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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgataagctcaagtatggtctttatatataccttaattagtatgtgccaaatgaaatacctgattacaaggctgttattcaatcaaaagGGGTCTGGTTGGAAAATTGTTGCAAGCTTTGAGGGGAAGTTTCCAGATAGGATCAAACAGCTTCCTTTGGACAGGCATTTTGATATTAACAATGTCAAAA

Basic information

species Oryza sativa
transcript LOC_Os02g50550.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA09G00430.1 (Glycine max), 3'ss of exon 8
----gttagtgataa---gctcaagtatggtctttatatataccttaattagtatgtgccaaatgaaatacctgattacaaggctgttattcaatcaaaagGGGTCTGGTTGGAAAATTGTTGCAAGCTTTGAGGGGAAGTTTCCAGATAGGATCAAACAGCTTCCTTTGGACAGGCATTTTGATATTAACAATGTCAAAA
     || |||| ||   | |    | | ||  | ||  |||    | ||  ||| ||     ||       |  | | |   || ||| | |    | |||| |||||||||||||||||| |  | ||||||||||  ||||| ||||| || || ||  | ||||| || |||||||||||||| |||||||| || |
agcatttggtgacaatttgttttcatgttgtgctaatgaataatgaattttatatatgttgcttgggcctttttttgatata-ctattaattatctgacagGGATCTGGTTGGAAAATTGTTTCTTGTTTTGAGGGGAGATTTCCTGATAGAATGAAGCAATTACCTTTAGATAGGCATTTTGATATCAACAATGTGAAGA

upper sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 8
---gttagtga---taagctcaagtatgg---tctttatatataccttaattagtatgtgccaaatgaaatacctgattacaaggctgttattcaatcaaaagGGGTCTGGTTGGAAAATTGTTGCAAGCTTTGAGGGGAAGTTTCCAGATAGGATCAAACAGCTTCCTTTGGACAGGCATTTTGATATTAACAATGTCAAAA
   |||||  |   | |  |   ||||||   ||     || |||  ||   || ||        |     | || | | |    || |||||   |   | ||    |||||||||| ||||||| || ||||| ||||| |||||  | || ||||| || |||||| | ||||| || ||||| || ||||||||||| |
gaagttagatactttgattttgggtatgggaatccaccaatgtacagta-caagaatcctattttttctgcatctaaattctttcct-ttatttccttgcagGGTAA-TGGTTGGAAAGTTGTTGCTAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATCGACAGACACTTTGACATAAACAATGTCAAGA

upper sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 8
---gttagtga---taagctcaagtatggtcttt-atatatacctta-attagtatgtgccaaatgaaatacctgattacaaggctgttattcaatcaaaagGGGTCTGGTTGGAAAATTGTTGCAAGCTTTGAGGGGAAGTTTCCAGATAGGATCAAACAGCTTCCTTTGGACAGGCATTTTGATATTAACAATGTCAAAA
   |||||  |   | |  |   ||||||  ||| |   ||    |  |  |  ||        |     | || | | |    || |  |||  |    ||||   |||||||||| ||||||| || ||||| ||||| |||||  | || ||||| || |||||| | ||||| || ||||| || ||||||||||| |
gaagttagatactttgattttgggtatgggatttcaccaatgtactgtacaaaaatccttttttttctgcatctaaattctttcctttatttc--tttgcagGGTAATGGTTGGAAAGTTGTTGCCAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATTGACAGACACTTTGACATAAACAATGTCAAGA

upper sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 8
----gttagtgataa---gctcaagtatggtctttatatataccttaattagtatgtgccaaatgaaatacctgattacaaggctgttattcaatcaaaagGGGTCTGGTTGGAAAATTGTTGCAAGCTTTGAGGGGAAGTTTCCAGATAGGATCAAACAGCTTCCTTTGGACAGGCATTTTGATATTAACAATGTCAAAA
     || |||| ||   | |    | | || || ||  |||    | |   ||| ||     ||  |    |  ||| |   || ||| | |      ||||  ||||||||||||||||| |  | ||||||||||  ||||| ||||| || || ||  | ||||| || |||||||||||||| |||||||| || |
agcatttggtgacaatttgttttcatgttgtgttaatgaataatgaattatatatatgttgcttgggacttttttttatata-ctattaattatctggcagGGAGCTGGTTGGAAAATTGTTTCCTGTTTTGAGGGGAGATTTCCTGATAGAATGAAGCAATTACCTTTAGATAGGCATTTTGATATCAACAATGTGAAGA

