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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGGTGGGTGGAAAGACAGAACAACAGTGGAAGATATGGACCTTGCTGTTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAGgttaatcaatgctccatctacttacctattagtacttccaaagttaacaattaacggagaatatgaatgacatatgattatgaattatcatttcaattttcttatactaagtaatggtgccttttttttaaatggtaactttatatag

Basic information

species Glycine max
transcript GLYMA11G19490.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19490.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G22740.1 (Arabidopsis thaliana), 5'ss of exon 5
AGCTGGTGGGTGGAAAGACAGAACAACAGTGGAAGATATGGACCTTGCTGTTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAGgttaatcaatgctccatctacttacctat-tagtacttccaaagttaacaattaacggagaatatgaatgacatatgatta-tgaattatcatttcaattttcttatactaagtaatggtgccttttttttaaatggtaactttatatag
||||||||||||||||||  | || || |||||||||||||| || || || || || |||||| | || ||||||||| | ||||| |||||||| ||||||      |  |  || ||||| |  ||  | || ||  | |||||  ||  ||   |  | |   || ||| ||  | | |   |   ||    | || ||| ||                                           
AGCTGGTGGGTGGAAAGATCGGACCACCGTGGAAGATATGGATCTCGCCGTCCGAGCAAGTCTTCGCGGCTGGAAATTTCTCTACCTCGGTGACCTTCAGgtt-----tttatttatttactttctaatacaatatttagatagttag-aacaaattaa--acacacataacaaatagtaagttggtgcacaagatacttctctcatt------------------------------------------

upper sequence: GLYMA11G19490.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv06s0061g01230.t01 (Vitis vinifera), 5'ss of exon 5
AGCTGGTGGGTGGAAAGACAGAACAACAGTGGAAGATATGGACCTTGCTGTTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAGgttaatc--aatg--ctccatctacttacctattagtacttccaaagttaacaattaacggagaatatgaatgacatatgattatgaattatcatttcaattttcttatactaagtaatggtgccttttttttaaatggtaactttatatag
 |||||||||||||| ||||||||||| ||||| || ||||| ||||| || ||||||||||| | ||| ||||||||  | || |||||||| || |||||  ||   |||      | |  | ||    |  | | | |  ||| | |    ||    |   || | |  |    || | ||                                                                    
GGCTGGTGGGTGGAAGGACAGAACAACCGTGGAGGACATGGATCTTGCCGTCCGTGCTAGTCTCAAGGGCTGGAAATTCGTTTATCTTGGTGATCTTCAGgtacatttaaataaatgtctttaagttggggaccatttcatttaaattgatagcttcttagttgatttaacggcttcatcaatag-------------------------------------------------------------------
















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|7478387|gb|AW666245.1|AW666245
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAG                         GCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAGgttaatcaat ... ctttatatagGCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|207797357|gb|GD769881.1|GD769881
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAG                         GCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAGgttaatcaat ... ctttatatagGCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|8283320|gb|BE020881.1|BE020881
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATNTTTGTACCTTGGTGACCTCCAA                         GCCAAGAGTGAGCTTGCCAGTACTGTGAGAGCCTTCAGATTCCAGCATCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAGgttaatcaat ... ctttatatagGCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|16346811|gb|BI972406.1|BI972406
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAG                         GCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAGgttaatcaat ... ctttatatagGCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|8284807|gb|BE022366.1|BE022366
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAG                         GCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAGgttaatcaat ... ctttatatagGCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
EST: gi|193422352|gb|FK389741.1|FK389741
EST:     TCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCCAG                         GCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGACAGC
genomic: TCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCC-AGgttaatcaat ... ctttatatagGCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAG-CAGC
EST: gi|10846450|gb|BF071342.1|BF071342
EST:     TTCGTGCTAGTCTTANGGGATGGAAATTTTTGTACCTTGGTGACCTCCAG                         GCCAAAAGTGAGC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAGgttaatcaat ... ctttatatagGCCAAAAGTGAGC
EST: gi|15337505|gb|BI498161.1|BI498161
EST:     TTCGTGCTAGTCTTAGGGGATGAAAATTTT-GTACCTTGGTGACCTCCAG                         GCCAAAAGTGAGCTTCCCA
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAGgttaatcaat ... ctttatatagGCCAAAAGTGAGCTTCCCA
EST: gi|6567149|gb|AW234774.1|AW234774
EST:     TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAG                         GCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC
genomic: TTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAGgttaatcaat ... ctttatatagGCCAAAAGTGAGCTTCCCAGTACTTTGAGAGCCTTCAGATTCCAGCAGCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGGTGGGTGGAAAGACAGAACAACAGTGGAAGATATGGACCTTGCTGTTCGTGCTAGTCTTAGGGGATGGAAATTTTTGTACCTTGGTGACCTCCAGgttaatcaatgctccatctacttacctattagtacttccaaagttaacaattaacggagaatatgaatgacatatgattatgaattatcatttcaattttcttatactaagtaatggtgccttttttttaaatggtaactttatatag

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