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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatggtttcatttgcttgtttgttgatgtttagcttacatatgaagtcttgagcttattatcaatttatgttattctatgactctttattttactgcagACAGGACCACTGGCTGCTTATTATAAGCTACCTCTTAATCAAGTGCTTGTG

Basic information

species Glycine max
transcript GLYMA08G12110.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G12110.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g00560.t01 (Vitis vinifera), 3'ss of exon 3
-----aaatggtttcatttgcttgtttgttgatgtttagcttacatatgaagtcttgagcttattatcaatttatgttattctatgactctttattttactgcagACAGGACCACTGGCTGCTTATTATAAGCTACCTCTTAATCAAGTGCTTGTG
     | |   |||  | | ||| || |  ||| ||    |   ||   |    ||     ||| |     |  | | ||| | | | |||| || | ||| ||| | || ||||| || |||||||||||||||||||||||||  ||| |||||
tttatagaaaatttagtgtccttattag--gatattagtttattattcaacaaatt---tctatgacatgatgctataattttgttattcttcatctaactccagGCTGGCCCACTTGCAGCTTATTATAAGCTACCTCTTAATCGTGTGGTTGTG

upper sequence: GLYMA08G12110.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0124g00260.t01 (Vitis vinifera), 3'ss of exon 2
-----aaatggtttcatttgcttgtttgttgatgtttagcttacatatgaagtcttgagcttattatcaatttatgttattctatgactctttattttactgcagACAGGACCACTGGCTGCTTATTATAAGCTACCTCTTAATCAAGTGCTTGTG
     |||   |||  | |  || || |  ||| || || |||  |||  || |       ||| |     |  ||| ||| | |   ||||  | | ||| |||   || ||||| || |||||||||||||||||||||||||   || |||||
tttacaaaaaatttagtgtctttattgg--gatatt-agtttat-tattgag-caaatttctataacatgatgttgtaattttgtttttcttcgtctaacttcagGTTGGCCCACTTGCAGCTTATTATAAGCTACCTCTTAATCGCATGGTTGTG
















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|192327645|gb|FK020664.1|FK020664
EST:     CTGTTTTCCTTGCAAAGCCTCAAACTTACATGAATCTCAGTGGTGAATCG                         ACAGGACCACTGGCTGCTTATTATAAGCTACCTCTTAATCAAGTGCTTGTG
genomic: CTGTTTTCCTTGCAAAGCCTCAAACTTACATGAATCTCAGTGGTGAATCGgtaaggaatt ... tttactgcagACAGGACCACTGGCTGCTTATTATAAGCTACCTCTTAATCAAGTGCTTGTG
EST: gi|192326838|gb|FK015110.1|FK015110
EST:     CTGTTTTCCTTGCAAAGCCTCAAACTTACATGAATCTCAGTGGTGAATCG                         ACAGGACCACTGGCTGCTTATTATAAGCTACCTCTTAATCAAGTGCTTGTG
genomic: CTGTTTTCCTTGCAAAGCCTCAAACTTACATGAATCTCAGTGGTGAATCGgtaaggaatt ... tttactgcagACAGGACCACTGGCTGCTTATTATAAGCTACCTCTTAATCAAGTGCTTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcttgagcttattatcaatttatgttattctatgactctttattttactgcagACAGGACCACTGGCTGCTTATTATAAGCTACCTCTTAATCAAGTGCTTGTG
                                     ctctttattttact  CT-rich tract
          ttattatcaatttatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatggtttcatttgcttgtttgttgatgtttagcttacatatgaagtcttgagcttattatcaatttatgttattctatgactctttattttactgcagACAGGACCACTGGCTGCTTATTATAAGCTACCTCTTAATCAAGTGCTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - -tgcttgt
- - - - - - - - - - - gttgatg
- - - - - - - - - - - - - - - - -gcttaca
- - - - - - - - - - - - - - - - - - - - tatgaag