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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCTTGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactcatttccgttaagtactatatatattgaagggtaaagggacaatgatacttaagtaattccatgtctgttctgatattttcttttgtttacatttctgcag

Basic information

species Glycine max
transcript GLYMA12G08990.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G08990.1 (Glycine max), 5'ss of exon 6
lower sequence: AT5G22740.1 (Arabidopsis thaliana), 5'ss of exon 6
TCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCTTGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactcatttccgttaagtactatatatattgaagggtaaagggacaatgatacttaagtaattccatgtctgttctgatattttcttttgtttacatttctgcag
||| |||||||| ||||||||| | || ||||| || |||||||||||||| ||||| ||| | ||  | |||||||| |||||||| || || |||||||||| || | ||  |    |  |||  | | | ||           ||  ||      | |  | || | ||  ||| ||||                            
TCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACATAGATGGTCTTGTGGACCTGCAAATCTCTTTAGGAAAATGGTTATGGAGATCGTAAGAAACAAGgtaa-taataataacaaaaatttacactttttctt------cttttggttaacttctttaatctgatcctattactgatctggcgcag----------------------

upper sequence: GLYMA12G08990.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv06s0061g01230.t01 (Vitis vinifera), 5'ss of exon 6
TCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCTTGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactcatttccgttaagtactatatatattgaagggtaaagggacaatgatacttaagtaattccatgtctgttctgatattttcttttgtttacatttctgcag
 ||||||||||| |  |||||| | || ||||| ||||| ||||| |||||||| || ||||||||| | |||||||||||||||||||| || |||||||| |||       |  ||| |   || | |  || |||  ||||  | | ||||  | | |  ||||     | ||    || ||          |  | | |  |||||
GCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGATTGTAAGAAACAAGgttagt-------ttagtttatatctttgtg-atagaaatgtaactg-agaatgtaattaagataat---gggactaagttgtta---------atcgataatcttgcag
















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|20811335|gb|BQ295813.1|BQ295813
EST:     GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAG                         AAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
genomic: GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactc ... atttctgcagAAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
EST: gi|6567058|gb|AW234685.1|AW234685
EST:     GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAG                         ANAGTTAAGTTTTGGAAGACAGTGTATGTTATATACAGCTNTCTCTTTGTT
genomic: GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactc ... atttctgcagAAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
EST: gi|22931749|gb|BU548888.1|BU548888
EST:     GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAG                         AAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
genomic: GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactc ... atttctgcagAAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
EST: gi|26057348|gb|CA800262.1|CA800262
EST:     GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAG                         AAAGTTAGGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
genomic: GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactc ... atttctgcagAAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
EST: gi|10235376|gb|BE804264.1|BE804264
EST:     GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAG                         AAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
genomic: GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactc ... atttctgcagAAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
EST: gi|120532206|gb|EH260339.1|EH260339
EST:     GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAG                         AAAGTTAGGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
genomic: GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactc ... atttctgcagAAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
EST: gi|7587930|gb|AW703736.1|AW703736
EST:     GTCCTGCTAATTTGTTCCGCANAATGGTGATGGAGATTGTGAGGAACAAG                         AAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTT
genomic: GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactc ... atttctgcagAAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTT
EST: gi|7588469|gb|AW704326.1|AW704326
EST:     GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAG                         AAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTNTNTCTTTGTT
genomic: GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactc ... atttctgcagAAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
EST: gi|298163139|gb|HO011872.1|HO011872
EST:     GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAG                         AAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
genomic: GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactc ... atttctgcagAAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
EST: gi|8283281|gb|BE020842.1|BE020842
EST:     GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAG                         AAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
genomic: GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactc ... atttctgcagAAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
EST: gi|151411882|gb|EV281693.1|EV281693
EST:     GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAG                         AAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
genomic: GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactc ... atttctgcagAAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
EST: gi|14259637|gb|BG882545.1|BG882545
EST:     GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAG                         AAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT
genomic: GTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactc ... atttctgcagAAAGTTAAGTTTTGGAAGAAAGTGTATGTTATATACAGCTTTTTCTTTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCTTGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGATTGTGAGGAACAAGgtaagtactcatttccgttaagtactatatatattgaagggtaaagggacaatgatacttaagtaattccatgtctgttctgatattttcttttgtttacatttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT