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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaaaacaagcaatgtcacgtggggattttgacttttttcatgtttgttgagctcattatagtcatttgcagATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGGTTGGAGCTCCTGAGGCTTTGGTAATTGGGGTCGTTGCTTTGTTGGTTTT

Basic information

species Glycine max
transcript GLYMA20G30120.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30120.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G52440.1 (Arabidopsis thaliana), 3'ss of exon 1
------------gtaacaaaacaagcaatgtcacgtggggattttg-acttttttcatgtttgttgagctcatta--tagtcatttgcagATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGGTTGGAGCTCCTGAGGCTTTGGTAATTGGGGTCGTTGCTTTGTTGGTTTT
            |  | |  |       | |      ||| ||||| |   || |    ||| |  || |   |   |  |  | |||||| |  ||| || | |||||| |||   || |   ||| ||||| ||||| |||||||| |||||||||||||| ||||| || ||||||||||| || ||
gtttcgatttcagagatatgattgcttctttacttctgggtttttgtaaagttgtttaatttctgaagttgggtggttttttgtgtgcagAGAAGAAGAGAAGATGTAAGAGTATGATGATTCGTGCGTCTCTGTTTGGTGTTGGAGCACCTGAGGCTTTGGTTATTGGTGTTGTTGCTTTGTTAGTCTT

upper sequence: GLYMA20G30120.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g00800.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------gtaacaaaacaagcaatgtcacgtggggattttgactttt-ttcatgtttgttgagctcattatag--tcatttgcagATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGGTTGGAGCTCCTGAGGCTTTGGTAATTGGGGTCGTTGCTTTGTTGGTTTT
                                      |  ||||     |   |    | |  ||||| |  ||||  |||| |  ||     |  |||| |  |  | |  ||  ||||  ||| |||| || || |||||||| ||||| ||||| ||||||||||| |||||||||||| |||| ||||| || || ||||||||||||||
gtgcttttttcatctgggtatttgggaattttgtttttttgcaaattgttcttggatttgagttgatttagggttttgctcatctgcgtatgcttgtttatggaattctatttagGAAGAAGAGGAAGGTGCAAAGGGAAAGTGGTTTATGCATCTCTGTTTGGGGTTGGGGCTCCTGAGGCTCTGGTTATTGGAGTGGTAGCTTTGTTGGTTTT
















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|298185172|gb|HO030385.1|HO030385
EST:     TTTAAAGCATCTGGGTATCTCAGCTAAACCAAAACCTCTTCTTCACATAG                         ATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGG
genomic: TTTAAAGCATCTGGGTATCTCAGCTAAACCAAAACCTCTTCTTCACATAGgtaacaaaac ... tcatttgcagATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGG
EST: gi|192311913|gb|FK004222.1|FK004222
EST:     TTTAAAGCATCTGGGTATCTCAGCTGAACCAAAACCTCTTCTTCACATAG                         ATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGG
genomic: TTTAAAGCATCTGGGTATCTCAGCTAAACCAAAACCTCTTCTTCACATAGgtaacaaaac ... tcatttgcagATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGG
EST: gi|151402645|gb|EV272458.1|EV272458
EST:     TTTAAAGCATCTGGGTATCTCAGCTAAACCAAAACCTCTTCTTCACATAG                         ATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGG
genomic: TTTAAAGCATCTGGGTATCTCAGCTAAACCAAAACCTCTTCTTCACATAGgtaacaaaac ... tcatttgcagATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGG
EST: gi|192334065|gb|FK026222.1|FK026222
EST:     TTTAAAGCATCTGGGTATCTCAGCTAAACCAAAACCTCTTCTTCACATAG                         ATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGG
genomic: TTTAAAGCATCTGGGTATCTCAGCTAAACCAAAACCTCTTCTTCACATAGgtaacaaaac ... tcatttgcagATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGG
EST: gi|19348858|gb|BM893390.1|BM893390
EST:     TTTAAAGCATCTGGGTATCTCAGCTAAACCAAAACCTCTTCTTCACATAG                         ATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGG
genomic: TTTAAAGCATCTGGGTATCTCAGCTAAACCAAAACCTCTTCTTCACATAGgtaacaaaac ... tcatttgcagATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGG
EST: gi|192311912|gb|FK004221.1|FK004221
EST:     TTTAAAGCATCTGGGTATCTCAGCTGAACCAAAACCTCTTCTTCACATAG                         ATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGG
genomic: TTTAAAGCATCTGGGTATCTCAGCTAAACCAAAACCTCTTCTTCACATAGgtaacaaaac ... tcatttgcagATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgtggggattttgacttttttcatgtttgttgagctcattatagtcatttgcagATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGGTTGGAGCTCCTGAGGCTTTGGTAATTGGGGTCGTTGCTTTGTTGGTTTT
         ttttgac  putative branch site (score: 3)
        attttgactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaaaacaagcaatgtcacgtggggattttgacttttttcatgtttgttgagctcattatagtcatttgcagATAGAAAGGGAGGGTGTAAGGGTAAAGTGGTATATGCTTCTCTCTTTGGGGTTGGAGCTCCTGAGGCTTTGGTAATTGGGGTCGTTGCTTTGTTGGTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT