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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttttttcctaaatatccatgtttcttacagtcaagctgacaatggtaggattagtgactgattattcgaagatttcattatcttttctggtttacagTTTGAACCTGAGACATCAAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG

Basic information

species Glycine max
transcript GLYMA06G16700.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g06300.1 (Oryza sativa), 3'ss of exon 12
tttttttttcctaaatatccatgtttcttacagtcaagctgacaatg---gtaggattagtga---ctgattattcgaagatttcattatcttttctggtttacagTTTGAACCTGAGACATCAAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
       | || || |  | |||||  ||   | | |  |  || ||    | | |||  | |    || || |   |||     |  |   |||    |   ||||||||||| ||  | |||||||||||||| |||||||| |||||||| ||||| || |||||||||||||| ||||| |||
----agatgccaaattgccaatgttgattggtgactaattagcattgtgcattgcatttctcatctttgcttttctaaaggcagtaacaaggttttcaat--gcagTTTGAACCAGAATCTTCAAGTGCCATGGGTTTTGGCTTCAGATGTGGATTTCTCGGTCTTCTTCATATGGAGATTGTGCAG

upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G003157_T02 (Zea mays), 3'ss of exon 3
----tttttttttcctaaatatccatgtttcttacagtcaagctgacaatggtaggattagtgactgattattcgaagatttcattatcttttctggtt-tacagTTTGAACCTGAGACATCAAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
    | | || |   |     ||  |  |  |     |        || |||||   |   |||    | |||      | ||   |||  | |   |  | ||||||||||| ||  | || ||||||||||| |||||||| ||||||||||| || || ||||| ||||||||||| ||||||
tgcatctgttctcatttggattctgtaatattggttattctttatgcattggtattttgtatgatacttcattt-----tctctaaatccatgccattaatgcagTTTGAACCAGAATCTTCTAGTGCCATGGGGTTTGGCTTCAGATGTGGGTTCCTTGGTCTTCTCCATATGGAAATAGTTCAG

upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G08650.1 (Arabidopsis thaliana), 3'ss of exon 12
---tttttttttcctaaatatccatgtttcttacagtcaagctgacaatggtaggattagtgactgattattcgaagatt-tcattatcttttctggtttacagTTTGAACCTGAGACATCAAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
   | | ||| |   |||||| ||  |||  |  |    |||  | |  | ||| ||||     |   |||  |    |  |||   |  ||| |    | |||||||| ||||| || || |||||||||||||||||||||||||| |||||| |||| ||||| || ||||||||||| |||
atgtatctttgttaaaaatattcacatttggtctaag-gagcgtata-cgttagcattaaca--tatctataggtttgtcctcaacttggtttttatcctgcagTTTGAGCCTGAAACTTCGAGTGCCATGGGATTTGGCTTTAGATGCGGGTTTTTGGGTCTTCTCCACATGGAAATTGTGCAG

upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv07s0031g03050.t01 (Vitis vinifera), 3'ss of exon 12
---tttttttttcctaa-atatccatgtttcttacagt-caagctgacaatggtaggattagtgactgattattcgaagatttcattatcttttctggtttacagTTTGAACCTGAGACATCAAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
   || |||  |  ||| |    | |  || | |  ||  | || ||   ||||     || |  || |  | | |          |    | ||   ||| |||||||| ||||||||||| ||||||||||| ||||||||||| ||||||||  |||| ||||| |||||||||||  |||||
ctattgtttggttgtaataagggcgtagttttaatggtatatgcagatcttggt-----tacttgctaaagaattgtgctcccttcttcaatgtccattttgcagTTTGAGCCTGAGACATCCAGTGCCATGGGCTTTGGCTTTAGGTGTGGGTTCTTGGGTCTTCTCCATATGGAAATCATTCAG

upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ20933 (Selaginella moellendorffii), 3'ss of exon 12
tttttttttcctaaatatccatgtttcttacagtcaagctgacaatggtaggattagtgactgattattcgaagatttcattatcttttctggtttacagTTTGAACCTGAGACATCAAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
                                ||   ||   | ||| || |  | |  ||  ||||  |   |||  |||| | | |     | | ||||||||||| || |  || ||||| ||||||||||| ||| ||||||| ||||| |||||| | || |||||||| || |||
--------------------------------gtatggcct-cgatgctaag--tcgccacctattaaacactgatgccattgtatctagaattctgcagTTTGAACCGGAAAGTTCGAGTGCAATGGGATTTGGATTTCGATGTGGATTTCTTGGCCTTTTGCACATGGAAATAGTACAG

upper sequence: GLYMA06G16700.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ32321 (Selaginella moellendorffii), 3'ss of exon 12
tttttttttcctaaatatccatgtttcttacagtcaagctgacaatggtaggattagtgactgattattcgaagatttcattatcttttctggtttacagTTTGAACCTGAGACATCAAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
                                ||   ||   | ||| || |    |  ||  ||||  |   |||  |||| | | |     | | ||||||||||| || |  || ||||| ||||||||||| ||| ||||||| ||||| |||||| | || |||||||| || |||
--------------------------------gtatggcct-cgatgctaagcc--gccacctattaaacactgatgccattgtatctagaattctgcagTTTGAACCGGAAAGTTCGAGTGCAATGGGATTTGGATTTCGATGTGGATTTCTTGGCCTTTTGCACATGGAAATAGTACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtaggattagtgactgattattcgaagatttcattatcttttctggtttacagTTTGAACCTGAGACATCAAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG
             gactgat  putative branch site (score: 3)
                              tttcattatcttttct  putative PPT
                             atttcattatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttttttcctaaatatccatgtttcttacagtcaagctgacaatggtaggattagtgactgattattcgaagatttcattatcttttctggtttacagTTTGAACCTGAGACATCAAGTGCCATGGGATTTGGCTTTAGATGTGGGTTTCTGGGCCTTCTTCATATGGAAATTGTTCAG

- - - - - - - - - ccatgtt
- - - - - - - - - - - - - - - - - - -gctgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgactg