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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcctattttcatagtattgatcactataactatacaagtaatcactttgaaagcattaaattgagaacatgttggatacattttgatcaatgaaatatagcaatgatacataacatatgcttcatttaacatcataatctttggggataccattgcag

Basic information

species Glycine max
transcript GLYMA20G36960.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36960.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G28640.1 (Arabidopsis thaliana), 5'ss of exon 3
GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcctattttcatagtattgatcactataactatacaagtaatcactttgaaagcattaaattgagaacatgttggatacattttgatcaatgaaatatagcaatgatacataacatatgcttcatttaacatcataatctttggggataccattgcag
||| ||| ||||||| ||  | || || |||||||||||||||||||| |||||||| || || ||| |     ||| | | |||||    |  | |||  | |||            || ||| | |  |||    ||| | |   | |||||||||  || |   |    |||| | | |                                                                   
GAATCAAGCAAGGCTTCAACGCAACCTAATGTACCTAGCTGCAATAGCAGATTCTCAGCCTCAGCCACCAAGTGTGCATAGCCAGgt----gattgtttatacagtg-----------aagtattcca--aattttgttgtatga--tcaattgagaaagtgatttgttttgtttggttattag-----------------------------------------------------------------

upper sequence: GLYMA20G36960.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv14s0081g00200.t01 (Vitis vinifera), 5'ss of exon 3
GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct-attttcatagtattgatcactataactatacaagtaatcactttgaaagcattaaattgagaacatgttggatacattttgatcaatgaaatatagcaatgatacataacatatgcttcatttaacatcataatctttggggataccattgcag
||||||  |||| || |||||||| ||||||||||| |||||||| ||||||||||||||||||||| |  | |||| || |||||||| |   | |||| |  | | |  |    ||||  || |  |    |   |     |   |||   ||| |  ||| |  |  ||| |  |      || | ||                                                           
GAACCAGGCAAGACTACAGAGAAACCTCATGTACCTGGCTGCAATCGCTGATTCTCAACCCCAACCACCCACCATGCATGCTCAGgtacgtatttcatttccggaatgtaaacttgtatattta-atgaaggctgtttgccgcatggttag--tgaaaggatgctcaac-catatcaact--caaatttta-----------------------------------------------------------
















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|298165632|gb|HO011681.1|HO011681
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|207842021|gb|GD817209.1|GD817209
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACT
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACT
EST: gi|298182194|gb|HO026369.1|HO026369
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|298165119|gb|HO011168.1|HO011168
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGGCTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|298198807|gb|HO042170.1|HO042170
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|192298039|gb|FG991319.1|FG991319
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|298165702|gb|HO008673.1|HO008673
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|298177026|gb|HO023387.1|HO023387
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|298195040|gb|HO043568.1|HO043568
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|213606189|gb|DB961333.1|DB961333
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|298196444|gb|HO041187.1|HO041187
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|192300839|gb|FG989736.1|FG989736
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|298181704|gb|HO025879.1|HO025879
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|193496739|gb|FK460757.1|FK460757
EST:     CTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: CTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|209701831|gb|BW652284.1|BW652284
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|151408071|gb|EV277879.1|EV277879
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|151409819|gb|EV279627.1|EV279627
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
EST: gi|298163796|gb|HO012529.1|HO012529
EST:     TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAG                         TATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG
genomic: TAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcct ... accattgcagTATCCTTCTAGTGGACTTATGCAGCAGGGAGCACACTACATGCAGGCTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACCAATCAAGGCTGCAGAGAAATCTCATGTACCTAGCTGCAATAGCTGATTCTCAACCCCAACCATCTCCAATGCCTGGTCAGgtacatgcctattttcatagtattgatcactataactatacaagtaatcactttgaaagcattaaattgagaacatgttggatacattttgatcaatgaaatatagcaatgatacataacatatgcttcatttaacatcataatctttggggataccattgcag

- - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - GCTGAT