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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgattatactaattgtccagagaaagtaccgaaattttgcagtgctaacatacagtttatgttcatttgtatattcattttctggctagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA

Basic information

species Oryza sativa
transcript LOC_Os06g36080.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgattatactaattgtccagagaaagtaccgaaatt--ttgcagtgctaacatacagtttatgttcatttgtatattcattttctggct--agATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA
                                     | |||||  || ||| |  | ||    || ||    | ||  | |   |||   || |||||| |   |  ||| |   || ||||| | ||      |  ||  ||||||| |   || |||||| |  | || ||||||||||| ||||| |||||||| ||||| ||||| ||||| |||||||| ||||||||||| ||
-----------------------------------aggttttaggattaattttttttat----cacagtttctccctgattaagttgttatgttaacattctaatgttgtactaatg-atattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA

upper sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgattatactaattgtccagagaa--agtaccgaaattttgcagtgctaacatacagtttatgttcatttgtatattcat---tttctggctagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA
             |  |  ||   |    ||| |  | | | | | || |||||  | ||| |    |  |   ||||     || |   ||   ||   | |||     || | || ||| |  ||   |||||   |||| ||  |||||||||| | ||||||| | ||| |||| ||||||||||| || ||||||||||| ||||| |||||||||||||| || || || |||||
----------gtactgcgtttttttttcttttctctttcatgattatt-attattattattattattattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA

upper sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 13
gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgattatactaattgtccagagaaagtaccgaaattttgcagtgctaacatacagtttatgttca-tttgtatattcat---tttctggctagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA
                            |||| || | ||||  | ||  | ||  | ||| |        |||||     || |   ||   ||   | |||  |||||||  || || ||  ||   |||||   |||  ||  |||||||||| | ||||||| | ||| |||| ||||||||||| || ||||||||||| ||||| ||||||||||| || || || || |||||
---------------------gtactgcatttttttttcttttctatt--tcatgattattatt----attagtacttgttttctattgttgaaattgatagta-atgttcaacttatacatcaatatttttctttgtagGGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACCGGCTCGGGAAAGACATA

upper sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G33390.1 (Glycine max), 3'ss of exon 9
----------gtaagaataaaagcgacacttaag--tgaaatttgttgtgctttagtgttgattatactaattgtccagagaaagtaccgaaattttgcagtgctaacat---acagtttatgttcatttgtatattcatt-ttctggct-----agATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA
           ||     |  |    |  ||| |  |  |||         |||  |  | || ||||||  | |  | | | | | || |  | |||   |    |  |   ||| |||||  |  | |  ||  | |||  |||   |     || |||||| |     || || ||| |  | ||  ||||||| |||||||| | |||||| ||||| ||||| ||||| || ||||| ||||||||||| ||
gtttatttctatatactcaccatttgccattaggctttgaatggaaaaacattttttcattataatactacctatttatatagact-ccaatttcttgttatttggattttttacactttattgttgtgttgattgttattactctaaatgatgcagCTGAGGTGTATGCTGACATACAAGCCTTTATACGATCAGTACTTGATGGGTTTAATGTATGTATATTTGCTTATGGCCAGACTGGTTCAGGGAAAACTTA

upper sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA05G35130.1 (Glycine max), 3'ss of exon 11
gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgattatactaattgtccagagaaagtaccgaaattttgcagtgctaacatacagtttatgttcatttgtatattcattttctggctagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA
                   |||||   ||||| ||   |     |  |   | |  || ||||          ||    ||  ||  | || |    |||   | || || | ||| ||| |            ||  ||||||| |   || |||||| |  | || ||||||||||| ||||| |||||||| ||||| ||||| ||||| |||||||| ||||||||||| ||
----------------gttttaagattaatttttttaacacagtttctcccttttttagttgt----------tatgttaaccttctaatgttg---tactaatgatattaaattgaataat----------gcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGGTATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA

upper sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G73860.1 (Arabidopsis thaliana), 3'ss of exon 12
----gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgattatactaattgtccagagaaagtaccgaaattttgcagtgctaacatacagtttat--------gttcatttgtatattcattttctggctagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA
    ||     |   | ||   ||    |  |   |  ||   || |||  || ||    | ||      |||||   |  | |  | |  ||   ||| ||    || ||        |||||||||    ||    |||| || || ||| || ||    || ||   ||| ||  |||| ||||| |||||||| || ||||||||||| ||||| ||||| || || |||||||||||||| ||
gtgtgttcatctgttaccggttctgttatatatccttatgcttttcagttctgttttgtgtgatctatgcgagaattcatggtacatctcgagaaataatattatattgatatcaccaagttcatttgatattttggattcttgc-agCTGACGTCTTTTCAGACATAAGACCGCTGGTTAGGTCAGTACTTGATGGGTACAATGTTTGTATATTTGCATATGGCCAGACAGGATCAGGGAAAACTTA

upper sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgattatactaattgtccagagaaagtaccgaaattttgcagtgctaacatacagtttatgttcat-ttgtatattcattttctggc-tagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA
                                                | ||| ||   || |||     | |||  |  |   |      |||  ||| |  | || ||||| |  |  ||   || |||    |||| ||||| |||   || | || |||| ||||| ||||  ||||||||||||||||||||||||| ||||| |||||||| ||||| || || ||||| ||
------------------------------------------------gtttaaacctctt-tccctcttatgtattgttagcgttttcctctataatata--tgatattcatatcctgaatctgttatcttatgtagAGGAGGTTTTCTTAGATACTCGACCATTAATTCGATCCATTCTTGATGGCTATAATGTTTGTATATTTGCCTATGGTCAGACTGGTTCTGGAAAAACTTA

