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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acggctgtttggtggcctcccaacagtaaatcaaacccgcatttaaaccttttttaatctctgctgttggcttgtatatgtattctctctctttctgcagATTGAAACTGATAGGGAAGCAGGAGGGAACAAAGGTGTCTCTGACAAGCAGATTCGACTCAAGATTTTTTCACCAAATGTTCTTGATATCACACTTGTTG

Basic information

species Glycine max
transcript GLYMA04G16340.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G16340.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 1
---acggctgtttggtggcctcccaacagtaaatcaaacccgcatttaaaccttttttaatctctgctgttggcttgtatatgtattctctctctttctgcagATTGAAACTGATAGGGAAGCAGGAGGGAACAAAGGTGTCTCTGACAAGCAGATTCGACTCAAGATTTTTTCACCAAATGTTCTTGATATCACACTTGTTG
     ||   |||| |   || |      | | | |     |   || |       ||| |     |    | |   | |    |  ||||   | | |||||   ||||| ||  | || ||||| || ||||||||||| || || | |||||| ||| | ||||||||||| |||||||||||| | || ||  | ||||
tgtttggtattttgtttcacttcttttctttagttag-tgtgggcttgagttgccattagtgct--ccacagaccattgttaaaagactctgcatctatgcagGCAGAAACAGACCGAGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAGATACGATTGAAGATTTTTTCTCCAAATGTTCTTAACATTACTTTGGTTG

upper sequence: GLYMA04G16340.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 1
--acggctgtttggtggcctcccaacagtaaatcaaacccgcatttaaaccttttttaatctctgctgttggcttgtatatgtattctctctctttctgcagATTGAAACTGATAGGGAAGCAGGAGGGAACAAAGGTGTCTCTGACAAGCAGATTCGACTCAAGATTTTTTCACCAAATGTTCTTGATATCACACTTGTTG
  |    | |    |            ||| | ||||     | ||||| ||||    ||   | |      |   |  |  |  | ||      ||| |||  ||| || ||||||||||| ||||  ||||||||||| || || |||||||||||  | ||||| || || |||||||| |||||||||||||| || |
ttatttttatcatctcaagctttgcatgtataccaaagtaatacttaaaactttgaagatagtttccccc--cccctcaaaattctttccaatcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAGATTCGTTTAAAGATATTCTCGCCAAATGTCCTTGATATCACACTAGTGG

upper sequence: GLYMA04G16340.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S49_216V6.1 (Physcomitrella patens), 3'ss of exon 3
acggctgtttggtggcctcccaacagtaaatcaaacccgcatttaaaccttttttaatctctgctgttggcttg-tatatgtattctctctcttt---ctgcagATTGAAACTGATAGGGAAGCAGGAGGGAACAAAGGTGTCTCTGACAAGCAGATTCGACTCAAGATTTTTTCACCAAATGTTCTTGATATCACACTTGTTG
   | || ||  |   | |  |  | |   |   |    || || |   |  ||  |  ||   | ||||| |  || |||   |  | ||  |     |||||  ||||||||| |||||    |||  |||||| ||  | ||||| |||||||||||||| || ||||||||||| |||||| |  | || || ||||| |
---gttgcttcttttgcacgaattattcgttgtcaaagacaattgagtatcgttggagttc-attcttggcgtactaaatgaggtgccacttctcgggttgcagGCTGAAACTGACAGGGAGCTTGGAACGAACAAGGGGATTTCTGAAAAGCAGATTCGACTGAAAATTTTTTCACCTAATGTTTTGAACATTACGCTTGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccttttttaatctctgctgttggcttgtatatgtattctctctctttctgcagATTGAAACTGATAGGGAAGCAGGAGGGAACAAAGGTGTCTCTGACAAGCAGATTCGACTCAAGATTTTTTCACCAAATGTTCTTGATATCACACTTGTTG
      ttttaat  putative branch site (score: 3)
                                 tgtattctctctcttt  putative PPT
     tttttaatct  TA-rich tract