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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatgagtctgctatgccttttgtgcccgagcgagtgcctttctttcagctgtgtaagctaatgagttgtatcttattttttttcag

Basic information

species Glycine max
transcript GLYMA07G06590.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G06590.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G25520.2 (Arabidopsis thaliana), 5'ss of exon 3
CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtat-ttatgagtctgctatgccttttgtgcccgagcgagtgcctttctttcagctgtgtaagctaatgagttgtatcttattttttttcag
                                         |   | ||||||||||| |||||||| ||||| |||||||||| || || |  || | |    ||  |     |   ||   | || ||   |     |  | ||   | |    ||  |   |   ||||
-----------------------------------------ATGTTGGAAATGGATGACGAGTATGAGGGAAACGTTGAGgtatgttgtgtgattggtttcatcttgat-----aataagaagcattgttattgtctctt--gttagaaactcaagtcacacaatgaatcag

upper sequence: GLYMA07G06590.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G25520.1 (Arabidopsis thaliana), 5'ss of exon 4
CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtat-ttatgagtctgctatgccttttgtgcccgagcgagtgcctttctttcagctgtgtaagctaatgagttgtatcttattttttttcag
|||| || ||||| || || ||||| ||  | ||  | || |   | ||||||||||| |||||||| ||||| |||||||||| || || |  || | |    ||  |     |   ||   | || ||   |     |  | ||   | |    ||  |   |   ||||
CTTACTGTACTGGCCTTCTTTTGGCTCGCCGTGTTTTAAAGATGTTGGAAATGGATGACGAGTATGAGGGAAACGTTGAGgtatgttgtgtgattggtttcatcttgat-----aataagaagcattgttattgtctctt--gttagaaactcaagtcacacaatgaatcag
















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|254340071|gb|GR858196.1|GR858196
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|254323520|gb|GR835966.1|GR835966
EST:     CAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
genomic: CAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|18039738|gb|BM308032.1|BM308032
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|308099024|gb|HO760865.1|HO760865
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|9203772|gb|BE329996.1|BE329996
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|37996752|gb|CF808341.1|CF808341
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|17964295|gb|BM271032.1|BM271032
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|8282908|gb|BE020469.1|BE020469
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|10844117|gb|BF067454.1|BF067454
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGTAACCTGCTGAGAGCATGAGGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|192333817|gb|FK025078.1|FK025078
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|8282719|gb|BE020280.1|BE020280
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|10847099|gb|BF069865.1|BF069865
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|10845936|gb|BF068951.1|BF068951
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAATGAAATGTTGAC                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAAGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|15815279|gb|BI787554.1|BI787554
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
EST: gi|9258280|gb|BE346427.1|BE346427
EST:     GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAG                         GCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC
genomic: GAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatga ... tttttttcagGCTACTGGAGAGGATTATTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAATGGATGAGGAGTATGAAGGAAATGTTGAGgtatttatgagtctgctatgccttttgtgcccgagcgagtgcctttctttcagctgtgtaagctaatgagttgtatcttattttttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA