttaatatttgttgttacaagtgtatatcatttttctgttttcttctttctccatataataaatattactatg---

upper sequence: GRMZM2G361847_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 7
ACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAGgta--------tcactaaatttcatctgtattagaacaa--attgagatgttctttttttgcttgaatgaagcgttatttggatatacgcatgatggcatgactagtttt-------------------------------------------------
||| |  |||||||||| |||||||||||||| || || ||||| || |||||||||||||||        ||  | ||||| |  || | | | | ||  |||| ||| |   ||  ||  |||    |   || || |   |  |  |   |   | |  |  |||||                                                 
ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAGgtaaggccttttctgttaattttagatgaacttggaaaattattgtgatataacttggttagttgttcaatatgtcatattattg-agacccaacaacttatcatgttttataaatatttctgaacttcttttttaaatccttgtttctattcattcag

upper sequence: GRMZM2G361847_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA19G31050.3 (Glycine max), 5'ss of exon 7
ACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAGgta--------tcactaaatttcatctgtattagaacaa--attgagatgt---tctttttttgcttgaatgaagcgttatttggatatacgcatgatggcatgactagtttt--------------------------------------------
||| |  |||||||||| |||||||||||||| || || ||||| || |||||||||||||||        ||  | ||||| |  || | | | | ||  |||| ||| |   |   ||| |  || |||    | |||||  ||   |   |   || ||||  |  | |                                             
ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAAAGgtaaggccttttccgttaattttagatgaacttgtaaaattattgtgatataggttggtttgttgttcaatatgtcattattgagaccca-ataatttgtcatgttttatatatattttttgacttattttttaaatccctctttctattcattcag

upper sequence: GRMZM2G361847_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G28400.1 (Glycine max), 5'ss of exon 2
ACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAGgta--------tcactaaatttcatctgtattagaacaa--attgagatgttctttttttgcttgaatgaagcgttatttggatatacgcatgatggcatgactagtttt-------------------------------------------------
||| |  |||||||||| |||||||||||||| || || ||||| || |||||||||| ||||        ||  | ||||  |  || | | | | ||  |||| ||| |   ||  ||  |||    |   || || |   |  |  |   |   | || |  |||||                                                 
ACATTAAGACGGCTTGCTCAAAATCGTGAGGCTGCCAGGAAAAGCCGACTGAGGAAAATGgtaaggccttttctgttaattgtagatgaacttggaaaattattgtgatataacttggttagttgttcaatatgtcatattattg-agacccaacaacttgtcatgttttataaatatttctgaacttcttttttaaatccttgtttctatttattcag

upper sequence: GRMZM2G361847_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT3G12250.5 (Arabidopsis thaliana), 5'ss of exon 5
ACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAGgtatcactaaatttcatctgtattagaacaaattg-----agatgttctttttttgcttgaatga-agcgttatttggatatacgcatgatggcatgactagtttt------------------
||  | ||  ||||||| ||||||||||||||||||||||||||  |  ||||||| |||||||   ||  || | | |||  | |     |||      | || ||| | || |       | | | |  ||   | ||||     ||     |     ||  |                   
ACCCTTCGTAGGCTTGCTCAAAATCGTGAGGCAGCAAGAAAAAGCAGATTGAGGAAGAAGgtatgtatattttgcttttgttcttgttttgatttttcttatatattcctcttatttccttgtaatatctctagaagaatatctatctgtcattaccttaagcatgttattgtttcctccatag

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|71428739|gb|DR809789.1|DR809789
EST:     GGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG                         GCATATGTGCAGCAGCTGGAGAGCAGTAAGCTGAAACTTGCACAACTGGAA
genomic: GGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAGgtatcactaa ... tctggtgaagGCATATGTGCAGCAGCTGGAGAGCAGTAAGCTGAAACTTGCACAACTGGAA
EST: gi|211145673|gb|FL260532.1|FL260532
EST:     GGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG                         GCATATGTGCAGCAGCTGGAGAGCAGTAAGCTGAAACTTGCACAACTGGAA
genomic: GGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAGgtatcactaa ... tctggtgaagGCATATGTGCAGCAGCTGGAGAGCAGTAAGCTGAAACTTGCACAACTGGAA
EST: gi|76913286|gb|DV165055.1|DV165055
EST:     GGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG                         GCATATGTGCAGCAGCTGGAGAGCAGTAAGCTGAAACTTGCACAACTGGAA
genomic: GGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAGgtatcactaa ... tctggtgaagGCATATGTGCAGCAGCTGGAGAGCAGTAAGCTGAAACTTGCACAACTGGAA
EST: gi|211145672|gb|FL260531.1|FL260531
EST:     GGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAG                         GCATATGTGCAGCAGCTGGAGAGCAGTAAGCTGAAACTTGCACAACTGGAA
genomic: GGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAGgtatcactaa ... tctggtgaagGCATATGTGCAGCAGCTGGAGAGCAGTAAGCTGAAACTTGCACAACTGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATGCGACGGCTTGCCCAAAATCGTGAGGCAGCAAGAAAAAGTCGGCTGAGGAAAAAGgtatcactaaatttcatctgtattagaacaaattgagatgttctttttttgcttgaatgaagcgttatttggatatacgcatgatggcatgactagtttt

- - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - -  AAGAAA