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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtattcatattgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgttgataattggtggttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

Basic information

species Glycine max
transcript GLYMA17G02640.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 11
gcaagtattcatattgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgttgataattggtggttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
    |||| | | ||   ||  |   |  ||||    || | |  ||  ||| ||  |||   |||  ||  |||| ||   || || |     |||||| ||||||| ||| ||||||||||| || ||||| |||||||| ||||| ||||||||||||||||||||||||||||||||||||
----gtatgc-tgttatgtgcaaattgttttct--tctgaacccatga-atatgt--atgttgaatatttagtgttaatg--tgttgatgtcttcagGAATCCACAAGCTGATCTGCAAGCTCAAGACCGTGCACATAGGATAGGTCAGAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 11
gcaagtattcatattgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttt--tgttgataattggtggttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
               |  ||||     | ||  || | | |    |  | | | |  |  | |  |    ||   | | ||  ||  | | | | ||||||| || ||||| || |||||||| || |||||||| ||||| ||||||||||||||||||||||||||||| || || |||||||||
---------------gtatgtc-----cttttcaaatcgtaattttttc-tcattctacaatttgtgaagttaaaggttatggttatttggtttcacagGAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCAAAAGAAAGAAGTTCAAGTTTTTCGTTTCTGCACTGAG

upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
gcaagtattcatattgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgttgataattggtggttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
                  | | ||         ||||||   | ||  | ||   | |  |  |||    |   |   | |||  ||    |  |||||| ||||||| ||| |||||||||||||| ||||| |||||||| ||||||||||||||||||||||| ||||| ||||||||||||
-----------------gtatgagactatgctaaacttgattctgttgcttaccctaagaatgaatctaatgcctctgttatttctgtgcctc-cagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG

upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 8
gcaagtattcatattg-attgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgttgataattggtggttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
| | |      | ||    |      ||  || |  |||  | |     ||| |   |||||  |  |  | ||  |  || ||    ||     |||||| || |||| ||| |||||||||||||| ||||| ||||| || ||||||||||||||||||||||| ||||| ||||||||||||
gtatgcgactttgttatgctaaatttagttttgttgcttataccctaagcatgaagccatga--accttatgttcctagtactt--ctgtgcctccagGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG

upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
gcaagtattcatattgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgt---tgataa--ttggtgg-ttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
                       | |    |||   |||   |  |    ||| || |||| |  ||  |||| |   | || |  | ||||| ||||  ||||||||| ||||||||| ||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || ||||| |||
-----------------------gtaaggctctt-tttgtgtccat--tgtaa-tttatgagtgttttcttttatgcctaatgaggtgggtggattatggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG

upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
gcaagtattcatattgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgtt-gataa--ttggtg-gttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
                       | |    ||| |       |    |  ||  ||    |||   ||||   ||| ||  |   |||    || |  ||||||||||||||| ||| ||||||||||||||||||| ||||||||||||||||| |||||||||||||| || ||||| |||||||||
-----------------------gtaagtctctcatcattgtc--cactgtagtttatgaactttctcttcacgtttgacgagtctggcatattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG

upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
gcaagtattcat--attgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgttgataattggtggttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
|  || |||  |  |||  || |       ||| ||   |||   ||     |   |  || | | |    | | ||||||   |       |    |||||||| ||||||||  ||||||| || |||||||||||| |||||||||||||||||||||||||||| || ||||| ||||| |||
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgt---tatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG

upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 11
gcaagtattcatattgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgttg-ataattggtggttata--acagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
                                              |  ||||  | |||| |  ||||   ||     |  || |   ||||    |||||| || ||||| ||  ||||||| || ||||| || ||| ||||||| || || |||||||||||||||||||||||||||||  ||
----------------------------------------------gtaataa--taatgatttgttctgagtggcatgtttttagaaattatgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG

upper sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 11
gcaagtattcatattgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgttgataattggtggttata--acagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
                                              |  |||   | |||| |  ||||   ||       || |   ||||    |||||| || ||||| ||  ||||||| || ||||| || ||| ||||||| || || |||||||||||||||||||||||||||||  ||
----------------------------------------------gtaatag--taatgatttgttctgagtggcatgttttagaaattatgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtgccataagttcatgactaattctttttgttgataattggtggttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
                    taattctttttgttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtattcatattgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgttgataattggtggttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT