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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtggtccttcttccttgtgagctgggaaatactgcatcacagttagtgatggatctattttgtttactatttgctgtactatttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGACCCTCCGAAAGGTGTCCTTTGCTATGGCCCACCTGGTACTGGCAAGA

Basic information

species Zea mays
transcript GRMZM2G110185_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110185_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 6
-------gtatgtggtccttcttccttgtgagctggga-aatactgcatcacagttagtgatggatctattttgtttactatttgctgtactatttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGACCCTCCGAAAGGTGTCCTTTGCTATGGCCCACCTGGTACTGGCAAGA
        |  |  || |   |   || | | |||  | |||   | ||   |||||   ||||  ||| ||| |||    |||  | |  ||| |    |||||||||| ||||| ||||| |||||||| || || || ||||| || ||||| ||||| || ||||| ||||||||||| ||||| || |||||||| |
gtaagtgattggaagttcccttcatttttaatctgttataattgaggatgcaagttac--atggcgctaatttattt----ttttatattttatctgc-tagGTTGTTGAGCTTCCCATGCTCCACCCAGAGAAATTCGTTAAGCTAGGAATTGATCCTCCAAAGGGTGTTCTTTGCTATGGTCCACCAGGGACTGGCAAAA

upper sequence: GRMZM2G110185_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 6
gtatgtggtccttcttccttgtgagctgggaaatactgca-tcacagttagtgatggatctattttgtttactatttgctgtactatttttgc-agGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGACCCTCCGAAAGGTGTCCTTTGCTATGGCCCACCTGGTACTGGCAAGA
||  ||| |      | |   |||  |   |  |  |  | |  | | |     |       |  |  ||    ||   | || | | | ||| |||||||||| ||||| ||||| ||||| || || || || ||||| || ||||| ||||| || ||||| ||||||||||| ||||| || |||||||| |
gttagtgattggaagttcccttgatttttaatctgttataattgcggatgtaagttacatggtgctaattttatttatttatattttatctgctagGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATTGATCCTCCAAAGGGTGTTCTTTGCTATGGTCCACCAGGGACTGGCAAAA

upper sequence: GRMZM2G110185_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 6
gtatgtggtccttcttccttgtgagctgggaaatactgcatcacagttagtgatggatctattttgtttactatttgct-gtactatttttgca-gGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGACCCTCCGAAAGGTGTCCTTTGCTATGGCCCACCTGGTACTGGCAAGA
           |   || ||| ||  |   |  || |  | ||    || ||| | |  ||  |    |   | |   | ||| | |   |||| ||||||||||||||| |||||||| ||||| || |||||||||||||| ||||| ||||| || ||||| ||||| |||||||| || || ||||| || |
----------gtaagtcattg-gaatttttacttatttta-catttataatgaagtagataagtcacgtgtcactaatttgtaatttcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGCCCCCCAGGAACTGGGAAAA

upper sequence: GRMZM2G110185_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 6
gtatgtggtccttcttccttgtgagctgggaaatactgcatcacagttagtgatggatctattttgtttactatttgctgtactatttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGACCCTCCGAAAGGTGTCCTTTGCTATGGCCCACCTGGTACTGGCAAGA
           |   || |||  |  |     ||  | ||| | | |   | ||| |  |||   |      |||||   |  |    |   |||||||||||||||| |||||||| ||||| || |||||||||||||| ||||| ||||| || ||||| ||||| ||||| || || || ||||| || |
----------gtaagtcattgaaatttcacttatcttacattataat-gataatgaagttatgcggcactaaatttgtcat--ttccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGTCCCCCAGGAACTGGGAAAA

upper sequence: GRMZM2G110185_T04 (Zea mays), 3'ss of exon 5
lower sequence: EFJ13722 (Selaginella moellendorffii), 3'ss of exon 6
gtatgtggtccttcttccttgtgagctgggaaatactgcatcacagttagtgatggatctattttgtttactatttgctgtactatttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGACCCTCCGAAAGGTGTCCTTTGCTATGGCCCACCTGGTACTGGCAAGA
                                  ||| || ||   ||     | | | |   | ||  || || |    |  ||    |  ||||||| || ||||||||||| || || || |||||| |||||||||| || || ||||| ||||| || |||||||| ||||| || || ||||| || |
-------------------------------gtaactacaccat--tttacatttggttt-cctcgtcgacgatcttaacttttacgcatatagGTTGTAGAGCTTCCTATGCTCCATCCTGAGAAGTTTATCAAGCTTGGAATCGATCCTCCCAAAGGAGTTCTTTGCTACGGCCCTCCGGGAACTGGGAAAA

upper sequence: GRMZM2G110185_T04 (Zea mays), 3'ss of exon 5
lower sequence: EFJ29161 (Selaginella moellendorffii), 3'ss of exon 6
gtatgtggtccttcttccttgtgagctgggaaatactgcatcacagttagtgatggatctattttgtttactatttgctgtactatttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGACCCTCCGAAAGGTGTCCTTTGCTATGGCCCACCTGGTACTGGCAAGA
                                  ||| || ||   ||     | | | | | | ||  || || |    |  ||    |  ||||||| || ||||||||||| ||||| ||||||||| |||||||||| || || ||||| ||||| || |||||||| ||||| || || ||||| || |
-------------------------------gtaactacaccat--tttacatttggttt-tctcgtcgacgatcttaacttttacgcatatagGTTGTAGAGCTTCCTATGCTCCACCCTGAAAAGTTTATCAAGCTTGGAATCGATCCTCCCAAAGGAGTTCTTTGCTACGGCCCTCCGGGAACTGGGAAAA

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|149015235|gb|EE045022.2|EE045022
EST:     CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
genomic: CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
EST: gi|211285323|gb|FL004422.1|FL004422
EST:     CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
genomic: CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
EST: gi|149015481|gb|EE045355.2|EE045355
EST:     CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
genomic: CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
EST: gi|211283517|gb|FL004412.1|FL004412
EST:     CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
genomic: CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
EST: gi|149087114|gb|EE176653.2|EE176653
EST:     CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
genomic: CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
EST: gi|211285334|gb|FL004433.1|FL004433
EST:     CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
genomic: CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
EST: gi|211283515|gb|FL004410.1|FL004410
EST:     CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
genomic: CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
EST: gi|19436438|gb|BM952848.1|BM952848
EST:     CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
genomic: CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
EST: gi|32846361|gb|CD986042.1|CD986042
EST:     ACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
genomic: ACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
EST: gi|33104358|gb|CF064318.1|CF064318
EST:     GTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
genomic: GTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
EST: gi|211283510|gb|FL004405.1|FL004405
EST:     CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
genomic: CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
EST: gi|78085799|gb|DV514192.1|DV514192
EST:     CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
genomic: CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
EST: gi|211285332|gb|FL004431.1|FL004431
EST:     CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
genomic: CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT
EST: gi|28930845|gb|CB334206.1|CB334206
EST:     CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAA                         GTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCT-GGTAT-
genomic: CGTACAATGATGTCGGTGGCTGCAAGGAGCAGATTGAGAAGATGCGTGAAgtatgtggtc ... atttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacagttagtgatggatctattttgtttactatttgctgtactatttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGACCCTCCGAAAGGTGTCCTTTGCTATGGCCCACCTGGTACTGGCAAGA
                                           ctattttt  CT-rich tract
                    tattttgtttactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtggtccttcttccttgtgagctgggaaatactgcatcacagttagtgatggatctattttgtttactatttgctgtactatttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGACCCTCCGAAAGGTGTCCTTTGCTATGGCCCACCTGGTACTGGCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA