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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtacctttttgttgttttggtttactttttttttctttgcctgtctgtttaattaacattatattgtgatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 15
gtcagta-cctttttgttgttttggtttactttttttttctttgcctgtctgtttaattaacattatattgt--gatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG
||| ||| |||||   ||||||||| | | | | || |  ||   || | |||| ||  || ||  |||| |  ||||||||||||  |||| || || ||||||||||||||||| || ||||| |||||||||||||| |||
gtcggtaacctttgcattgttttggctga-tctcttctctttaatctctgtgttaaaccaatatcgtattttctgatgcagCATTATTCAGAGTTGCCTGATATCAAGCGTGTCATTGTAAATACTCATGCCATTGAGCCCCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 17
gtcagtacctttttgttgt-tttggtttactttttttttctttgcctgtctg-----------tttaattaa---cattatattgtgatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG
|| || ||  |     ||| |||  ||       ||| ||| ||    |||             |||||| |   |||||| |  || ||||||||||||||||||||||||| ||||| || || || || ||||| ||||| ||||| || |||
gtaaggactctccaaatgtgttttattcttgcactttctctatgttaatcttaaaatcaaacccttaattgattgcattat-tcttggtgcagCATTACACAGAATTACCAGACATCAAACGCGTGATTGTTAATACACATGCAATTGAACCTCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 17
gtcagtaccttttt--gttgttttg---gtttactttttttttctttgcctgtctgtttaattaacattatattgtgatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG
||   |  ||| ||  ||| |  ||   || || |  | | || || |  | | | || ||       | |||  |  |||||||||| || || || || || ||||| |||||||| |||||||| ||||||||||||||||||
gttctttgcttcttaagttctgatgacagtataatgatctcttgttagaatatttcttgaaccgtgtctgtat-attgtgcagCATTATACTGAGTTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATTGAGCCACAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 16
----------gtcagtacctttttgttgtt-ttggtttactttttttttcttt--gcctgtctgtttaatta--acattatattgtgatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG
            ||      |||| || ||  |||||| ||| |||   |     ||||     |||| | |  ||| ||| || || |||||||||||||||| || |||||||| || ||||| || || ||||| ||||| ||||||||||||
gtaatgactcaccaaatgtgttttattattactggttttcttatttaacccaaaagccttctcttttactgattacactat-ttttggtgcagCATTACACAGAGTTGCCAGATATAAAACGTGTGATTGTAAATACACATGCAATTGAGCCACAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 17
gtcagtaccttttt--gttgttttggtt---tactttttttttctttgcctgtctgtttaattaacattatattgtgatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG
||   |  ||| ||  ||| |  ||  |   || | || | || || |  | | | || ||       | | |  |  |||||||||| || || || || || ||||| |||||||| |||||||| ||||||||||||||||||
gttctttgcttcttaagttctgatgactgtataatgttctctttttagaatatttcttgaaccttgtctgtgt-attgtgcagCATTATACTGAGTTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATTGAGCCACAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 16
----------gtcagtacctttttgttgtt-ttggtttactttttttttcttt-gcctgtctgtttaattaa---cattatattgtgatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG
            ||      |||| || ||  |||||| ||| |||   |    | |  ||| ||| ||| |   |||||| || || |||||||||||||||| || |||||||| || ||||| || || ||||| ||||| ||||||||||||
gtaatgactcaccaaatgtgttttattcttactggttttcttatttaacccaaaggccttctcttttattgattacattat-ttttggtgcagCATTACACAGAGTTGCCAGATATAAAACGTGTAATTGTAAATACACATGCAATTGAGCCACAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 17
gtcagtacctttttgttgttttggtttacttt--ttttttctttgcctgtctgtttaattaacattatattgtg---atgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG
||   |    |||| || || ||  | ||| |  ||| || |  |  |   |  || |      || | |  ||   |||||||||||  | ||||| || || ||||| |||||||| |||||||| |||||||| || ||||||
gttctt-tgcttttattcttatgactgactgtaatttcttgtcagaataatttcttgaaccttcttgtgtgttgcttatgcagCATTATTCCGAATTGCCTGACATCAAACGTGTCATTGTGAATACACATGCCATCGAACCACAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 17
gtcagtacctttttgttgt-tttggtttactttttttttctttgcctgtct----gtttaattaac-----attatattgt----gatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG
|| || ||  |     ||| |||  ||  |    ||| ||| ||   ||||    ||  ||          |||  ||| |    | ||||||||||||||||||||||||| ||||| ||||| || || ||| | ||||| ||||| || |||
gtaaggactctccaaatgtgttttattctcgcactttctctatgttagtcttaaagtcaaaccctttgttgattgcattattcttggtgcagCATTACACAGAATTACCAGACATCAAACGTGTGATTGTTAATTCACATGCAATTGAACCTCAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 17
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 17
-------gtcagtaccttttt--gttgttttggtttact---ttttttttctttgcctgtctgtttaattaacattatattgtgatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG
        ||| |  ||| ||   |  | ||||  || |   | | |||| ||| ||  |||   |   |  | || |  | || ||||||||||| |||| ||||| |||||||| ||||| || ||||| || ||||| ||||||||||||
gtttttgctcaatgtcttctttaatattcttggcctaatagatgtatttttttttcccctctaacttcgtttccttttgctttg-tgcagCATTACTCAGAGTTACCTGATATCAAACGTGTAATTGTGAACACACATGCTATTGAGCCACAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 17
------------------gtcagtacctttttgttgttttggtttactttttttttct----ttgcctgtctgt-ttaattaaca---ttatattgtgatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG
                   |   |    |||| || |||   |||  | || ||   |    ||   | |  || ||  |||| |   ||||||| || |||||||||| || || || |||||||| || || ||||| |||||||| ||||| ||||||||||||
gtgaaattggttcttgcaattcattttattttattttttaccttttttattgttacatgaaattaattatacgtcttggttaaaacacttatattttg-tgcagCATTATACTGAGTTGCCAGATATAAAACGCGTCATTGTGAATACACATGCAATTGAGCCACAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 17
----gtcagtacctttttgttgttttggtttactttttttt-----tctttgcctgtctgtttaattaac--attatattgtgatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG
        ||  ||   | |    ||| |  ||||| |||       |||||  ||| | ||  |||||   |||    | | ||||||||||| || ||||| || |||||||| |||||||| ||||| || ||||||||||||||||||
gtataatggtttctcactatctgattgatgaactttatttcacagacctttgattgtttcttggattaaatgattcatctcttatgcagCATTATACTGAATTGCCCGATATCAAACGTGTCATTGTGAACACACATGCCATTGAGCCACAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 63 (downstream exon)
Score: 167

TGCTGATGCCATCCTTGCTAATGGTATGTTCAGTCATTATGATCGCCCTCGTGTTGCTCAGCTTTGTGAAAAGGCTGGCTTGTACTTGCGAGCTCTCCAGgtcagtacct ... tgtgatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttactttttttttctttgcctgtctgtttaattaacattatattgtgatgcagCATTACACAGAATTACCAGATATCAAGCGTGTCATGGTGAATACCCATGCCATTGAGCCACAG
                               aattaac  putative branch site (score: 167)
                            tttaattaacattata  TA-rich tract