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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggttgttagccattttcttcaaaactgccttgaatttcttttttaacatattttatatacactctatgttcttaaacatatgccattcatcag

Basic information

species Zea mays
transcript GRMZM2G119725_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119725_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 5
TGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggttgtt-----agccattttcttcaaaactgccttgaattt-----cttttttaacatattttatatacactctatgttcttaaacatatg-ccat-tcatcag
|||||| |||||||| ||||||||||| || || |||||||||||||| || |||||||||||||||| ||| || ||| | ||||||||||||||||||||| ||||||  |      |  | |||  |||  |  || |||||||       || | || ||| |||  | ||   | ||   ||| |||||||||  | |    ||||
TGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATTGTTGTTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtttcttttgttgtaactttgctcagtagggcattgaattagatggtttctatatcatttttcttctatgatatacaatctgaaacatatggtcgtactgtcag

upper sequence: GRMZM2G119725_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA12G29800.1 (Glycine max), 5'ss of exon 5
TGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggttgttagccattttcttc---aaaactgccttgaatttcttttttaacatattttatatacactctatgttcttaaacatatgccattcatcag
|||| |  |||| ||    || |||||   ||| || || || || || || || ||| ||||| |||||   ||||||||||||||||| |||||||||||  ||       ||  ||||        | || |   |||    |  |       |  | | |||||   | ||       ||| | | | | || | || 
TGTTGCATCAAATCCTCGTGGAGCTGAATCACTACCCCCTGGAATCGTTGTATCAGAATCAGATTTTTATTTACGAAGACTATGGGGTGAACCTAGTGAGgtatgttacaaacagttatttatgatgcgagaaattatttgtggcttgtagccgttaagtctcatatatgatatagtactacaaatacaagac-ttaaaca-
















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|148930418|gb|EE284901.2|EE284901
EST:     TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAG                         GACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGG
genomic: TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggtt ... cattcatcagGACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGG
EST: gi|149108358|gb|EE292696.2|EE292696
EST:     TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAG                         GACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTT
genomic: TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggtt ... cattcatcagGACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTT
EST: gi|76930436|gb|DV172388.1|DV172388
EST:     TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAG                         GACCTTACTAGCGAGCC
genomic: TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggtt ... cattcatcagGACCTTACTAGCGAGCC
EST: gi|148937093|gb|EC881269.2|EC881269
EST:     TGTCTGACACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAG                         GACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGG
genomic: TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggtt ... cattcatcagGACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGG
EST: gi|148961302|gb|EE012027.2|EE012027
EST:     TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAG                         GACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGG
genomic: TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggtt ... cattcatcagGACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTGTTGGTATTGGG
EST: gi|149104738|gb|EE290190.2|EE290190
EST:     TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAG                         GACCTTACTAGCGAGCCGAGGTATCTTGGTACTTTTACTG
genomic: TGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggtt ... cattcatcagGACCTTACTAGCGAGCCGAGGTATCTTGTTACTTTTACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggttgttagccattttcttcaaaactgccttgaatttcttttttaacatattttatatacactctatgttcttaaacatatgccattcatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA