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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAAACATTTCACAGCTTGAACAGTGAGTTGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataattctacactgaccctatacttttgtgatgttttatttctttaaaacagtattctttacctatcccatgtctggggaaaagtgcaaaatatt...

Basic information

species Arabidopsis thaliana
transcript AT3G06670.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06670.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv05s0077g01200.t01 (Vitis vinifera), 5'ss of exon 6
GCGAAACATTTCACAGCTTGAACAGTGAGTTGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataattctacactgaccctatacttttgtg-atgttttatttc----tttaaaacagtattct-ttacct---atcccatgtctggggaaaagtgcaaaatatt
| ||  ||||||||||| | |||||||||||||||||| | ||||| || |||||  | || |||||| | |||||||||||   ||       ||  ||  |  || || | |  ||  ||| ||||    ||| |    ||||  | || | |   ||    || |   |||  ||||         
GTGACTCATTTCACAGCATCAACAGTGAGTTGAGGGAGTTGCCTGCAGTTGAGCTGTCCACCCTTCCCTTGATACTGAAGgtaacattggatgccatggatgccttagttctcttcatactttgtttcatctttttatttggtatgttattgcttgttattttttggccaaggaggagtg---------
















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|116447731|gb|EG490323.1|EG490323
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116423237|gb|EG465829.1|EG465829
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGG
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGG
EST: gi|116412443|gb|EG455035.1|EG455035
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116411545|gb|EG454137.1|EG454137
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116407356|gb|EG449948.1|EG449948
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116413313|gb|EG455905.1|EG455905
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116444990|gb|EG487582.1|EG487582
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116449085|gb|EG491677.1|EG491677
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116449109|gb|EG491701.1|EG491701
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116407371|gb|EG449963.1|EG449963
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116417526|gb|EG460118.1|EG460118
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116448708|gb|EG491300.1|EG491300
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTCACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116411537|gb|EG454129.1|EG454129
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116449103|gb|EG491695.1|EG491695
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116460005|gb|EG502597.1|EG502597
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116434816|gb|EG477408.1|EG477408
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
EST: gi|116379504|gb|EG422096.1|EG422096
EST:     TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAG                         ATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT
genomic: TGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataat ... ttccttgcagATTGTTACAGAGAGTGGCATTACAGATCAGATGCGCCTAACTGAACTTATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGAAACATTTCACAGCTTGAACAGTGAGTTGAGGGAGCTTCCTGCTGTAGAGCTTACTACTCTTCCCCTAATACTGAAGgttttataattctacactgaccctatacttttgtgatgttttatttctttaaaacagtattctttacctatcccatgtctggggaaaagtgcaaaatatt

- - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctatccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaaaata