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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggattatttgttgtcttattggaaatttagtgtcataactaataactacttggttttgttttttgtaatgcaactaggcctcattttatgttaattttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG

Basic information

species Glycine max
transcript GLYMA08G18760.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 4
gtaggattatttgttgtcttattggaaatttagtgtcataactaataa-ctacttggttttgttt-tttgtaatgcaactaggcctcattttatgttaattttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG
||| |  |||| ||||    ||  ||  | || |      |     || ||  |  |  | |||  ||||| |   || |     | |||  || |    |||  ||||| ||||||||||| ||||| |||||||  || |||||||| || ||||| || |||||||| || ||    ||||| ||  |  ||||||| |||
gtatg-ctattagttgagacatgagacctctattacttgtatggtcaatctgttaagagtcgttaatttgtgaactaagtgaaaataattc-atttgctctttttcagGTCGTTGCAGCTGGTGCCAATCCTGTGCAAATTACACGTGGTATCGAGAAAACTGCGAAAGCACTAGTTGAAGAGCTAAAGAAATTGTCAAAGGAG

upper sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 4
------gtaggattatttgttgtcttattggaaatttagtgtcataactaa-taactacttggttttgttttttgtaatgc-aactaggcctcattttatgttaattttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG
       |  | |||  | || | ||     ||  | |    ||||   |  |||  |  || |     | | | |  ||| ||||| |  |||||        |||    ||||| || |||||||| || |||||||| || ||||| || ||||||||||||||  | ||| |||| ||  |||||||||| | ||| |||||||||
gtctgtttttgcttaactcttttgtttggtaaacatgaagaacatagtaatctaaggaaatgataacactgtgtttgttgctaactaaga-tcattc-------attcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAG
















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|120530535|gb|EH258668.1|EH258668
EST:     CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAG                         GTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
genomic: CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAGgtaggattat ... attttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
EST: gi|207747526|gb|GD717907.1|GD717907
EST:     CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAG                         GTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
genomic: CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAGgtaggattat ... attttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
EST: gi|193564338|gb|FK519201.1|FK519201
EST:     CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAG                         GTTGTTGCAGCGTGGGGCCAACCCTGTGCTCAT
genomic: CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAGgtaggattat ... attttcgcagGTTGTTGCAGC-TGGGGCCAACCCTGTGCTCAT
EST: gi|193653960|gb|FK596948.1|FK596948
EST:     CGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAG                         GTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
genomic: CGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAGgtaggattat ... attttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
EST: gi|193528896|gb|FK483628.1|FK483628
EST:     CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAG                         GTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGC
genomic: CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAGgtaggattat ... attttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGC
EST: gi|120530550|gb|EH258683.1|EH258683
EST:     CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAG                         GTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
genomic: CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAGgtaggattat ... attttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
EST: gi|17401201|gb|BM177983.1|BM177983
EST:     CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAG                         GTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
genomic: CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAGgtaggattat ... attttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
EST: gi|20207910|gb|BQ133999.1|BQ133999
EST:     CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAG                         GTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
genomic: CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAGgtaggattat ... attttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
EST: gi|15201304|gb|BI424801.1|BI424801
EST:     CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAG                         GTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
genomic: CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAGgtaggattat ... attttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
EST: gi|193655361|gb|FK596651.1|FK596651
EST:     CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAG                         GTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
genomic: CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAGgtaggattat ... attttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
EST: gi|192323269|gb|FK015275.1|FK015275
EST:     CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAG                         GTTGTTGCAACTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG
genomic: CCACGACCTCGGTTGTTCTTGCTCAGGGTCTTATAGCGGAAGGTGTCAAGgtaggattat ... attttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggttttgttttttgtaatgcaactaggcctcattttatgttaattttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG
                                        tgttaat  putative branch site (score: 3)
                                              ttttcgc  CT-rich tract
                                tcattttatgttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggattatttgttgtcttattggaaatttagtgtcataactaataactacttggttttgttttttgtaatgcaactaggcctcattttatgttaattttcgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACACGTGGCATTGAGAAGACAGCGAAAGCTCTTGTATCTGAGCTTAAACAGATGTCAAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG