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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtattgccatacttttatcactagtttttttagcgaaagggcctttagctgagttggttacgtggtctgagtagcactccttaggtcctgagttcgaatc...

Basic information

species Zea mays
transcript GRMZM2G177912_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 5
GTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtat-tgccatacttttatcactagtttttttagcgaaagggcctttagctgagtt-----ggttacgtggtctgag----tagcac--tccttaggtcctgagttcgaatc----------------------
|| |||| ||||||||| || ||||||||||||||||||| ||| |||||||||||||||| ||| |||||  |  ||| |   |     |     ||| ||| ||       ||   | | ||     |  |  |   |  |||    | |     || || | |  | |  || |||                       
GTTCGAGGAGCGGAATACAATAATGTAAGGAGCCAGCTTAGTGCGATCAACAGAAAGCAAACTGGAAGgtagattgcatgccactgagtttttggctttaagccaattctttcttgttttatttcaaaggactcagaaatgcgagggtatggtttcatcttttgttagtcaactctaattagtttgttttccttctgtatag

upper sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv17s0000g00460.t01 (Vitis vinifera), 5'ss of exon 5
GTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtattgccatacttttatcactagtttttttagcgaaagggcctttagctgagttggttacgtggtctgagtagcactccttaggtcctgagttcgaatc---
|| || |  || || |||||||||||| | || ||||||| ||| || ||||||||||||| ||| ||||||||   || |  | | |  |        |   |      ||||  |  | ||  | |     | ||  |  |  ||   |     | | |    ||    
GTTCGTGTTGCTGAGTATAACAATGTACGCAGTCAGCTTAATGCCATAAACAGAAAGCAAACTGGAAGgtattgaattattgctgtaatcatcaacagaaattatttcaacttt--ccaaatttataa-aaattttgtttgcctgtcagaaataaataaataaacattcaa
















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|211359331|gb|FL325567.1|FL325567
EST:     AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCAGTTCGTGA
genomic: AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtattgccat ... tctgtgacagCTTAGCAGTTCGTGA
EST: gi|9953349|gb|BE639932.1|BE639932
EST:     AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACC
genomic: AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtattgccat ... tctgtgacagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACC
EST: gi|78120131|gb|DV538515.1|DV538515
EST:     AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCTG
genomic: AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtattgccat ... tctgtgacagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCTG
EST: gi|211267792|gb|FL344631.1|FL344631
EST:     AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCAGTTCGTGACCTTTCCAAT
genomic: AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtattgccat ... tctgtgacagCTTAGCAGTTCGTGATCTTTCCAAT
EST: gi|148969238|gb|EE019992.2|EE019992
EST:     AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCTG
genomic: AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtattgccat ... tctgtgacagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCTG
EST: gi|149104624|gb|EE290073.2|EE290073
EST:     AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCTG
genomic: AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtattgccat ... tctgtgacagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCTG
EST: gi|67016433|gb|CO445182.1|CO445182
EST:     AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCAGTTCGTGACCTTTCCAATCTGGTAAAACCAGAGGATATGGTCTG
genomic: AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtattgccat ... tctgtgacagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCTG
EST: gi|211460898|gb|FL364621.1|FL364621
EST:     AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCAGTTCGTGACCTTTCCAATC
genomic: AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtattgccat ... tctgtgacagCTTAGCAGTTCGTGATCTTTCCAATC
EST: gi|76288290|gb|DV027858.1|DV027858
EST:     AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAG                         CTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCTG
genomic: AACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtattgccat ... tctgtgacagCTTAGCAGTTCGTGATCTTTCCAATCTGGTAAAACCAGAGGATATGGTCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCGAGCAGCGGAATATAACAATGTAAGGAGCCAGCTTACTGCAATCAACAGAAAGCAAAGTGGGAGgtattgccatacttttatcactagtttttttagcgaaagggcctttagctgagttggttacgtggtctgagtagcactccttaggtcctgagttcgaatc

- - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG