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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacgaattggtcctttattgcttcatgttcttactagttctcaggctggtgtatatctaacaattttccccttatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG

Basic information

species Oryza sativa
transcript LOC_Os02g37080.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G444643_T01 (Zea mays), 3'ss of exon 3
gtaatacgaattggtcc------tttattgcttcatgttcttactagttctcaggctggtgtatatctaacaattttccccttatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
||||| |  ||   |||       || ||| |  |  |||||| |  ||||||||||||| || ||||||   ||   ||||||    ||||| ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||
gtaattcttatccttccactgtactttttgatagaaattcttaatgcttctcaggctggtataaatctaatggttgcacccttactctcagATTGAAACTTAAGGCTGTATATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTG

upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G170868_T01 (Zea mays), 3'ss of exon 2
gtaatacgaattggtcc--tttattgcttcatg----ttcttactagttctcaggctggtgtatatctaacaattttccccttatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
||||| |  ||   |||  | || |  || ||     |||| ||| ||| |||  ||| | || ||||||   || | ||||||    ||||| ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||
gtaattctgatccttccactgtactttttaataaaaattctcactggttttcaatctgctctagatctaatggttgtgcccttactctcagATTGAAACTTAAGGCTGTATATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGACTTTGGAGTG

upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G36370.1 (Glycine max), 3'ss of exon 2
------------gtaatacgaattggtcctttattgcttcatgttcttactagttctcaggctggtgtatatctaacaattttccccttat---ctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
             |  ||          ||  |||  |    |   || | |       || |     | |   ||  |   |      ||    | ||| | |||| | ||||| ||||||||||| ||||||||||| ||| |||| ||||| |||||  | || ||||||||||| ||||| || || ||||| |||
attcttgatcagtttttattgccgaactctgaattagtcagagccgtttccaacaagagggttaagacaaaaagaaataaccttttaacatacattgcagGTTGAAATTGAAGGCAGTCTATATGTACGCTGCTGGATTTTACTCATACTCCATTTTTGCTTTGATATTTTGGGAAACGAGGCGCTCCGACTTTGGAGTG

upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G14040.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------gtaatacgaattggtcctttattgcttcatgttcttacta-gttctcaggctggt---gtatatctaacaattttccccttat-ctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
                                                           ||  |   |||||    | | |  | |  | |  || | | ||  |||   |      ||  ||  | ||||   |   | |   | ||||| |||| | || |   |||||||||||||||||||||| || ||||| |||||| ||||  |  | ||||||||||| | ||| || || ||||  || 
gtaagattttcatttacttgcacaacttttgtggcttttctgttacaatctttaatctagttttgttaattgtctttatttgtccttctttgatttccatgtgttcaacttaagttggttgattgagcaataaccttttaacatttcagATTGAAATTGAAAGTGCTCTATATGTATGCTGCTGGATTTTATACATACTCCATACTTGCTTTAGTATTTTGGGAAACGAAGCGCTCTGACTTTGTGGTT

upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 2
gtaatacgaattggtcc---tttattgcttcatgttcttactagttctcaggctggtgtatatctaacaattttccccttat-ctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
    || | |||  |||   |   |  |||     || |      | ||    || | |  || ||  |  |||   | ||   | ||| | |||| | ||||| ||||||||||| ||||||||||| ||| |||| ||||| |||||  | || ||||||||||| ||||| || |||||||| |||
---gtaagtatttctccacatgcctcacttatgaatcatttgttctttccatatgattttaatttataaccttttaacatacatttcagGTTGAAATTAAAGGCAGTCTATATGTACGCTGCTGGATTTTACTCATACTCCATTTTTGCTTTAATATTTTGGGAAACGAGGCGCTCCGATTTTGGAGTG

upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G25540.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatacgaattggtcctttattgc--ttcatgttcttactagttctcaggctggtgtatatctaacaattttccccttatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
        | ||| | | |||| |   |  || |  ||  |  |  |||   | |   | || | | | |     |  | | | |||   |||  | |||  | | ||||||| |||||||||||||||||| || || ||||| ||  |  |||||||||||||||| || || ||||| || || 
-----gtaagttgtttcgttatggtcatcgatatcttttgtgatggtca--tttgctaaaatatgatactg----ctatgtgtgcagGATGAAGTTGAAGTTTTTATATATGTTTGCTGCTGGATTCTACACGTACTCTATATTCGCGTTGGTGTTTTGGGAAACAAGACGGTCTGATTTCGGAGTT

upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0010g01110.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------gtaatacgaattggtcctttattgcttcatgttcttactagttctcaggct--ggtgtatatctaacaattttcccct-tatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
                                                      |  |   |  |   | |||     |   ||| |||   |   ||||| ||  |  ||   |  |   ||  |    |  |  | ||| | |||| | |||| | | |||||||||  || ||||||||||||||| |||||||||||  | || ||||||||||||||||| || |||||||| |||
gtaaggttttcacaagccatacattaaaagcttatggttgttaaattctggcttttgtgttagcttaactttttcctttagctgtgctttgaatagctcagcctatgaagtcagttgagtgatgatatattgcaaattcagGTTGAAATTGAAGGGTTTGTATATGTATTGTGGTGGATTCTACACATACTCCATATTTGCTTTGATTTTTTGGGAAACAAGGCGGTCTGATTTTGGAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcttactagttctcaggctggtgtatatctaacaattttccccttatctacagATGGAAACTTAAGGCTGTCTATATGTATGCTGCTGGATTCTACACATATTCCATATTTGCACTTATGTTTTGGGAAACAAGGCGTTCAGATTTTGGCGTG
                            atctaac  putative branch site (score: 2)
                                     ttttccccttatctac  putative PPT
                         tatatctaacaatttt  TA-rich tract