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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagctttttgctagtttctatggaaatcacataatttttttgtcattcatttgactaaggtgaatttttgctttagGTTGTAGATTCCCTCTATGATTGCAAAAGTGAAGTTATTGGGCCTGGATTCTTCAGATTTAAGGCAGAAATAG

Basic information

species Glycine max
transcript GLYMA08G23740.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23740.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os04g23180.1 (Oryza sativa), 3'ss of exon 9
gtacaagctttttgctagtttctatggaaatcacataat--ttttttgtcattcatttgactaaggtgaatttttgctttagGTTGTAGATTCCCTCTATGATTGCAAAAGTGAAGTTATTGGGCCTGGATTCTTCAGATTTAAGGCAGAAATAG
||  ||  || | | ||   |   |  | ||| || | |   | | ||| ||  |  ||| |    || ||  |      ||||||||||| | || ||||||||||||||||| || ||||| || |||||||| ||||| || || ||||| |
gtgaaaatttgtggatatccttattccatatcgcacactggatctatgttatggagctgattttcttgcatcatg----cagGTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTG

upper sequence: GLYMA08G23740.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G065839_T01 (Zea mays), 3'ss of exon 9
gtacaagctttttgctagtttctatggaaatcacataatttttttgtcattcatttgactaaggtgaatttttgctttagGTTGTAGATTCCCTCTATGATTGCAAAAGTGAAGTTATTGGGCCTGGATTCTTCAGATTTAAGGCAGAAATAG
     ||||||    |  |   | ||||| |  | ||     | | | ||  |  | | |  |||   || ||||   ||||||||||| | || ||||||||||||||||| || |||||||| || || || ||||| ||||| ||||| |
--gtgagctttgacattataattttggaact-gcttagaagctcttttatgaaactaatt--ggtatcttcttgc---agGTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTG

upper sequence: GLYMA08G23740.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G032293_T02 (Zea mays), 3'ss of exon 1
gtacaagctttttgctagtttctatggaaatcacataatttttttgtcattcatttgactaaggtgaatttttgctttagGTTGTAGATTCCCTCTATGATTGCAAAAGTGAAGTTATTGGGCCTGGATTCTTCAGATTTAAGGCAGAAATAG
    |||||||    |  |   |  |||| |  | ||    |||| | ||  |  | | ||   |   || ||||   |||| |||||| | || |||||||||||||| || || |||||||| ||||| || ||||| ||||| ||||| |
--gtaagctttggcattataatttcggaact-gcttagaagtttttttatgaagctaatta---tatcttcttgc---agGTCGTAGATGCTCTTTATGATTGCAAAAGCGAGGTGATTGGGCCAGGATTTTTTAGATTCAAGGCTGAAATTG

upper sequence: GLYMA08G23740.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G032293_T01 (Zea mays), 3'ss of exon 2
gtacaagctttttgctagtttctatggaaatcacataatttttttgtcattcatttgactaaggtgaatttttgctttagGTTGTAGATTCCCTCTATGATTGCAAAAGTGAAGTTATTGGGCCTGGATTCTTCAGATTTAAGGCAGAAATAG---------------------------
    |||||||    |  |   |  |||| |  | ||    |||| | ||  |  | | ||   |   || ||||   |||| |||||| | || |||||||||||||| || || |||||||| ||||| || ||||| ||||| ||||| |                           
--gtaagctttggcattataatttcggaact-gcttagaagtttttttatgaagctaatta---tatcttcttgc---agGTCGTAGATGCTCTTTATGATTGCAAAAGCGAGGTGATTGGGCCAGGATTTTTTAGATTCAAGGCTGAAATTGGTAGTCTTTATATTCTGGCATTTCACC

upper sequence: GLYMA08G23740.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G51610.1 (Arabidopsis thaliana), 3'ss of exon 9
gtacaagctttttgctagtttctatggaaatcacataatttttttgtcattcatttgactaagg-tgaatttttgcttt----agGTTGTAGATTCCCTCTATGATTGCAAAAGTGAAGTTATTGGGCCTGGATTCTTCAGATTTAAGGCAGAAATAG
||||||  | ||       |  | | |||||| ||||  |      |       | | || ||  | || | |||  ||    |||||||||||||  | ||||| |||||||||||||| ||||| ||||||| |||||||||||| || |||||||
gtacaaattcttcttatcataatttagaaatctcatatatgacgcatgtagaggtgggctcagaatcaaatattgtgttgtgtagGTTGTAGATTCTTTATATGACTGCAAAAGTGAAGTGATTGGTCCTGGATCCTTCAGATTTAAAGCTGAAATAG

upper sequence: GLYMA08G23740.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0054g00220.t01 (Vitis vinifera), 3'ss of exon 9
-----------------gtacaagctttttgctagtttctatggaaatcacataatttttttg---tcattcatttgactaaggtga---atttttgctttagGTTGTAGATTCCCTCTATGATTGCAAAAGTGAAGTTATTGGGCCTGGATTCTTCAGATTTAAGGCAGAAATAG
                 | | ||   | |  | | |  |||  |  || ||||| || |       | |    |  ||||    | |   ||||||  | ||||| || ||| | || |||||||| |||||||| || ||||| ||||| ||||| || ||||||||||||||||
gtattgttttctacactgaataactctatcccaattagctactgttat-acatatttgtcccagtttgacgggtacgactctatttatttattttttttgtagGTAGTTGATGCTCTATATGATTGTAAAAGTGAGGTGATTGGACCTGGGTTCTTTAGGTTTAAGGCAGAAATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaaatcacataatttttttgtcattcatttgactaaggtgaatttttgctttagGTTGTAGATTCCCTCTATGATTGCAAAAGTGAAGTTATTGGGCCTGGATTCTTCAGATTTAAGGCAGAAATAG
                           atttgac  putative branch site (score: 4)
                                           tttttgcttt  putative PPT
         ataatttttttgtcat  TA-rich tract