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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccatattttcactgttttcatcattcaatatgatatcccctcgaagttatcagtggctggtttcgatttgttcgtgtaaggtaaactgaccccatgttatgttttacatgccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G51690.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G51690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 9
gtccatattttcactgttttcatcattcaatatgatatcccctcgaagttatcagtggctggtttcgatttgttcgtgtaaggtaaactgaccccatgttatgttttacatgccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG
    | | ||| |    ||       | | | | |||   | |   |  ||| |||||     | |          || || || |  |   ||  || |   |||       ||||||||||| || ||||||||  |||| ||||| ||||||||||| |||||||||||||| | ||| |||
----aaacttttatatattctgcagctgattctaatactacgtatca--tataagtggtatactgct---------tgaaatgtca-ttagtccgttgctccttttctttcttcagTTATGGGATATAAACATGGATTCAGGCCCAGTTGCAACTTTCCAAGTTCATGAATATTTAAGACCTAAG

upper sequence: AT1G51690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 9
gtccatattttcactgttttcatcattcaatatgat--atcccctcgaagttatcagtggctggtttcgatttgttcgtgtaaggtaaactgaccccatgttatgttttacatgccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG-------------------------------
                     | ||| | || | ||  ||    || |  || |  |         ||  ||| ||      |       | |   |   |    | ||   |  ||||||||||||||||| |||||  | |||||||| ||||| |||||||||||||| ||||| |  ||||||                               
------------------cagagcatgctatgtaattcattaattctactttgtttggatacacactctgtttcttatcaacaaaatccttcaagtctcatctcatcttgtttttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAGGTTAGATTCCCATGTTTGGATGAGCAATGAA

upper sequence: AT1G51690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G20830.3 (Glycine max), 3'ss of exon 9
gtccatattttcactgttttcatcattcaatatgat--atcccctcgaagttatcagtggctggtttcgatttgttcgtgtaaggtaaactgaccccatgttatgttttacatgccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG
                     | ||| | || | ||  ||    || |  || |  |         ||  ||| ||      |       | |   |   |    | ||   |  ||||||||||||||||| |||||  | |||||||| ||||| |||||||||||||| ||||| |  ||||||
------------------cagagcatgctatgtaattcattaattctactttgtttggatacacactctgtttcttatcaacaaaatccttcaagtctcatctcatcttgtttttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACGTTCCAGGTTCATGAGTATTTAAGGCCAAAG

upper sequence: AT1G51690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 9
gtccatattttcactgttttcatcattcaatatgatatcccctcgaagttatcagtggctggtttcgatttgttcgtgtaaggtaaactgaccccatgttat--gttttacatgccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG
                    ||        ||||  || |  |     |||    ||  ||| |||  | ||||  | | |   |||     |   | | ||  || ||  ||  ||||||||||||||||| |||||  | |||||||| ||||| ||||||||||| || ||||| |  ||||||
------------------ggcagagcatgctatgtaattcatttttttttacttttgtttggattccctctgtttttatcaacaaaatcccactagtctcatctgtcttgtatttcagTTATGGGACATCAATATGGATTCTGGTCCAGTTGCAACATTCCAGGTTCACGAGTATTTAAGGCCAAAG

upper sequence: AT1G51690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 9
gtccatattttcactgttttcatcattcaata-tgatatcccctcgaagttatcagtggctggtttcgatttgttcgtgtaaggtaaactgaccccatgttatgttttacat-gccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG
                |   |||| |||| |  |||  |    | |  | | ||  |   ||  |   ||   ||| |  |   | | || |   ||  | |||  ||   | | ||||| |||||||| || |||||  |||| || || |||||||||||||||||||| ||||||| ||| |||
---------------atcgacatctttcatttctgactttgtttgggggatttc--ttcttgtatgttataaattcttaaagcttcatctcatttcac-taatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTGAGACCCAAG

upper sequence: AT1G51690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 9
gtccatattttcactgttttcatcattcaata-tgatatcccctcgaagttatcagtggctggtttcgatttgttcgtgtaaggtaaactgaccccatgttatgttttacat-gccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG
                    || | |||| |  |||  |    | |  | | ||  |   ||  |   ||   ||| |  |   | | || |   ||  | |||  ||   | | ||||| |||||||| || |||||  |||| || || |||||||||||||||||||| ||||| | ||| |||
---------------accgacacctttcatttctgactttgtttgggggatttc--ttcttgtatgttataaattcttaaagcttcatctcatttcac-taatgacttgttttgtcagTTGTGGGACATTAATATGGATTCAGGCCCCGTTGCAACTTTCCAGGTTCATGAGTATTTAAGACCCAAG

upper sequence: AT1G51690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 9
gtccatattttcactgttttcatcattcaatat-gatatcccctcgaagttatcagtggctggtttcgatttgttcgtgtaaggtaaactgaccccatgttatgtt--ttacatgccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG
              | ||| |||||      || |||||   ||   | || ||  |  |||| ||   || |  | | | |  |||  | ||   |  || | ||  || | |  |||||||||||||| || |||||| |||| |||||  |||| |||||||||||||||||||| | ||| |||
-----------aggtctttgcatcacaaggaattgatatgtact---atttgtc--tttctggcttaagttagggcct-tgaactaa--tcactggaatttgttttacttgcttttcagTTATGGGACATTAATATGGACTCAGGCCCAGTTTCAACCTTCCAGGTTCATGAATATTTAAGACCTAAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86070772|gb|DR366529.1|DR366529
EST:     TTGCAAAAGAAGGAAGATATCTACTTAGCNNTGACTATATGACACTTAAG                         TTATGGGACATCAACATGGACGCAGGTCCAGTAGCA
genomic: TTGCAAAAGAAGGAAGATATCTACTTAGCCGTGACTATATGACACTTAAGgtccatattt ... tacatgccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCA
EST: gi|86070771|gb|DR366528.1|DR366528
EST:     TTGCAAAAGAAGGAAGATATCTACTTAGCCGTGACTATATGACACTTAAG                         TTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCAT
genomic: TTGCAAAAGAAGGAAGATATCTACTTAGCCGTGACTATATGACACTTAAGgtccatattt ... tacatgccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCAT
EST: gi|86070769|gb|DR366526.1|DR366526
EST:     TTGCAAAAGAAGGAAGATATCTACTTAGCCGTGACTATATGACACTTAAG                         TTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCAT
genomic: TTGCAAAAGAAGGAAGATATCTACTTAGCCGTGACTATATGACACTTAAGgtccatattt ... tacatgccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCAT
EST: gi|86070768|gb|DR366525.1|DR366525
EST:     TTGCAAAAGAAGGAAGATATCTACTTAGCCGTGACTATATGACACTTAAG                         TTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCAT
genomic: TTGCAAAAGAAGGAAGATATCTACTTAGCCGTGACTATATGACACTTAAGgtccatattt ... tacatgccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcgatttgttcgtgtaaggtaaactgaccccatgttatgttttacatgccagTTATGGGACATCAACATGGACGCAGGTCCAGTAGCAACTTTCCAGGTTCATGAATATTTGAAACCAAAG
                        aactgac  putative branch site (score: 2)
                                     ttatgtttta  TA-rich tract