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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattagcacagttgcaataacttttagtcatctatatctagaatggtaatggagaggcaaactcaatcaagaatttagtacattcttattgacaattttgaaatgtatagCTTCTTGCAGAGAAAGGTGAGCTCCCTACAAGATTTGGCTCAGCAACCTTGGGAATTCTTCTTCTACAG

Basic information

species Arabidopsis thaliana
transcript AT4G04850.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G04850.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g42300.1 (Oryza sativa), 3'ss of exon 5
gtattagcacagttgcaataacttttagtcatctatatctagaatggtaatggagaggcaaactcaatcaagaatttagtacattcttattgacaattttgaa----atgtatagCTTCTTGCAGAGAAAGGTGAGCTCCCTACAAGATTTGGCTCAGCAACCTTGGGAATTCTTCTTCTACAG
        ||| |||    | |    | |  |   |   || | | ||  || |  | ||  ||  |   | ||||   |  ||| ||   |    ||||| |    || |  |||||||||| ||||||||||| ||||| ||||||||||||||||| ||  ||||||| || || || |||
------atacaattgttcaagc----aatacttcctgcttacagtagt--tgtattgtcactctttacacataatt--attgatttttggag-tgtttttggatgtcatatgcagCTTCTTGCTGAGAAAGGTGAACTCCCAACAAGATTTGGCTCAGCTACACTGGGAATCCTCCTCCTGCAG

upper sequence: AT4G04850.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G009715_T01 (Zea mays), 3'ss of exon 5
gtattagcacagttgcaataacttttagtcatctatatctagaatggtaatggagaggcaaactcaatcaagaatttagtacattcttattgacaattt-tgaaatgtatagCTTCTTGCAGAGAAAGGTGAGCTCCCTACAAGATTTGGCTCAGCAACCTTGGGAATTCTTCTTCTACAG
          |||| ||  ||   | | |||   | |  |   ||| | |   | ||  | | |   | ||   ||| | || |  | |||||  ||   |   || |  |||||||||| ||||||||||| || || ||||||||||| ||||| ||  ||||||||||||| || |||
-------tttagttacacaaa---tcattcacgca-acttgtcatgcttaca-acagttacattttttaaaactttttgcacttggtgattgattatgaataccatctgcagCTTCTTGCCGAGAAAGGTGAACTTCCAACAAGATTTGGTTCAGCTACACTGGGAATTCTTCTCCTGCAG

upper sequence: AT4G04850.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G06890.3 (Glycine max), 3'ss of exon 6
gtattagcacagttgcaataacttttagtcatctatatctagaatggtaatggagaggcaaactcaatcaagaatttagtacattcttattgaca-attttgaaatgtatagCTTCTTGCAGAGAAAGGTGAGCTCCCTACAAGATTTGGCTCAGCAACCTTGGGAATTCTTCTTCTACAG
            | |   ||  | ||   |||  ||   |  | ||  |   | |||  | ||| ||| | | ||   |||  || | |   | | ||    | || | |||||||||||||||| ||||||||| |||||||||||||||||||||||  | ||||| |||||| | |||
-----------atggttttaggtgttccccatgcatgagtccattgtgatatgtgagtgacactaaat-atggataatgtaacttatcaagcatatatgcatatatttgtagCTTCTTGCAGAGAGAGGTGAGCTTCCTACAAGATTTGGCTCAGCAACTCTTGGAATACTTCTTTTGCAG

upper sequence: AT4G04850.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G30360.2 (Glycine max), 3'ss of exon 7
gtattagcacagttgca-ataacttttagtcatctatatctagaatggtaatggagaggcaaactcaatcaagaatttagtacattcttattgaca-attttgaaatgtatagCTTCTTGCAGAGAAAGGTGAGCTCCCTACAAGATTTGGCTCAGCAACCTTGGGAATTCTTCTTCTACAG
            |   |  | ||  | | |      |||| || ||    ||  | |   | |   |   |   || || || ||   |||  | | || |  | || | |||||||||||||||| ||||||||| ||||| |||||||| ||||||||  | ||||| |||||| | |||
------------tgatatgtgacactaaatgcaacttatcaagcatatatatatatatatatatatatatatatatata-tatatatatatatatatatatatatatttgtagCTTCTTGCAGAGAGAGGTGAGCTTCCTACGAGATTTGGTTCAGCAACTCTCGGAATACTTCTTTTGCAG

upper sequence: AT4G04850.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s0282g00020.t01 (Vitis vinifera), 3'ss of exon 6
gtattagcacagttgcaataactt-ttagtcatctatat-ctagaatggtaatggagaggcaaactcaatcaagaatttagtacattcttattgacaattttgaaatgtatagCTTCTTGCAGAGAAAGGTGAGCTCCCTACAAGATTTGGCTCAGCAACCTTGGGAATTCTTCTTCTACAG
  | |     |  ||||  || || ||  |  ||| ||   ||||||  |  |  | ||    |||  ||  || | |    |   |||||   |  |      ||| ||||||||||||||||||||||||||||||| ||| ||||||| |||||||| |||||||| ||||| ||||||
-gagtgaattatatgcagaaatttctttcttgtctgtagattagaatattgctacaaag----acttgatatagcagtctaga---tcttaccaagcac-----aatatatagCTTCTTGCAGAGAAAGGTGAGCTCCCAACACGATTTGGTTCAGCAACTTTGGGAATACTTCTACTACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaaactcaatcaagaatttagtacattcttattgacaattttgaaatgtatagCTTCTTGCAGAGAAAGGTGAGCTCCCTACAAGATTTGGCTCAGCAACCTTGGGAATTCTTCTTCTACAG
                               tattgac  putative branch site (score: 2)
                                      aattttgaaatgtata  TA-rich tract