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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtaaatgttttaaggattttatttgctttaacgtagatgcccacagatatataccattatgcgttcgtataaattgcctaaatttctatttagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA

Basic information

species Glycine max
transcript GLYMA11G12280.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 10
-----------------------------------------------------gtatgtgtaaatgttttaaggattttatttgctttaacgtagatgcccacagatatataccattatgcgttcgtataaattgcctaaat-ttctatttagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA
                                                      ||||    |    |     | |||    || || | | ||  |  | |  |  || |     |||   | ||| ||| ||   | |||  | | |  || |||||||||| |||||   |||||| |||||||||||||| ||||| || || ||||||||  | || |||| ||||||||||||||| |||||||| |
gtaagcaactcaataatttaaatttatttcattcaaaagcatggaacattcagatatgaaacagcactcctgagttttgtgatgattcaccttacttatcaatggtgatgt----ctataaatccgtttaa-ttatatgaatactatgtgcagGTTTTGAAGATTAACCCTTTGAAGAAGGATATAGATTCTTTCGTGGCATCAGACTTCAAGCTGGTCGGTTATGATCCTCACCAGAAGATTGAAATGAAAA

upper sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os12g26060.1 (Oryza sativa), 3'ss of exon 8
-------------gtatgtgtaaatgttttaag--gattttatttgctttaacgtagatgcccacagatatataccattatgcgttcgtataaattgcctaaatttc-tatttagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA
             |  |   | | ||  | ||   ||| |  |||  || || |||  ||   |      ||| | | |  |  ||  | | | ||   |  ||  | | |  |||||||||||||||| ||   |||||||||||| |||||||||||  | || || ||||| ||  |  | |||| ||||||||| ||||||||||||||||
gtaagcaaatgttgattaatttactgcataaaaatgatatatttttattcaaagtacctgattatttgattattcaact--gattttttgtgagtt--ttggatcccatctgcagATTTTGAAGATAAATCCTGTGAAGAAAGATATTGATTCTTTTGTAACATCAGACTTCAAACTGGTTCGCTATGATCCTCACCATAAGATAGAAATGAAGA

upper sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G157586_T01 (Zea mays), 3'ss of exon 1
gtatgtgtaaatgttttaaggattttatttgctttaacgtagatgcccacagatatataccattatgcgttcgtataaattgccta---aatttctatttagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA
   || |  | |  |   || | | | ||    ||    |   ||   ||   | | |   |  |||| |   | ||| ||   |       || |    |||||||||||||||| ||    || || ||||||||||||||| |||| || || ||||||||  | || |||| ||| |||||||||||||| ||||| |
--gtgagccactcctaatagaactgttttgatgtttctttt--tgtttac---tttctgtgaccatgcatct-tctaagttctatgtgggccttatgcacagATTTTGAAGATAAATCCTTCAAAAAAGGATATAGATTCTTTTATGGCATCAGACTTCAAGCTGGTTGGCTATGATCCCCACCAGAAGATAGAGATGAAAA

upper sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G139880_T01 (Zea mays), 3'ss of exon 9
-------------------------------------gtatgtgta---aatgttttaaggattttatttgctttaacgtagatgcccacagatatataccat---tatgcgttcgtataaattgcctaaa---tttctatttagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA
                                      ||| || |    ||| ||| | | |||| ||||  |    ||   ||        ||  | |  |    |||| |   | ||| |||  |       || | |  |||||||||||||||| ||   ||| || ||||||||||||||  |||| || || ||||||||  | || |||| ||||||||||||| |||| ||||| |
gtgagccaaccatttttacgaaaaatatgaaatctgcatatatgaacttgatgctttgatgtttttttttgtgtgtgtgtgtgtgtgtgtgtttactttctgtgcccatgcatct-tctaagttgtatgtgggtcttatgtgcagATTTTGAAGATAAATCCTTCGAAAAAGGATATAGATTCTTTCATGGCGTCAGACTTCAAGCTGGTTGGCTATGATCCTCACCAGAAGCTAGAGATGAAAA

upper sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 11
----gtatgtgtaaa----tgttttaaggatttt---atttgctttaacgtagatgcccacagatatataccattatgcgttcgtataaat-tgcctaaatttct-------attta--gATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA
    ||||    |||    || |||   |||| |   || |  ||| |  | ||||    || | || ||||| ||    || | |   || ||| ||  | |||       |||||  | ||||||||||||| ||| ||||||||||||||||||||||||| ||   ||| ||  ||||||| || |||| ||||||| |||| ||||| ||||| |
gtgagtataaacaaacacatgatttgctgattcttcaatcttgtttgagtttgatgaatgcata-atctaccaataattctttgcaactatatgcttatttatctttgggatatttacagGTTTTGAAGATAAATCCAGAGAAGAAAGATATAGATTCTTTTGTTGCGGATGACTTTGAGCTCATTGGCTATGATCCTCACAAGAAAATAGATATGAAAA

upper sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgtgtaaatgttttaaggattttatttgctttaacgtagatgcccacagatatataccat-tatgcgttcgtataaattgcctaaatttctatttagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA
      |||| | | |    ||   |  |          |  ||   |||  ||   |||| | | |  ||| ||    || | || | |     |  || |  |||||||||||||  |||||||| | || |||||||||||||||||||| ||  | |||| ||| |||| ||||||| |||||||||||||||| |
------gtaagtatatcgccgacaatgatcatcgaggaatgcatattcacctatccttaccgtgtttttgtttgtcgtcatgggctcactac---tgcagGTAATGAAGATAAACCCGGAGAAGAAACAAATCGATTCTTTTGTGGCTTCTGACTTTGACCTCACAGGCTATGATCCTCACAAGAAGATAGAAATGAAAA

upper sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 9
----gtatgtgtaaatgttttaaggattttatttgctttaacgtagatgcccacagatatataccattatgcgttcgtataaattgcctaaatttctatttagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA
    |||  | |   | |||     ||   ||||  ||||| |||  | | |  || ||    || || ||   |  |||    |   |   | |   |  ||||||||||||| || ||| ||||||| ||||| || || ||||||||  |||||||  |||| ||||| |||  ||||||||||||||| |||||||| |
caaggtagctctgcctttttcttatataccattt--tttaa-gtactttctcctagctactaccctttctgaacttctatgttgtctttgcctgttcctgcagATTTTGAAGATCAATCCACAGAAGAAGGATATTGAATCATTTGTGGCAGCTGATTTTGAGCTTATAGGTTATAATCCTCACCAGAAGATTGAAATGAAAA

upper sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 11
---------------------------------------gtatgtgtaaatgttttaaggattttatttgc-----tttaacgtagatgcccacagatatataccattatgcg------ttcgtataaa---ttgcctaaatttctatttagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA
                                        ||| |||||    | |||    ||| ||        ||| ||    || |   |  || | |  |  |||  |      | | || |     || |    | ||  ||  ||||||||||||| || ||| |||||||  | || ||||||||||||||  |||||||| | |||||||| |||| |||||| ||||| ||||| ||||| |
gttagtattcttgaattgattagttctattccaaattttttatttgtaaggagtataattcctttcttcttgtgtttttcactcttattctttcgtatttttctctctatttgagttgttccatacatcctcttactcgcactttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCTGATTTCCAACTCATAGGTTATGATCCTCATCAGAAAATAGAGATGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcccacagatatataccattatgcgttcgtataaattgcctaaatttctatttagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA
                                     gcctaaa  putative branch site (score: 3)
                                            tttctattt  CT-rich tract
                                        taaatttctattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtaaatgttttaaggattttatttgctttaacgtagatgcccacagatatataccattatgcgttcgtataaattgcctaaatttctatttagATTTTGAAGATAAACCCAAAGAAGAAAGATATAGATTCTTTTGTGGCTTCTGATTTCAAGCTCATAGGATATGTTCCTCACCAGAAGATAGAAATGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA