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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcctttagtttacctcttgtcagtaatcttggatcgtaagagtatatagaatgaaggttagggcatatcttagcttcttagctgatcattattcataaaaattcactagatttacatcaatgcagGTTTTTGCACGGACTAGTTACTTTCCTTACATGCTGTGGACTTTCAACATATTTTTTCTCTTCTGCAATCGCATTTATGAAGGATATTCTTTCTCCATTT

Basic information

species Arabidopsis thaliana
transcript AT1G57600.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G57600.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G25100.1 (Glycine max), 3'ss of exon 5
gtatgtttcctttagtttacctcttgtcagtaatcttggatcgtaagagtatatagaatgaaggttagggcatatcttagcttcttagctgatcattattcataaaaattcactagatttacatcaatgcagGTTTTTGCACGGACTAGTTACTTTCCTTACATGCTGTGGACTTTCAACATATTTTTTCTCTTCTGCAATCGCATTTATGAAGGATATTCTTTCTCCATTT
                               ||| ||   | || |     ||||   |     |||       | ||  |  |||  |  |   |||| |||  ||    ||||    |   |||  |||| | ||||||| ||     |||||||||    |  | |||| || ||||||||| |||||  |||| ||||| ||||||||||||||||| ||||| || |
------------------------aacagacaatgttt--ttgtcaatcattatattgtagcatttaattaccttatttacaacttttcctacagttat-catgtaag---actaatcctgtttca--gcagATCTTTGCACAGAAGGAGTACTTTCCTCTTGTAGTTTGGAGTTACAACATATTGTTTCTTCTCTGTAATCGGATTTATGAAGGATATTCATTCTCTATGT

upper sequence: AT1G57600.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G41940.2 (Glycine max), 3'ss of exon 4
---------------------------------gtatgtttccttta-gtttacctcttgtca---gtaatc--ttggatcgtaag-----agtatatagaatgaaggttagggcatatc--ttagcttcttagctgatcattattcataaaaat-tcact--agatttacatcaat---gcagGTTTTTGCACGGACTAGTTACTTTCCTTACATGCTGTGGACTTTCAACATATTTTTTCTCTTCTGCAATCGCATTTATGAAGGATATTCTTTCTCCATTT
                                    |||||| || | |||||  |||    |    |||||  || | || |||      | | | |      |   |||     || |  |||  | | |   | |  | | ||| |  |  | |||    ||| | |      |   |||| | ||||||| ||     |||||||||    |  | |||| || ||||||||| |||||  |||| ||||| ||||||||||||||||| ||||| || |
gtgcgtgtaatggaacaacttttgatgcttgaccattgtttcattaatgtttaagtctcaataaatataatccatttgttcctaaacagataatgtttttgtcaatcattatattgtagcatttaattaccttatttacaacttttcctgcagttatcatgtaagactaatcctgtttcagcagATCTTTGCACAGAAGGAGTACTTTCCTCTTGTAGTTTGGAGTTACAACATATTGTTTCTTCTCTGTAATCGGATTTATGAAGGATATTCATTCTCTATAT

upper sequence: AT1G57600.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0507g00010.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtttccttta-gtttacctcttgtcagtaatcttggatcgtaagagtatatagaatgaaggttagggcatatcttagcttcttagctgatcattattcataaaaattcactagatttacatcaatgcagGTTTTTGCACGGACTAGTTACTTTCCTTACATGCTGTGGACTTTCAACATATTTTTTCTCTTCTGCAATCGCATTTATGAAGGATATTCTTTCTCCATTT
||  || || |  | ||||      ||| | || |  |  || ||    ||   |   ||  |   | |   || |  |   ||   |  |         | | |  |||| || ||| |||  |   ||||| | |||||||| || |  |||||  | |   | || |||||||||||| ||||||||||  | |  ||||| ||| ||||||||||||| ||||||| ||
gtgggtctcatgaaagttttggatgtgtgactatttctttattgttgttgttgttgttatatatcattgttgatgttgttattttgcaatt------cccttacattaatttaccagacttatgtttctgcagATATTTGCACGAACAAAGTACTTCTCATCAGTACTTTGGACTTTCAACTTATTTTTTCTTATGTATAATCGTATTCATGAAGGATATTCATTCTCCACTT

upper sequence: AT1G57600.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0559g00010.t01 (Vitis vinifera), 3'ss of exon 7
gtatgtttccttta-gtttacctcttgtcagtaatcttggatcgtaagagtatatagaatgaaggttagggcatatcttagcttcttagctgatcattat-tcataaaaattcactagatttacatcaatgcagGTTTTTGCACGGACTAGTTACTTTCCTTACATGCTGTGGACTTTCAACATATTTTTTCTCTTCTGCAATCGCATTTATGAAGGATATTCTTTCTCCATTT
||  || |  |  | ||||      ||||| |  |  |  |||||    || | |   || |    ||   |||   | |  || |||  |    |||   | | |  |||| |||||| |||  |   ||||| | |||||||| || |  |||||  | |     || |||||||||||| ||||||||||  | |  ||||| ||| ||||||||||||| ||||||| ||
gtgagtcttatgaaagttttggatgtgtcactgtttctttatcgtt---gtttttgttatta----tatatcattgttgatgttgttattttgcaattcccttacattaatttactagacttatgtttctgcagATATTTGCACGAACAAAGTACTTCTCATCAGCACTTTGGACTTTCAACTTATTTTTTCTTATATATAATCGTATTCATGAAGGATATTCATTCTCCACTT

upper sequence: AT1G57600.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s1281g00010.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtttccttta-gtttacctcttgtcagtaatcttggatcgtaagagtatatagaatgaaggttagggcatatcttagcttcttagctgatcattattcataaaaattcactagatttacatcaatgcagGTTTTTGCACGGACTAGTTACTTTCCTTACATGCTGTGGACTTTCAACATATTTTTTCTCTTCTGCAATCGCATTTATGAAGGATATTCTTTCTCCATTT
||  || || |  | ||||      ||| | || |  |  || ||    ||   |   || ||   | |   || |  |   ||   |  |         | | |  |||| || ||| |||  |   ||||| | |||||||| || |  |||||  | |   | || |||||||||||| ||||||||||  | |  ||||| ||| ||||||||||||| ||||||| ||
gtgggtctcatgaaagttttggatgtgtgactatttctttattgttgttgttgttgttataaatcattgttgatgttgttattttgcaatt------cccttacattaatttaccagacttatgtttctgcagATATTTGCACGAACAAAGTACTTCTCATCAGTACTTTGGACTTTCAACTTATTTTTTCTTATGTATAATCGTATTCATGAAGGATATTCATTCTCCACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcttcttagctgatcattattcataaaaattcactagatttacatcaatgcagGTTTTTGCACGGACTAGTTACTTTCCTTACATGCTGTGGACTTTCAACATATTTTTTCTCTTCTGCAATCGCATTTATGAAGGATATTCTTTCTCCATTT
         agctgat  putative branch site (score: 4)
                 attattcataaaaatt  TA-rich tract