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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaaactattttaattcatttttgtctttgaactcacaaagtgaattttgtttctagcattccatttcttatttgttatttaattgtgtatacttattttgcagCCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG

Basic information

species Glycine max
transcript GLYMA20G38810.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g61860.1 (Oryza sativa), 3'ss of exon 8
gtttgtaaactattttaattcatttttg--tctttgaac-tcacaaagtgaattttgtttctagcattccatttcttatttgttatttaattgtgtatacttattttgcagCCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG
|||||   | |||| |  ||  | ||    | | || |  |||  |  ||   | | | | || |   | ||||     |   || ||  || || ||  || ||||||||  ||||| |||||||| || || || || || ||||||||||||||||||||||| || || || ||  |||||||||| || ||||||||||
gtttgcgcattattcttgtttgtattaaaatatctgtatatcatgacttggcatatatgt-taaccgacaattt-----tgactactt--ttatgcatggtt-ttttgcagTAAATCACCTGGATTACCTCGGCGTTCAAGTTGCATGGGTTACTGGACCATGGTTTCTATCTATATTCATGAACATGCTACCATGGGAAAGTG

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g38950.2 (Oryza sativa), 3'ss of exon 8
gtttgtaaactattttaattcatttttgtctttgaactcacaaagtgaattttgtttctagcattccatttcttatttgttatttaattgtgtatacttattttgcagCCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG
||| | ||  ||||  || |    | | |   ||   |  |       |||| | |  || | ||| |     || |  |||   |  ||  |    || || |||||| ||||| |||||||| || ||  | || || |||||||||||||||||||||||||| ||||||||    ||  ||||||||||||| ||||
gttcgcaacttattgcaaatatgatatattggtg---tggcgtgcctcatttagctagtaac-ttcaaaaatataataattaaa-agctgatttccttttttgtgcagCAAATCACCTGGATTACCTTGGTCTTCAAGTTGCATGGGTTACTGGACCATGGTTCCTATCCATTTTCACCAATGTGCTTCCTTGGGAGAGTG

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G096470_T01 (Zea mays), 3'ss of exon 8
gtttgtaaactattttaattcatttttgtctttgaactcacaaagtgaattttgtttctagcattccatttcttatttgttatttaattgtgtatacttattttgcagCCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG
|| ||| |  ||||  |  | |||| |  |     | |  || |        | ||   ||||    |||               ||        |  |||||| |||  |||||||| ||||| || || || || || |||||||| ||||| ||||||||||| || |||||| ||||||||||||| ||||||||||
gtgtgtgacttattcca--ttatttgtaccacatgattgtcaga------catattaacagcacaagattgac------------aagaacactcatgtattttccagTAAATCATCTTGATTACCTTGGTGTACAAGTTGCATGGGTCACTGGTCCATGGTTCCTATCTATTTTTATGAACATGCTTCCCTGGGAAAGTG

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G051050_T01 (Zea mays), 3'ss of exon 8
gtttgtaaactattttaattcatttttgtctttgaactcacaaagtgaattttgtttctagcattccatttcttatttgttatttaattgtgtatacttattt--tgcagCCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG
||| | || ||||  | | | | ||      |||    ||    |||| | ||  | |    ||   |      |  | |||    |||    ||||||  ||   ||||| ||||| |||||||| || ||| | || || |||||||||||||| ||||||||| | ||||| ||   |||  ||||||||||||||||||
gttagcaacctatcatgaataaattgaaatattggtggcat---gtgactctttgtgccctaataaaaaaatccaagtattag--gatttaacatactttcttgacgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACGAATGTGCTTCCTTGGGAAAGTG

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G094951_T01 (Zea mays), 3'ss of exon 8
gtttgtaaactattttaattcatttttgtctttgaactcacaaagtgaattttgtttctagcattccatttcttatttgttatttaattgtgtatacttattt--tgcagCCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG
||| | || ||||  | | | | || |    |||    ||         || |||  | |    |  |      |    | |    |||    ||||||  ||  |||||| ||||| |||||||| || ||| | || || |||||||||||||| ||||||||| | ||||| ||    ||  ||||||| ||||||||||
gttagaaacctatcatgaatgaattgtaatattggtggcatgtgactctttctgtccc-attggtaaaaaatccaagcataag--gatttaacatacttccttgatgcagCAAATCACCTGGATTACCTTGGACTTCAAGTTGCATGGGTTACTGGGCCATGGTTCTTATCCATCTTCACAAATGTGCTTCCCTGGGAAAGTG

