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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAATTGAAGAAGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagcttttgtttttccagtggtaggaattgcctcaagtgatttatcttgagttttgacaataccagtttgcatagtgattacttgttttattggggtc...

Basic information

species Zea mays
transcript GRMZM2G540403_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540403_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g15860.1 (Oryza sativa), 5'ss of exon 8
TCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAATTGAAGAAGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagcttttgtttttccagtggtaggaattgcctcaagtgatttatcttgagtttt---gacaataccagtttgcatagtgattacttgttttattggggtc
 || ||||| || |||||| | || ||||||||| ||||||| ||||| |||||||| ||||||||||| ||||||||||||||| |||||||||||||||||||||||||  |||    |  |  |   || ||    | |||  |   || || |   || |  |||| |||||||  || | ||||| |  ||||||| |
CCCTGCAATCCAATTCATGTTGTACGAGACTCTTTTGAAGAAGTTGAAAAAGAGACGTGCCTCTAATTTGAAGGGAGCTGATGGACTGACTGCTCTTGAAgtaagcttttggcttttggcttttctgg--tgactgggatcatt-gtacagatttattaggatataaccaatttgcatcatgctaacttgctgcattggggcc
















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|149071943|gb|EE160330.2|EE160330
EST:     AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|211285343|gb|FL118292.1|FL118292
EST:     AGAGACGAGCCTCTAATTTCAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTNTTMTTCTTGGTGCTGTTGCGAAACTTGGTGCAA-CGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|32929166|gb|CF033978.1|CF033978
EST:     AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|60343577|gb|DN210550.1|DN210550
EST:     AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|24934302|gb|CA452520.1|CA452520
EST:     AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|91877626|gb|EB407583.1|EB407583
EST:     GAGACGAGCCTCTAA-TTTAAGGGGAGCGGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: GAGACGAGCCTCTAATTTTAA-GGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|60340184|gb|DN207157.1|DN207157
EST:     AGAGACGAGCCTCTAATTTCAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|32929640|gb|CF034452.1|CF034452
EST:     AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|78121536|gb|DV539920.1|DV539920
EST:     AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|32935002|gb|CF039814.1|CF039814
EST:     AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|211285345|gb|FL118294.1|FL118294
EST:     AGAGACGAGCCTCTAATTTCAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|29543455|gb|CB603851.1|CB603851
EST:     AGAGACGAGCCTCTATTTTTAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTGGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|71422917|gb|DR805896.1|DR805896
EST:     AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|32868675|gb|CF008357.1|CF008357
EST:     AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|71422924|gb|DR805897.1|DR805897
EST:     AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|211285341|gb|FL118290.1|FL118290
EST:     AGAGACGAGCCTCTAATTTCAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|211285344|gb|FL118293.1|FL118293
EST:     AGAGACGAGCCTCTAATTTCAAGGGAGCTGATGGATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: AGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
EST: gi|211378309|gb|FL452851.1|FL452851
EST:     ATTGACTGCTCTTGAA                         ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT
genomic: ATTGACTGCTCTTGAAgtaagctttt ... tcttattcagATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCGCAATTCAGTTCATGCTATATGAGACTCTTCTGAAGAAATTGAAGAAGAGACGAGCCTCTAATTTTAAGGGAGCTGATGGATTGACTGCTCTTGAAgtaagcttttgtttttccagtggtaggaattgcctcaagtgatttatcttgagttttgacaataccagtttgcatagtgattacttgttttattggggtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA