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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaatcactttggattggattgctaattatcttttaaagttactgtagctgtagaaacatccttatttaactccagtaatatttgctgataatttcccagGTCCTGGATGCTCATCGATTGCGTATGGAGCATCTGAAGAGATTGGCCCATTTAGGATTAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATG

Basic information

species Oryza sativa
transcript LOC_Os02g55130.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g55130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G879749_T02 (Zea mays), 3'ss of exon 1
---ctaatcactttggattggattgctaattatcttttaaagttactgtagctgtagaaacatccttatttaactccagtaatatttgctgataatttcccagGTCCTGGATGCTCATCGATTGCGTATGGAGCATCTGAAGAGATTGGCCCATTTAGGATTAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATG
   |||    |||  | ||       ||   || |        | || |||    ||     |  |  | |   | ||||  |  | ||     | |  | ||||||||||||||| ||| | ||||||||||| || || ||||| ||||| ||  |||| ||  ||||||||||||| || |  || ||||||||||||||
tctctacatgcttccgcttccgcctatatgcatatgcattgcctgctatagtaccagctgtgtaatagtatg--tacagttctgatggcctggcactggc-agGTCCTGGATGCTCGTCGGTGGCGTATGGAGCGTCGGAGGAGATCGGCCCGTTCCGGATCAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATG

upper sequence: LOC_Os02g55130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G26930.1 (Glycine max), 3'ss of exon 1
ctaatcactttggattggattg---ctaattatcttttaaagttactgtagctg-tagaaacatccttatttaac-tccagtaatatttgctgataatttcccagGTCCTGGATGCTCATCGATTGCGTATGGAGCATCTGAAGAGATTGGCCCATTTAGGATTAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATG
   || |||||  | |  |||     || |||||||   | |||        |  |  |    | || ||||| | | || |||| |||  || ||| ||   |||||| ||||| |||||  | || |||||||||||||||||||||||||||||||| || || | ||  |   | || || ||    ||||||| ||||||
--cattactttatactttattcaatttatttatcttactaggttttgacttttaatccattttttctaatttagcgtgcaataatcttttgtggtaaatt---agGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGTCTATACAAAAACAAGTTCTCATG

upper sequence: LOC_Os02g55130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA18G50170.1 (Glycine max), 3'ss of exon 1
ctaatcactttggattggattgctaattatcttt----taaagttactgtagctgtagaaacatcctt---atttaactc--cagtaatatttgctgataatttcccagGTCCTGGATGCTCATCGATTGCGTATGGAGCATCTGAAGAGATTGGCCCATTTAGGATTAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATG
      |||||  | |  |||  | | | | |||    || | |   |  |  | ||||  |||  ||   | |||| |   || |||| |||| || ||| ||   |||||| ||||| |||||  | || |||||||||||||||||||||||||||||||| || || | ||  |   | ||||| ||  | |||||||  || ||
-----tactttatacttcattattcaatttatttatattagaatgttttgacttttagatccatttttttaacttaagtgtgcaataatttttg-tggtaaatt---agGTCCAGGATGTTCATCAGTGGCATATGGAGCATCTGAAGAGATTGGCCCATTTAGAATAAACAAAACAGCTTCTGGGCTATACATTAACAAGTTTTCGTG

upper sequence: LOC_Os02g55130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv14s0068g00260.t01 (Vitis vinifera), 3'ss of exon 1
ctaatcactttggattggattgctaattatcttttaaagttactgtagctgtagaaacatccttatttaactccagtaatatttgctg----ataatttcccagGTCCTGGATGCTCATCGATTGCGTATGGAGCATCTGAAGAGATTGGCCCATTTAGGATTAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATG
    |   |    ||    |||   ||||   | ||       | |     |  | | ||   || |        || | | ||| |      ||| ||   ||||||||| ||||| ||  | |||||||| ||||||||||| || |||||||||||||| || |  |  |   |||| || || || ||||||| ||||||
--gctttttaaaaatcaagttg--gattaatatataggacccgtctcataatgtatatatatatagtatctgatggtgagacttgttttgttgtaacttgtaagGTCCTGGTTGCTCTTCTGTGGCGTATGGGGCATCTGAAGAAATAGGCCCATTTAGGATCAACAAGACTGCTTCAGGCCTGTACCTTAACAAGTTCTCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctgtagaaacatccttatttaactccagtaatatttgctgataatttcccagGTCCTGGATGCTCATCGATTGCGTATGGAGCATCTGAAGAGATTGGCCCATTTAGGATTAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATG
                                      tgctgat  putative branch site (score: 3)
                                               tttccc  putative PPT
                 ttatttaact  TA-rich tract