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G39280.1 (Arabidopsis thaliana), 3'ss of exon 8
gtttgtaaactattttaattcatttttgtctttgaactcacaaagtgaattttgtttctagcattccatttcttatttgttatttaattgtgtatacttattttgcagCCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG
    || |  | ||| |   || | |||  ||| | || || ||   || ||||    | |   |        || |||| ||||   |||  ||        |||||   ||||||| |||||||| |||||||||||||| || ||||| || |||||||| ||  |||| ||  | || |||||||| ||||||||||
----gttagttttttca---cagtcttg--tttcatcttaccaa---aaatttggagttggtgctaa---cactacttgtgattt--ctgtccat-------ctgcagTTCATCATCTAGATTATCTTGGAGTGCAGGTGGCTTGCGTTACAGGGCCATGGTTTCTTACCATCTTCATTAATATGCTTCCATGGGAAAGTG

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 8
gtttgtaaactattttaattcatttttgtctttgaactcacaaagtgaattttgtttctagcattccatttcttatttgttatttaattgtgtatacttattttgcagCCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG
    || |  |   | ||   | |||| | ||| | ||   | | ||   ||      ||| | |    |       ||  | ||   | ||| |||         ||   |||||||||||||||| |||||||| ||||| |||||||| || |||||||| || ||||| ||  |||| |||||||| ||||||||||
----gtgagttccctcaa---agttttttgtttcatcttgtagaatg---ttcacagttagtactaagctc------tgcaacttttctatgtctac---------agTTCATCATCTGGATTATCTTGGAGTGCAAGTGGCTTGGGTTACAGGGCCATGGTTTCTTTCCATCTTCATGAATATGCTTCCATGGGAAAGTG

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 8
gtttgtaaactattt--taattcatttttgtctttgaactcacaaagtgaattttgtttctagcattccatttcttatttgttatttaattgtgtatacttattttgcagCCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG
||||||    | ||   || || ||| | ||        ||  |   | | ||||  ||         |||||   ||   || ||   |    | |   |  | |||||  ||||| ||||||| ||||||||||||||||||||||||||||||||| ||||| || ||||||||| |||| |||||||| ||||||||||
gtttgtttcttgttgcatattttattatcgttgcccttttccaattattattttttctttatatgaggcattttggatggcttcttatttcacctttgtgtcatgtgcagTTAATCACCTGGATTTTCTGGGAGTGCAGGTGGCATGGGTTACTGGACCGTGGTTTCTTTCCATTTTTATGAATATGCTTCCATGGGAAAGTG

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S31_313V6.1 (Physcomitrella patens), 3'ss of exon 8
---gtttgtaaactattttaattcatttttgtctttgaactcacaaagtgaattttgtttctagcattccatttcttatttgttatttaattgtgtatacttattttgcagCCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG
     | |||   || | |   |  |||   |  ||||  ||    |||  |   | |     | ||||        |||  | || || ||||||         ||||||| | |||||||||    || ||||||||||| |||||||||| ||| || |||||||| ||||| ||||||||| |  | || ||||| | ||
gtgagtcgtatcatactcttgattttttacctacttgatttcgtttagtataggatataataggaattctcagaaaaattgctaatgtatttgtgt-------cattgcagCAACTCATCTGGAGAGCCTTGGAGTGCAGGTAGCATGGGTTAGTGGCCCTTGGTTCCTTTCCATCTTTGTGAACGTCGTACCATGGGAGACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctagcattccatttcttatttgttatttaattgtgtatacttattttgcagCCAATCATCTGGATTATCTGGGAGTGCAGGTGGCATGGGTTACTGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTG
                            atttaat  putative branch site (score: 4)
                                           cttatttt  putative PPT
              atttcttatttgttat  TA-rich tract