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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatcattgcgctctaaaatattttagaaaagcataagtgggaagtactatcttttcctttcattttgtgttttgattaatgccatctaaccttcaatagGTATGAAGCTTGCATGGATGTCACAGATAGTGACCACAAGCCTGTCCGCTGCATATTTTCTATAGATATTGCTCGAGTAGATGAACCAATCCGGAGGCAG

Basic information

species Glycine max
transcript GLYMA20G36090.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os09g32440.1 (Oryza sativa), 3'ss of exon 9
ttatcattgcgctctaaaatattttagaaaagcataagtgggaagtactatcttttcctttcattttgtgttttgattaatgccatctaaccttcaatagGTATGAAGCTTGCATGGATGTCACAGATAGTGACCACAAGCCTGTCCGCTGCATATTTTCTATAGATATTGCTCGAGTAGATGAACCAATCCGGAGGCAG
              | | ||  | ||  |   | |          |  | | ||  |      | ||   | ||||| | |     |   | ||  ||||||||| ||||||||||||||||||||| ||||||||||| |||||  | |||| ||||    | || |||||  |||| |||||   |||  | || || 
-------------gtcagatgctataacacttccttttc------tcttcttttgactccctttctttgatattgatcatttttgccct-cttttgatagGTATGTAGCTTGCATGGATGTCACAGAGAGTGACCACAAACCTGTGAGATGCACATTTAGCGTTGACATTGCAAGAGTGGATGAGTTAATAAGAAGACAA

upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os08g41270.2 (Oryza sativa), 3'ss of exon 10
---------------ttatcattgcgctctaaaatattttagaaaagcataagtgggaagtactatcttttcctt-------tcatt---ttgtgttttgattaatgcc--atctaaccttcaatagGTATGAAGCTTGCATGGATGTCACAGATAGTGACCACAAGCCTGTCCGCTGCATATTTTCTATAGATATTGCTCGAGTAGATGAACCAATCCGGAGGCAG
               ||| || |   | ||    |     || | |   ||||    |  |  | | || || |        ||| |   |  |   |   || |||    ||    | |    |||||||||||||||||||| ||||||||||||||| || || || ||  | ||   ||||  | | ||||||||  |||| |||||    |   | || |||
gtaagattctacaacttaccagttaccactcgttttgagaaggagaatctaagacacacatgttgttttgtcttgatcataatcactccctcatacataatttgatgttttattgctcttctggtagGTATGAAGCTTGCATGGGTGTCACAGATAGTGATCATAAACCAGTGAGGTGTGCATTTAGTGTTGATATTGCAAGAGTGGATGAGTTTACAAGAAGACAG

upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G065225_T01 (Zea mays), 3'ss of exon 9
--------------------ttatcattgcgctctaaaatattttagaaaagcataagtgggaagtactatcttttcctttcattttgtgttttgattaatgccatctaaccttcaatagGTATGAAGCTTGCATGGATGTCACAGATAGTGACCACAAGCCTGTCCGCTGCATATTTTCTATAGATATTGCTCGAGTAGATGAACCAATCCGGAGGCAG
                       || |||   |||  |  ||| |      |  |    |   || ||||     |   ||||| |  |  |||  ||         |   |||  | ||||| ||| ||||||||||||||||||| |||||||| || || ||  | || | |||     | ||||||||  ||||||| || |  ||  ||||||| 
gtaagatttgacagagccaggcgtctttgta-tctttaccattctgtgtgtgtgtggaggaagagaactac----tgggttcatgtgatccttttttt--------ttgctctttgacagGTACGAATCTTGCATGGATGTCACAGACAGTGACCATAAACCCGTGAGATGTACATTCAGCGTCGATATTGCAAGAGTAGACGAGCTGATAAGGAGGCAA

upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G422045_T01 (Zea mays), 3'ss of exon 9
ttatcattgcgctctaaaatattttagaaaagcataagtgggaagtactatcttttcctttcattttgtgttttgattaatgccatctaaccttcaatagGTATGAAGCTTGCATGGATGTCACAGATAGTGACCACAAGCCTGTCCGCTGCATATTTTCTATAGATATTGCTCGAGTAGATGAACCAATCCGGAGGCAG
      |      |||  | | ||        |       |    |        ||||||| ||      |  ||||| ||         ||||  |||||||||  || ||||||||||||||||| |||||||| || |||||  | || | |||   | | ||||||||| |||| || ||   |||  | ||||| 
-----gtgagatactatcacacttccttttccccctttcagatgat--cggtaattcctttgatcc---atactgattgatttt------cctttgatagGTATGTGGCATGCATGGATGTCACAGAGAGTGACCATAAACCTGTGAGGTGTACATTCAGTGTTGATATTGCTAGAGTTGACGAGTTAATAAGAAGGCAA

upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G65580.1 (Arabidopsis thaliana), 3'ss of exon 9
--ttatcattgcgctctaaaatattttagaaaagcataagtgggaagtactatcttttcctttcattttgtgttttgattaatgccatctaaccttcaata-gGTATGAAGCTTGCATGGATGTCACAGATAGTGACCACAAGCCTGTCCGCTGCATATTTTCTATAGATATTGCTCGAGTAGATGAACCAATCCGGAGGCAG
    ||||||    | |        ||| ||   | ||  |||  | |||| |    |  |   |   |      | |  | |  | | |  | ||   || ||||||| || |||||||| || ||||| |||||||||||||| || |||||  |||||  | |  | ||||| || || |||||  || || |||| || 
gtaaatcattttttttttgtgacccttataa---cgtatatggttactactcttgaattgtcaaaggattaagacttaaaattctcgtttttctttttgtaagGTATGATGCCTGCATGGAAGTGACAGACAGTGACCACAAGCCCGTACGCTGTGTATTTAGTGTCAAGATTGCCCGGGTTGATGAGTCAGTCAGGAGACAA

upper sequence: GLYMA20G36090.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0220g00160.t01 (Vitis vinifera), 3'ss of exon 8
ttatcattgcgctctaaa-atattt-tagaaaagcataagtgggaagtactatcttttcctttcattttgtgttttgattaatgccatctaaccttcaa-tagGTATGAAGCTTGCATGGATGTCACAGATAGTGACCACAAGCCTGTCCGCTGCATATTTTCTATAGATATTGCTCGAGTAGATGAACCAATCCGGAGGCAG
      |  | ||||| | |||| | || | |     |||     |      | ||||  |||  ||     |||       ||  ||||    || || |||||| ||||||||||||||||| ||||| ||||| || |||||||| || ||||| |||  | | ||||||||||||||||| ||  || || | || |||
---ctctctctctctatatatatatatatatatattgaagccttcacactcctatttttgtttttttccccttttaagactttgatatcttcttttgaactagGTACGAAGCTTGCATGGATGTGACAGACAGTGATCATAAGCCTGTTCGTTGCATGTTTAGTGTTGATATTGCTCGAGTAGACGAGTCAGTCAGAAGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactatcttttcctttcattttgtgttttgattaatgccatctaaccttcaatagGTATGAAGCTTGCATGGATGTCACAGATAGTGACCACAAGCCTGTCCGCTGCATATTTTCTATAGATATTGCTCGAGTAGATGAACCAATCCGGAGGCAG
                                       atctaac  putative branch site (score: 2)
                                             ccttc  CT-rich tract
                         ttttgattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatcattgcgctctaaaatattttagaaaagcataagtgggaagtactatcttttcctttcattttgtgttttgattaatgccatctaaccttcaatagGTATGAAGCTTGCATGGATGTCACAGATAGTGACCACAAGCCTGTCCGCTGCATATTTTCTATAGATATTGCTCGAGTAGATGAACCAATCCGGAGGCAG

- - - - - - - - - - - - - gaaaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccatc