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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaataatgggccaatttagtttacgattctaatagacgatcctatgtgcttgcctgtttttattgagatagaattgacaatagtttgcatgcttttcagAGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG

Basic information

species Glycine max
transcript GLYMA09G06890.1
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 27
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 29
---tgaataatgggccaattt-agtttacgattctaat---agacgatcctatgtgcttgcctgtttttattgagatagaattgacaatagtttgcatgcttt----tcagAGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG
     | |  |   |  | || ||  | ||  |  | |      | |   ||      |  | |||| | || |  | | |   | ||| |  |  ||  |||    |||||||||||||||| |||||||| |||||||| || ||| | ||||| 
gtaccacttcttatcagacttgagcatgcgtgttaagtcttgttcaactatagagtgctctcagtttctcttcaatttgcac-aataattggatttatcttttgctctcagAGAACCTCTCATCACAAATATCATGTGGAGAAACTTGTTTATACAA
















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|17020701|gb|BM091735.1|BM091735
EST:     ACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAG                         AGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG
genomic: ACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAGgtcagaattt ... tgcttttcagAGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG
EST: gi|15337121|gb|BI497777.1|BI497777
EST:     ACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAG                         AGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG
genomic: ACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAGgtcagaattt ... tgcttttcagAGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG
EST: gi|193572068|gb|FK532375.1|FK532375
EST:     ACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAG                         AGAACCTCTCATAACAAATATTATGTGGAGG
genomic: ACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAGgtcagaattt ... tgcttttcagAGAACCTCTCATAACAAATATTATGTGGAGG
EST: gi|9820234|gb|BE555744.1|BE555744
EST:     ACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAG                         AGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG
genomic: ACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAGgtcagaattt ... tgcttttcagAGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG
EST: gi|17020693|gb|BM091727.1|BM091727
EST:     ACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAG                         AGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG
genomic: ACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAGgtcagaattt ... tgcttttcagAGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG
EST: gi|207771638|gb|GD744317.1|GD744317
EST:     ACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAG                         AGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG
genomic: ACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAAGgtcagaattt ... tgcttttcagAGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcttgcctgtttttattgagatagaattgacaatagtttgcatgcttttcagAGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG
                           aattgac  putative branch site (score: 3)
                                             tgcttttc  putative PPT
            tttttattgagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaataatgggccaatttagtttacgattctaatagacgatcctatgtgcttgcctgtttttattgagatagaattgacaatagtttgcatgcttttcagAGAACCTCTCATAACAAATATTATGTGGAGGAATTTGCTGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttgca