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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaattgttttttcttttttctttgcagtaattttatgtccttcactatgttttcaatttcttacaagtttcaaaataatacagagcatatatttttataaatcagGTTGGTGGTGTTCATTTTAGCCTGCTTTCTAAAGTTCGCTATGACATTGGGGATTCTTGTTCACTGGATTACCTTATAGATAGCATTTTTCCATTATTTA

Basic information

species Glycine max
transcript GLYMA20G02060.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G02060.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g21110.1 (Oryza sativa), 3'ss of exon 5
gttaattgttttttcttttttctttgcagtaattttatgtccttcactatgttttcaatttcttacaagtttcaaaataatacagagcatatatttttataaatcagGTTGGTGGTGTTCATTTTAGCCTGCTTTCTAAAGTTCGCTATGACATTGGGGATTCTTGTTCACTGGATTACCTTATAGATAGCATTTTTCCATTATTTA
                         | |  |||| ||  | |   |  || ||||  |||    |  ||||  |   ||   ||     |  |    |  |  ||||||||||||||||||||||||||| || |||||||| |   |||| ||||| |||||||| ||  |||| || || || |||||||| ||||| || ||||
-------------------------gtaaaaattataattgccctaa-atatttttcattatagaacagtt--attttatctcaataatttcacccatgaacttcagGTTGGTGGTGTTCATTTTAGCCTTCTGTCTAAAGTCCAGCATGATATTGGAGATTCTTGCTCGTTGGACTATCTGATTGATAGCATATTTCCCTTGTTTA

upper sequence: GLYMA20G02060.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G473385_T01 (Zea mays), 3'ss of exon 2
--------gttaattgttttttcttttttctttgcagtaattttatgtccttcactatgttttcaatttcttacaagtttcaaaataatacagagcatatatttttataaatcagGTTGGTGGTGTTCATTTTAGCCTGCTTTCTAAAGTTCGCTATGACATTGGGGATTCTTGTTCACTGGATTACCTTATAGATAGCATTTTTCCATTATTTA
        | || ||| ||  | | | |   ||    |  ||  |  | | |    |       |   | ||||  |||    ||  |||||  |   ||||   | |    |||||||| || ||||||||||||||||||||||||||||   |||| ||||| |||||||| ||| |||| || || || || || || |||||||| ||||
gtaaacatgatagttgcttactttctataagttattttgtttagacttgcattctcacagaacaatagtattacctgttatgtaaccatacaaggtgcatatgagttt----cagGTTGGCGGCGTTCATTTTAGCCTGCTTTCTAAAGTTCAGCATGATATTGGAGATTCTTGCTCATTGGACTATCTAATCGACAGTATATTTCCATTGTTTA

upper sequence: GLYMA20G02060.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G01460.1 (Arabidopsis thaliana), 3'ss of exon 5
gttaattgttttttcttttttctttgcagtaattttatgtccttcactatgttttcaatttcttacaagtttcaaaataatacagagcatatatttttataaatcagGTTGGTGGTGTTCATTTTAGCCTGCTTTCTAAAGTTCGCTATGACATTGGGGATTCTTGTTCACTGGATTACCTTATAGATAGCATTTTTCCATTATTTA
                         | |  | |||    ||||  |  | ||| |     |||  | | | |  ||  |  | |     |||  | |      | ||||||| || |||||||||||||| || |||||||| || ||||| ||||| ||||| ||||| || ||||||||||| || |||||||| || || ||||
-------------------------gtaagattttctcctcctagagca-gttattgg--tctagctaatgtacaaccatgatatcatttattctctctgtggttagGTTGGGGGCGTTCATTTTAGCCTTCTCTCTAAAGTCCGTTATGATATTGGAGATTCGTGTTCGCTTGATTACCTTATCGACAGCATTTTCCCTTTGTTTA

upper sequence: GLYMA20G02060.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g04960.t01 (Vitis vinifera), 3'ss of exon 5
---------------gttaattgttttttcttttttctttgcagtaattttatgtccttcactatgttttcaatttcttacaagtt-tcaaaataatacagagcatatattttt--ataaatcagGTTGGTGGTGTTCATTTTAGCCTGCTTTCTAAAGTTCGCTATGACATTGGGGATTCTTGTTCACTGGATTACCTTATAGATAGCATTTTTCCATTATTTA
               |||  |||   |  | || |  |||    | |   | |||       ||  |  |   ||  | | ||  | |||| |||||    ||   | ||| ||   | |  |||||||||||||||||||||||||| ||||| |||||||| ||||| ||||| |||||||||||  |||| |||||||| || |||||||| |||||||| |
gtaatattttccttggttccttggggtcacattctgtttttttatgaccctttgttaact--taaatcattggttgttaagaaaatatcaatataatgttaagtgaaaattgtttggtgagacagGTTGGTGGTGTTCATTTTAGCCTTCTTTCCAAAGTTCGATATGATATTGGAGATTCTTGTTCTTTGGACTACCTTATTGACAGCATTTTCCCATTATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaatttcttacaagtttcaaaataatacagagcatatatttttataaatcagGTTGGTGGTGTTCATTTTAGCCTGCTTTCTAAAGTTCGCTATGACATTGGGGATTCTTGTTCACTGGATTACCTTATAGATAGCATTTTTCCATTATTTA
       ttcttac  putative branch site (score: 2)
                                       tattttt  putative PPT
                 tttcaaaataatacag  TA-rich tract