upper sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgattatactaat-tgtccagagaaagtaccgaaattttgcagtgctaacatacagtttatgttcatttgtatattcattttctggctagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA
    |  |      |          ||| |||  |    | || | ||  ||  | |  | ||| |   | |   | | |||           ||| ||||   ||||||    |||||| ||    |||| || || |||||||||    || ||  |||| || ||| ||||||||||||| || || ||||| ||||| ||||| |||||||| || |||||||||||||| ||
----gtgttcttttgtttgcctgaggaatttttcttcaatatactttttgttggattggtgtgttcttgggactaatcaaaa-------aaattaatatac---ttatgtc--attgtatcttttaattcttgc-agCTGAGGTATTTTCAGATATAAAACCTCTTATTCGATCAGTTCTTGACGGGTACAATGTATGTATCTTTGCATATGGTCAGACAGGATCAGGGAAAACTTA

upper sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv17s0000g03700.t01 (Vitis vinifera), 3'ss of exon 12
gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgattatactaattgtccagagaaagtaccgaaattttgcagtgctaacatacagtttatgttcatttgtatattcattttctggctagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA
                             ||| |  | | |||   || || ||    ||   |  ||  |  |  |    |||         |  |||  | ||   |    || |   |  |   | |   ||| |||||| ||    || | ||||||  |  |  |||| |||||||||||||||||||| ||||| ||||| |||||||||||||| || || || |||||
----------------------------gtttttcat-ccttatattttataatttggat--ccttgaatagatctc----tttcaagaaatcattataatgcttgactcatattatgcttggaaaatgtttgtagCTGAGGTGTTTTCTGACACTCAACCCTTGGTACGATCTGTTCTTGATGGCTATAATGTATGTATATTTGCTTATGGTCAAACTGGTTCGGGCAAGACATA

upper sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 14
gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgat-tatact-aattgtccagagaaagtaccgaaattttgc--agtgctaacatacagtttatg---ttcatttgtatattcattttctggctagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA
|| |   |   |   | | ||   |  | || |   || ||   | ||  | ||| || |  | || |    |  || |    |||||    |    ||| |  |  |||     || |||||||||| |||| | |    ||| ||||||||    || | ||||||| ||||| |||| || |||||||| || ||||| ||||| ||||| |||||||||||||| || || ||||| ||
gttatcttctta-taatattt---tatatttggccttgtttctttatttgtatatcctcagatttctattccacttagcatgcttttgttaggaaagaacttttaacttactacctttatttgtatatacattgtgttatcagAGGAGGTATTTTTAGACACTCAACCATTAATTCGATCTGTACTTGATGGATACAATGTCTGTATATTTGCCTATGGTCAAACTGGCTCTGGAAAAACCTA

upper sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ19920 (Selaginella moellendorffii), 3'ss of exon 8
gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgattatactaattgtccagagaaagtaccgaaattttgcagtgctaacatacagtttatgttcatttgtatattcattttctggctagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA
                                                                                   | | |  |||  | |  |  |    || || | || | |   | | |    |||  | ||||||  ||| | ||| ||| | ||  | |||||||||||||| || || || ||||||||||||||||||||||| || || || ||||| ||
----------------------------------------------------------------------------------gtagtaaagcttccgttaaagtc---ttgatgtataaacttgatatgtttgcagAACAAGTATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTA

upper sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ12333 (Selaginella moellendorffii), 3'ss of exon 8
gtaagaataaaagcgacacttaagtgaaatttgttgtgctttagtgttgattatactaattgtccagagaaagtaccgaaattttgcagtgctaacatacagtttatgttcatttgtatattcattttctggctagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA
                                                                                   | | |  |||  | |  |  |    || || |  | | |   | | |    |||  | ||||||  ||| | ||| ||| | ||  | |||||||||||||| || || || ||||||||||||||||||||||| || || || ||||| ||
----------------------------------------------------------------------------------gtagtaaagcttccgttaaagtc---ttgatgtagaaacttgctatgtttgcagAACAAGTATTCCTGGATACTCAGCCATTGATACGGTCAGTTCTTGATGGTTACAACGTGTGTATTTTTGCGTATGGTCAAACAGGCTCGGGAAAAACGTA

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: 67 (upstream exon), 19 (downstream exon)
Score: 4

GATAATGGTGAACTAATTTTAGCAAATCCTGCAAAACGAGGAAAGGAAGGACATAAGTTGTTCAAATTCAACAAAGTTCTTGGCCCCTCTGCTAGTCAAGgtaagaataa ... ttctggctagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcagtgctaacatacagtttatgttcatttgtatattcattttctggctagATGAGGTATTCAAGGAAATTCAACCACTAATTAGATCAGTTCTTGATGGCTATAATGTTTGTATTTTTGCGTATGGTCAAACTGGATCAGGGAAAACATA
        tgctaac  putative branch site (score: 4)
                                       ttcattttct  putative PPT
                              atttgtatattcattt  TA-rich tract