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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatgaatgttccatctacttacttattagtacttccaaagtcagcaattaatgttctgcatgcaattaatggagaatattaattacatgtgattatgaattatcatttcaattttcttatactaagtcatggtgttttttttttcaatggcaactttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCTTGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGA

Basic information

species Glycine max
transcript GLYMA12G08990.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G08990.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgaatgaatgttccatctacttacttattagtacttccaaagtcagcaattaatgttctgcatgcaattaatggagaatattaattacatgtgattatgaattatcatttcaattttcttatactaagtcatggtgttttttttttcaatggcaactttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCTTGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGA
||| | | | | | ||| | || | |||| | || || || || ||||| | | | | | ||| | |||| ||||| |||||||||||||| |||||||| ||||||||| | || ||||| || |||||||||||||| ||||| ||| | || | |||||||| |||||||
------------------------------------------------------------tcattttacctttttaaga-agtaaagatattttgttattactt---gttgaaaaattggtatacatcataaatatatgagtcctttttac--tttctttgcatagGTGAAAAGTGAGCTTCCAAGTACTTTTAGAGCCTTCCGTTTTCAGCAACATAGATGGTCTTGTGGACCTGCAAATCTCTTTAGGAAAATGGTTATGGAGA

upper sequence: GLYMA12G08990.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 5
gtgaatgaatgttccatctacttacttattagtacttccaaagtcagcaattaatgttctgcatgcaattaatggagaatattaattacatgtgattatgaattatcatttcaattttcttatactaagtcatggtgttttttttttcaatggcaactttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCTTGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGA
| | ||| | | | || | | | || || || ||| | | | | | || || || || ||| | | | ||||| ||||||||||| ||||||||||| | |||||| | || ||||| ||||| ||||| |||||||| || ||||||||| | ||||||||||||||||
----------------------------------------------------------------------------gtacatttaa-ataaatgtctttaagttgg-ggaccatttcatttaaattga--tagcttcttagttgatttaacggcttcatca-atagGTGAAAAGTGAGCTGCCTAGTACTTTCAAGGCCTTCCGCTTTCAGCAACACAGGTGGTCCTGTGGTCCAGCCAATTTGTTCAGAAAAATGGTGATGGAGA
















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:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAG                         GCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|6567058|gb|AW234685.1|AW234685
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAG                         GCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|22931749|gb|BU548888.1|BU548888
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAG                         GCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|26057348|gb|CA800262.1|CA800262
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAG                         GCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|10235376|gb|BE804264.1|BE804264
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAG                         GCCAAAAGTGAGCTTTCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|120532206|gb|EH260339.1|EH260339
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAG                         GCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|13477899|gb|BG507587.1|BG507587
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAG                         GCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|7587930|gb|AW703736.1|AW703736
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAG                         GCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|7588469|gb|AW704326.1|AW704326
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAG                         GCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|15815411|gb|BI787686.1|BI787686
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAG                         GCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|33390688|gb|CA853883.1|CA853883
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAG                         GCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCA
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCA
EST: gi|22522995|gb|BU081806.1|BU081806
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAG                         GCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|13477774|gb|BG507518.1|BG507518
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAG                         GCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|298163139|gb|HO011872.1|HO011872
EST:     GGGGATGGAAATTTTTGTACCTTGGAGACCTCCAG                         GCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: GGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|8283281|gb|BE020842.1|BE020842
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAG                         GCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|151411882|gb|EV281693.1|EV281693
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAG                         GCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|14259637|gb|BG882545.1|BG882545
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAG                         GCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGAGACCTCCAGgtgaatgaat ... ctttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattttcttatactaagtcatggtgttttttttttcaatggcaactttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCTTGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGA
                        tgttttttttttcaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatgaatgttccatctacttacttattagtacttccaaagtcagcaattaatgttctgcatgcaattaatggagaatattaattacatgtgattatgaattatcatttcaattttcttatactaagtcatggtgttttttttttcaatggcaactttatatagGCCAAAAGTGAGCTTCCTAGTACTTTGAGAGCCTTCAGATTCCAGCAGCACAGATGGTCTTGTGGTCCTGCTAATTTGTTCCGCAAAATGGTGATGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA