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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttttgcacaatagttttcatattccggtactttttggttattgtaaggttatgaggataggaaattatataagtgtttattttgtaagtgtct...

Basic information

species Glycine max
transcript GLYMA02G11960.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G11960.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttttgcacaatagttttcata-ttccggtactttttggttattgtaag-gttatgaggataggaaattatataagtgttt--attttgtaagtgtct
|||||||| || |||||||| || |  |||||  |||||||||||||||||| ||||||||| || |||||||||| ||  ||      |    ||   | || | || ||     |      || | | | |    ||   |  |  | | |  |     |   || ||||    
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgttattttttttcctttccactttctgtcctcaggaggctgcatatgtgctttttaaatcacatttcctttgatgggcccaaacctgcaagt----
















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|193302127|gb|FK266962.1|FK266962
EST:     AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAG                         CCATATCAACCTGGGTATACTGCCCCCC-ACCTCGTCCTAATCCTGAAGAA
genomic: AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttt ... gactctccagCCATATCAACCTGGGTATACTGCCCCCCCACCTCGTCCTAATCCTGAAGAA
EST: gi|15814866|gb|BI787141.1|BI787141
EST:     AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAG                         CCATATCAACCTGGGTATACTGNNNNNNNACCTCGTCCTAATCCTGAAGAA
genomic: AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttt ... gactctccagCCATATCAACCTGGGTATACTGCCCCCCCACCTCGTCCTAATCCTGAAGAA
EST: gi|193480374|gb|FK444680.1|FK444680
EST:     TGAGATATGTCATCAG                         CCATATCAACCTGGGTATACTG-CCCCCCACCTCGTCCTAATCCTGAAGAA
genomic: TGAGATATGTCATCAGgtatgctttt ... gactctccagCCATATCAACCTGGGTATACTGCCCCCCCACCTCGTCCTAATCCTGAAGAA
EST: gi|16346362|gb|BI971957.1|BI971957
EST:     AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAG                         CCATATCAACCTGGGTATACTGNNNNNNNACCTCGTCCTAATCCTGAAGAA
genomic: AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttt ... gactctccagCCATATCAACCTGGGTATACTGCCCCCCCACCTCGTCCTAATCCTGAAGAA
EST: gi|23052679|gb|BU577171.1|BU577171
EST:     AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAG                         CCATATCAACCTGGGTATACTGNNNNNNNACCTCGTCCTAATCCTGAAGAA
genomic: AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttt ... gactctccagCCATATCAACCTGGGTATACTGCCCCCCCACCTCGTCCTAATCCTGAAGAA
EST: gi|15284721|gb|BI468612.1|BI468612
EST:     AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAG                         CCATATCAACCTGGGTATACTGNNNNNNNACCTCGTCCTAATCCTGAAGAA
genomic: AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttt ... gactctccagCCATATCAACCTGGGTATACTGCCCCCCCACCTCGTCCTAATCCTGAAGAA
EST: gi|23057292|gb|BU577966.1|BU577966
EST:     AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAG                         CCATATCAACCTGGGTATACTGNNNNNNNACCTCGTCCTAATCCTGAAGAA
genomic: AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttt ... gactctccagCCATATCAACCTGGGTATACTGCCCCCCCACCTCGTCCTAATCCTGAAGAA
EST: gi|18039590|gb|BM307884.1|BM307884
EST:     AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAG                         CCATATCAACCTGGGTATACTGNNNNNNNACCTCGTCCTAATCCTGAAGAA
genomic: AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttt ... gactctccagCCATATCAACCTGGGTATACTGCCCCCCCACCTCGTCCTAATCCTGAAGAA
EST: gi|193418267|gb|FK383485.1|FK383485
EST:     TATGTCATCAG                         CCATATCAACCTGGGTATACTG-CCCCCCACCTCGTCCTAATCCTGAAGAA
genomic: TATGTCATCAGgtatgctttt ... gactctccagCCATATCAACCTGGGTATACTGCCCCCCCACCTCGTCCTAATCCTGAAGAA
EST: gi|9564988|gb|BE474497.1|BE474497
EST:     AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAG                         CCATATCAACCTGNGTATACTGNNNNNNNACCTCGTCCTAATCCTGAAGAA
genomic: AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttt ... gactctccagCCATATCAACCTGGGTATACTGCCCCCCCACCTCGTCCTAATCCTGAAGAA
EST: gi|14258749|gb|BG881657.1|BG881657
EST:     AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAG                         CCATATCAACCTGGGTATACTGNNNNNNNACCTCGTCCTAATCCTGAAGAA
genomic: AGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttt ... gactctccagCCATATCAACCTGGGTATACTGCCCCCCCACCTCGTCCTAATCCTGAAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttttgcacaatagttttcatattccggtactttttggttattgtaaggttatgaggataggaaattatataagtgtttattttgtaagtgtct

- - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - -  AGGAGA