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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtttcattttgtgctgaacaagcatatgcatttttcttgataattatttcaagaacacattcgcatcaagatacaatctcactgtgttaaatgttaactgcattgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA

Basic information

species Oryza sativa
transcript LOC_Os03g12950.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G063994_T01 (Zea mays), 3'ss of exon 3
gtgtttcattttgtgctgaacaagcatatgcatttttcttgataattatttcaagaacacattcgcatcaagatacaatctcactgtgttaaatgttaactgcattgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA----------
                            | | |||  |  ||  | |||  ||        | |      ||| |   ||||| |||   | | | ||||||||||||||||| |||||||| |||||||||||  |||||||||| ||||| ||||| ||||||||  | || |||| |||||| |          
---------------------------gttcgtttgcccagactactatgccaccgcattttgcttccttagagatcgtctcaatgt---acacgctaactgcattgcagGCACCACCAGCAAGGAAGATGGCAGTCTCGGATTGGAAGGGTCGCTGGAAACAAGGATCTATACCTCGACACTTTTAGTAAGAAAGA

upper sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G021573_T02 (Zea mays), 3'ss of exon 6
gtgtttcattttgtgctgaacaagcatatgcatttttcttgataattatttcaagaacac---attcgcatcaagatacaatctcactgtgttaaatgttaactgcattgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA
  |||    | ||    ||    ||    |||| |  |||  | ||||||    | |||    |      | |||| |   ||||| ||    | | | ||||||||||||||||| |||||||| |||||||||||  |||||||||| || || ||||| ||||||||  | || |||||||||||||
--gttcgtctgtgcagggattgcgccaccgcatctcgcttccttattattgtgcggacaactaacgtaagtgaagagatcgtctcaatgc---acacgctaactgcattgcagGCACCACCAGCAAGGAAGATGGCAGTCTCGGATTGGAAGAGTCGCTGGAAACAAGGATCTATACCTCGGCACTTTCA

upper sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA04G05080.1 (Glycine max), 3'ss of exon 7
gtgtttcattttgtgctgaacaagcatatgcatttttcttgataattatttcaagaacacattcgcatcaagatacaatctcactgtgttaaatgttaactgcattgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA
         || |||  |  |   |     | |||||||| || | || |  ||    |  ||        |   |||  | | | |  | ||| |||     ||| |||||||||||| |||||||||||||||||  |||| ||||| |||||||| ||||| ||| | || || || || ||||
--------gttggtgtggttctgccc----cctttttcttcattagtagtggaactttagtttgatgatttgtgtcaagtttatttt--ttaatattattattatt-cagGCATCACCAACATGGAAGATGGCAAGCGAGGATAGGCAGAGTTGCTGGGAACAAAGACCTTTACCTTGGGACGTTCA

upper sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G05170.1 (Glycine max), 3'ss of exon 8
gtgtttcattttgtgctgaacaagcatatgcatttttcttgataattatttcaagaacacattcgcatcaagatacaatctcactgtgttaaatgttaactgcattgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA
         || |||  |  |   | |   |  |||| ||  || | ||   |   | || |  |  | | |||      | | | | ||   |  ||     ||| |||||| ||||| |||||||||||||||||  |||| ||||| |||||||| ||||| ||| | || || || || ||||
--------gttcgtgtggttc--tcctgcaccctttttttattagtaataatagtgatacttcagtttgatgatttgtgttaagtttattttttaatattattatt-cagGCACCACCAACATGGAAGATGGCAAGCGAGGATAGGCAGAGTTGCTGGGAACAAAGACCTTTACCTTGGGACATTCA

upper sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 6
gtgtttcattttgtgctgaacaagcatatgcatttttcttgataa---ttatttcaagaacacattcgcatcaagatacaatctcactgtgttaaatgttaactgcattgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA
  | |    |||   | | | | ||||    ||||    | | ||   |||   | |||  | | |   |    | |  || |||| |   ||     ||||||   | ||||||| ||||| |||||||| ||||||||||| ||||| ||||| || || ||||| ||  | ||||| || || || |
--gctagcatttacacagtatatgcattgtaatttaatgtaacaagatttacacctagagaagaatta-actttgttctaaactcagttgattctg-attaacttggtagcagGCACCACCAACATGGAAGGTGGCAAGCTCGAATTGGAAGGGTAGCCGGAAACAAAGATCTATATCTTGGAACCTTTA

upper sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT4G37750.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgtttcattttgtgctgaacaagcatatgcatttttcttg-ataattatttcaagaacacattcgcatcaagatacaatctcactgtgttaaatgttaactgcattgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA
                        | | |  |||    ||  |||| | | |  |  ||| | |   |  ||  |  |   | ||| |||   | |||   || | |  || ||||||||||||||||| |||||||| |||||||| || || ||||| ||||| ||  | || || || |||||  
---------------------gtccttttaaattacatttatataactttatataatacatagtt-taataatgtgaatattgactttgtgtga-gttttttgtact--agACATCACCAGCATGGAAGGTGGCAAGCACGGATTGGTAGAGTCGCTGGAAACAAAGATCTCTACCTTGGAACTTTTG

upper sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 7
gtgtttcattttgtgctgaacaagcatatgcatttttcttg---ataattatttcaagaacacattcg---catcaagatacaatctcactgtgttaaatgttaactgcat---tgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA
        |||| | || |   | | | |   || | || |      ||| ||  |  |  | | | |   | | || || |  | |   | ||||   | ||   |   |   | ||||||||| || |||||||||||||| ||||||||||| ||||||||||| ||||||||| | |||||||| || ||||
-------gttttattcttatataacttcttttttctcctagcacgccattgttcaagcattaaagttggccccttaaaattctttttttgtttgtttttttttttttttttaaatacagGCATCATCAACATGGAAGATGGCAGGCTCGGATTGGGAGGGTTGCTGGAAACAAGGACCTTTATCTCGGGACATTCA

upper sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv07s0151g00440.t01 (Vitis vinifera), 3'ss of exon 6
---gtgtt-tcattttgtgctgaacaagcatat-gcatttttcttgataattatttcaagaacacattcgcatcaagatacaatctcactgtgttaaatgttaactgcattgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA
    |  | | ||||| |||| |     ||| | | | || | |||  |  |  |   |||  | |  || |  || || |  |   |     ||     ||   | | | |||| |||||||| |||||| | ||||||||||| |||||||| ||||| || ||||||||| | ||||| || || ||||
gtcttactattattttctgcttatgtctcatcttgtaattgtattgtcatgttctctgagagaaaaggcgaaaaaaaatcccctgaaatctctttcctgcttcgattcttagcagACATCACCAACATGGACGGTGGCAAGCTCGAATTGGCAGAGTTGCAGGGAACAAGGACCTTTATCTTGGGACATTCA

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: 30 (upstream exon), 21 (downstream exon)
Score: 1

GAGAAGCAGCGGGTTCTCTCGCGGTGCTTCCATCTACCGGGGAGTAACAAGgtgtttcatt ... tgcattgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacacattcgcatcaagatacaatctcactgtgttaaatgttaactgcattgcagGCATCACCAGCATGGAAGATGGCAAGCTCGGATTGGCAGGGTTGCTGGCAACAAGGACTTGTATCTCGGCACTTTCA
                                      tgttaac  putative branch site (score: 1)
                                 ttaaatgttaa  TA-rich tract