upper sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 8
gttagtgataagctcaagtatggtctttatatataccttaattagt-atgtgccaaatgaaatacctgattac----aaggctgttattcaatcaaaa---------gGGGTCTGGTTGGAAAATTGTTGCAAGCTTTGAGGGGAAGTTTCCAGATAGGATCAAACAGCTTCCTTTGGACAGGCATTTTGATATTAACAATGTCAAAA
         | | |   | || |  | | |    |   |      | ||||||  || |   |    |||| |    ||   | || |  ||| ||||         |||   |||||||||| |||||||||| ||||| || || || ||  || | |||||| ||||||| ||||| || ||||||||  | |||||||||||||
--------aaggtttttgaattgcatgtctggtgattgtgcccgttcatgtgctgaaggcctttttggatttcggtaaatatttttctctaataaaaatttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAA

upper sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 8
---gttagtgataagctcaagtatggtctttata--tatacct-taattagtatgtgccaaatgaaatacctgattacaaggctgttattcaatcaaaagGGGTCTGGTTGGAAAATTGTTGCAAGCTTTGAGGGGAAGTTTCCAGATAGGATCAAACAGCTTCCTTTGGACAGGCATTTTGATATTAACAATGTCAAAA
     |  | ||    ||   |   ||  |||||  |||| |  || |||||         ||    |     |||  |    |   ||| |      ||||  ||||||||||  | ||||| || ||||||||||| |||||  | |||||||| ||||| ||||| |||||||||||||| || |||||||||||||
caatatcataattctttcctatcctgtgcttatagttatagcaatatttagtgctatgattattcgttcttaaattttatatgttacatttacgtggcagGGTGCTGGTTGGAAGGTCGTTGCCAGTTTTGAGGGGAATTTTCCTAACAGGATCAAGCAGCTCCCTTTAGACAGGCATTTTGACATCAACAATGTCAAAA

upper sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 8
gttagtgataagctcaagtatggtctttatatataccttaattagtatgtgccaaa-tgaaatac--ctgattacaag--gctgttat----tcaatcaaaagGGGTCTGGTTGGAAAATTGTTGCAAGCTTTGAGGGGAAGTTTCCAGATAGGATCAAACAGCTTCCTTTGGACAGGCATTTTGATATTAACAATGTCAAAA
  |  |   |    |   |||   | || |  |  | |||   | ||      ||  ||   |||  |  ||||  ||  ||||| ||    |   |    ||||    ||||||||| |||||||||| ||||| || || || ||  | |||||||| ||||| ||||| || |  ||||||||||| |||||||||||||
--ttctagcattgactgctatcaaccttgtgcac-cattagacattacaacagaatctgttctactgcccattattagctgctgtcataaattttctttgcagGGTAGCGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAACAGGATCAAGCAGCTACCTTTAGATAAACATTTTGATATAAACAATGTCAAAA

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), 68 (downstream exon)
Score: 33

AGAACAGATGGTATCAAGCGCTGAAGGAACCAGGGCTGTTGCTTTGGAGCTTTGCCGTGAATTCGAAGACAAGTTTCTTGCCCATGTTACTTCTGGTGAGgttagtgata ... caatcaaaagGGGTCTGGTTGGAAAATTGTTGCAAGCTTTGAGGGGAAGTTTCCAGATAGGATCAAACAGCTTCCTTTGGACAGGCATTTTGATATTAACAATGTCAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattagtatgtgccaaatgaaatacctgattacaaggctgttattcaatcaaaagGGGTCTGGTTGGAAAATTGTTGCAAGCTTTGAGGGGAAGTTTCCAGATAGGATCAAACAGCTTCCTTTGGACAGGCATTTTGATATTAACAATGTCAAAA
                       acctgat  putative branch site (score: 33)
                                        ttattcaatcaaaa  TA-rich tract