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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagctgcatttattcttcatgttgactatttttcagttcaattataggaaaccagtggattattattatttggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTCGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAACAGTCCATTGCCTTGTCAAAGAAAGATA

Basic information

species Glycine max
transcript GLYMA11G35460.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 25
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
------------gttagctgcatttattcttcatgttgactatt-tttcagttcaattataggaaaccagtggattattattatttggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTCGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAACAGTCCATTGCCTTGTCAAAGAAAGATA
            | |   || | |  || || |||||   | |  |||   ||  ||| |    ||| | |||  |   ||   |||     ||| |||| ||||||||  | |||||||||||  |  ||||||| || |||||||||||||| || |||||||| || || |||||| |||| |||||||| |
gtaaagcgattagatgattgtactgcttattgatgttatttttccttttttttttattttgaataactaatgg-ctggaatgccttgat---cagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA

upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 25
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
------------gttagctgcatttattcttcatgttgactat--ttttcagttcaattataggaaaccagtggattattattatttggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTCGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAACAGTCCATTGCCTTGTCAAAGAAAGATA
              |   || | |  || || |||||   | |  ||||   ||  ||| |    ||| | |||  |   ||   |||     ||| |||| ||||||||  | |||||||||||  |  ||||||| || |||||||||||||| || |||||||| || || |||||| |||| |||||||| |
gtaaagcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaataactaatgg-ctggaatgccttgat---cagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA

upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 25
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 26
gttag---ctgcatttattcttcatgttgactatttttcagttcaattataggaaaccagtggattattattatttggaatg---cagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTCGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAACAGTCCATTGCCTTGTCAAAGAAAGATA
|| ||    |  || |||   ||  ||  || |||| |   | |  |||    | || | |  ||  ||||    |||   |    ||||||| || || |||||| |||| ||||||||||| ||||||||||| || ||||| || ||||||||||| || || ||||| ||||||||||||||||
gtaagagtttaaatctatctatcgagtacac-atttatatttcccctta---aatactaatttatcgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA

upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 25
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 26
gttagctgcatttattcttcatgttgactatttt-tcagttcaattataggaaaccagtggatt------------attattatttggaatg-------cagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTCGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAACAGTCCATTGCCTTGTCAAAGAAAGATA
|| |  | ||  ||| || |   || | |||||| ||  || ||  || | |||  | |||  |            | | ||  |  |||||       ||||| || || || || ||| |||| ||||||||||| ||||||||||| |||||||| || || |||||||| || || ||||| || ||||||||||| |
gtaaagttcaaatatactacccctttaatattttctctctttaaaaatggaaaaagaatggccttagagatgatataatcttcctgtgaatggtgcgaacagATCGAGAAACACGAACTTGTTGAAATGAGACGTGTGGCTGCTTATATCTACAAGAAAGCGGGCAGATGGAAGCAATCAATTGCATTATCAAAGAAAGACA

upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 25
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
---------------gttagctgcatttattcttcatgttgactattttt-cagttcaattataggaaaccagtggattattattatttggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTCGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAACAGTCCATTGCCTTGTCAAAGAAAGATA
                |||| |||| || || ||| |  ||  | | |   | | |  |||  |  |  |  || | | ||   | ||||    ||||||||| || || ||||||||||||||||||||||| |||||||||||||||||||| ||||| |||||||| || || ||||| ||||| |||||||| |
gtggagtataatttctttaggtgcaattgtttttctttgtggttctatgcactggttgatttcataagccttgttggt-atg--tgtttga---gcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatttttcagttcaattataggaaaccagtggattattattatttggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTCGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAACAGTCCATTGCCTTGTCAAAGAAAGATA
                                 attattattatttgga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagctgcatttattcttcatgttgactatttttcagttcaattataggaaaccagtggattattattatttggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTCGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAACAGTCCATTGCCTTGTCAAAGAAAGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA