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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtacgattcagtttgattcaatgcttggaaattgcaaatccatatgtgaaagcatcttcatcactttaagaagagttatgatcccttaccctctcagAATTTTCTGTTCAAATCAACCGAAGAAGGTTCATCTCTAAAGGCTACAGATTTTGGTCTGTCGGACTTCATAAAGCCAG

Basic information

species Arabidopsis thaliana
transcript AT4G36070.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 4
gtaggtacgattcagtttgattcaatg-cttggaaat---tgcaaatccatatgtgaaagcatc-ttcatcactttaagaagagttatgatcccttaccctctcagAATTTTCTGTTCAAATCAACCGAAGAAGGTTCATCTCTAAAGGCTACAGATTTTGGTCTGTCGGACTTCATAAAGCCAG
    |||  | |        ||||||| ||||| |||   || | ||     ||  |   |||   |  |||  | | | |    | |      || || || ||||| || || |||||||||||| | || |  ||| || ||||||| ||||||||||||||||| ||||||||||| ||||
----gtagaaattgaacgctttcaatgtcttggcaattagtgtacattttggtgatatttcattacttctcaggtcatgtaagaatgtacctattttccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG

upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os07g22710.3 (Oryza sativa), 3'ss of exon 3
gtaggtacgattcagtttgattcaatgcttggaaattgcaaatccatatgtgaaagcatcttcatcactttaagaagagttatgatcccttaccctctcagAATTTTCTGTTCAAATCAACCGAAGAAGGTTCATCTCTAAAGGCTACAGATTTTGGTCTGTCGGACTTCATAAAGCCAG
                              | |   |  |||   | | |   |||  |  | || |   |||       | ||||   |     |  ||||| || || |||||||||||| |||| |  ||||| || |||||||||||||||||||| || || || ||||  ||||
------------------------------gtatgctctaaaagtacaagactaagtcttcttataagagtaattgatcatttgatatgt-gtatttacagAACTTCCTCTTCAAATCAACCAAAGAGGACTCATCCCTCAAGGCTACAGATTTTGGTCTTTCAGATTTTATAAGACCAG

upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G365035_T01 (Zea mays), 3'ss of exon 4
gtaggtacgattcagtttgattcaatgcttggaaattgcaaatccatatgtgaaagcatcttcatcactttaagaag-agtta-tgatcccttaccctctcagAATTTTCTGTTCAAATCAACCGAAGAAGGTTCATCTCTAAAGGCTACAGATTTTGGTCTGTCGGACTTCATAAAGCCAG
    |||   |        ||   ||         |   ||||   ||  ||  |  | |||  | | |  ||| || || || | |||   |        |||| || || ||||||||||   | || |  ||  | || |||||||||||||||||||| || ||||||||||| ||||
----gtatactctgaaagtataagatagaatcctgtcataaata-gtagttgctaataccttt-ttattaaaaggagtagctaataatcttattggtgtgtagAACTTCCTATTCAAATCAAAAAAGGAGGACTCGCCCCTTAAGGCTACAGATTTTGGTCTTTCAGACTTCATAAAACCAG

upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G37100.1 (Glycine max), 3'ss of exon 5
gtaggtacgattcagtttgattcaatgcttggaaattgcaaatccatatgtgaaagcatcttcatcactttaagaagagttatgatcccttaccctctcagAATTTTCTGTTCAAATCAACCGAAGAAGGTTCATCTCTAAAGGCTACAGATTTTGGTCTGTCGGACTTCATAAAGCCAG
    ||| | |  |||| | |   ||   |    | |    ||   ||| ||  |  ||       || |||| |              |   | |  ||||||||||| ||||| |||||| |||||| |||| || |||||||||| ||||||||| |||| || |||||||| || |
----gtatggtcaagttcgctagcatatctacgcaatatggatttgtatatgctactat-------acattaaaa-----------ttttcctctttgcagAATTTTCTTTTCAAGTCAACCAAAGAAGATTCACCTTTAAAGGCTACCGATTTTGGTTTGTCTGATTTCATAAAACCTG

upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 4
gtaggtacgattcagtttgattcaatgcttg--gaaattgcaaatccatatgtgaaagcatcttcatcactttaagaagagttatgatcc--cttaccctctcagAATTTTCTGTTCAAATCAACCGAAGAAGGTTCATCTCTAAAGGCTACAGATTTTGGTCTGTCGGACTTCATAAAGCCAG
    ||| |||  ||     ||  ||   ||   || |||      |  |  |  |  |  ||  ||    |  |  ||| | ||| |    | ||  ||  ||||||||||| || ||||||| | |||||| |||| || ||||||| |||||||||||| |||| || |||||||| || |
----gtatgatcaagcacatttgcatatctgccaaatttgtgtgaactgagatctatactactagatgctatataatagattaatgtttttacctattcttgcagAATTTTCTTTTTAAATCAATCAAAGAAGATTCACCTTTAAAGGCCACAGATTTTGGTTTGTCAGATTTCATAAAACCTG

upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 6
gtaggtacgattcagtttgattcaatgcttg--gaaattgc---aaatcc-atatgtgaaagcatcttcatcactttaagaagagttatgatcccttaccctctcagAATTTTCTGTTCAAATCAACCGAAGAAGGTTCATCTCTAAAGGCTACAGATTTTGGTCTGTCGGACTTCATAAAGCCAG
    ||| |||  ||     ||  ||   ||   || |||    ||||   || | |   |  |  | |   || | |   |    |||  |  | ||  ||  ||||||||||| || ||||||||| |||||| |||| || ||||||| || ||||||||| |||| || |||||||| || |
----gtatgatcaagcacatttgcatatctgccaaatttgtgtgaaatgagatctatactactagatgctatacataatatattaatatttttacctattcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG

upper sequence: AT4G36070.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G08180.1 (Glycine max), 3'ss of exon 5
gtaggtacgattcagtttgattcaatgcttggaaattgcaaatccatatgtgaaagcatcttcatcactttaagaagagttatgatcccttaccctctcagAATTTTCTGTTCAAATCAACCGAAGAAGGTTCATCTCTAAAGGCTACAGATTTTGGTCTGTCGGACTTCATAAAGCCAG
    ||  | |  |||||| |   ||   |    | |    |    | |        || ||  ||  | ||  ||   ||    |||  |   |   ||||||||||| ||||| |||||| |||||| |||| || |||||||||| ||||||||| |||| || || ||||| || |
----gtgtggtcaagtttgctggcatatctacgcaatatggagttgtgta-------attttactctatatattaaatttt----tcctctttgcatgcagAATTTTCTTTTCAAGTCAACCAAAGAAGATTCACCTTTAAAGGCTACCGATTTTGGTTTGTCTGATTTTATAAAACCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgaaagcatcttcatcactttaagaagagttatgatcccttaccctctcagAATTTTCTGTTCAAATCAACCGAAGAAGGTTCATCTCTAAAGGCTACAGATTTTGGTCTGTCGGACTTCATAAAGCCAG
                                        cccttac  putative branch site (score: 3)
                                       tcccttaccctctc  CT-rich tract
                      tttaagaa  TA-rich tract