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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacatagttggacttaaaagtttcattttcagctgttttcttcctgattttttggacatatatctagGTGTGGGATTACATAAGTGGAAAGCTGAAGAAAGATCTACAGTACCAGGCTGAT

Basic information

species Glycine max
transcript GLYMA08G13560.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 7
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------gtatacatagttggacttaaaagtttcattttcagctgttttcttcct--gattttttggacatata------tctagGTGTGGGATTACATAAGTGGAAAGCTGAAGAAAGATCTACAGTACCAGGCTGAT
                   ||||  ||  |   ||     | |    |||  |    || | |  ||  ||||  |  ||| |  |      |  |||| ||||||||||||||||||||||| ||||| ||| | || || || ||||||
gtgagttgatccggaatctgtatgtatgataatacaagttattagtctttaaaataattctgtgactaggattgctcagacttgaaaagcattacagGTATGGGATTACATAAGTGGAAAGCTCAAGAAGGATTTGCAATATCAAGCTGAT
















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|207732274|gb|GD705269.1|GD705269
EST:     CACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG                         GTGTGGGATTACATAAGTGGAAAG
genomic: CACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAGgtatacatag ... atatatctagGTGTGGGATTACATAAGTGGAAAG
EST: gi|193465598|gb|FK432503.1|FK432503
EST:     CACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG                         GTGTGGGATTACATAAGTGGAAAGCTGAAGAAAGATCTACAGTACCAGGCT
genomic: CACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAGgtatacatag ... atatatctagGTGTGGGATTACATAAGTGGAAAGCTGAAGAAAGATCTACAGTACCAGGCT
EST: gi|192300449|gb|FG987906.1|FG987906
EST:     CACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG                         GTGTGGGATTACATAAGTGGAAAGCTGAAGAAAGATCTACAGTACCAGGCT
genomic: CACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAGgtatacatag ... atatatctagGTGTGGGATTACATAAGTGGAAAGCTGAAGAAAGATCTACAGTACCAGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaaaagtttcattttcagctgttttcttcctgattttttggacatatatctagGTGTGGGATTACATAAGTGGAAAGCTGAAGAAAGATCTACAGTACCAGGCTGAT
                             tcctgat  putative branch site (score: 3)
        tttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacatagttggacttaaaagtttcattttcagctgttttcttcctgattttttggacatatatctagGTGTGGGATTACATAAGTGGAAAGCTGAAGAAAGATCTACAGTACCAGGCTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT