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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCTGCTCAGTGAGAACGACGACTGGGACCTGCAGCCTGGTGGCCGCTACTTCTTCACGCGCAACATGTCCTGCTTGATTGCCTTTGCAGTAGGGGAAAAgtaagtcagcgacattggcttctgattatttaacttatcactaagaatctgcaacgaatgtggtgttcaaataccatttgaaagtcaatgcctttgattt...

Basic information

species Oryza sativa
transcript LOC_Os01g73680.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73680.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G32790.1 (Glycine max), 5'ss of exon 1
CGCTGCTCAGTGAGAACGACGACTGGGACCTGCAGCCTGGTGGCCGCTACTTCTTCACGCGCAACATGTCCTGCTTGATTGCCTTTGCAGTAGGGGAAAAgtaagtcagcgacattggcttctgattatttaacttat--cactaagaatctgc--aacgaatgtggtgttcaaataccatttgaaagtcaatgcctttgattt
   |||||   |||||| |||||||| ||||  |||| || || |||||||||||||| |||||||||||||| ||| |||| || ||  | || || |||| |||   |  | ||     |    | | |   || |  |  || |  | ||    |||   || || ||    ||                           
ACATGCTCGACGAGAACCACGACTGGCACCTCAAGCCCGGCGGACGCTACTTCTTCACCCGCAACATGTCCTGTTTGGTTGCTTTCGCCATCGGAGATAAgtcagttcacttctttcttcgccttctctcttctttgttccgttacggttttgtttgacggg-gtcgtttttgcctag--------------------------

upper sequence: LOC_Os01g73680.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA10G34800.1 (Glycine max), 5'ss of exon 1
CGCTGCTCAGTGAGAACGACGACTGGGACCTGCAGCCTGGTGGCCGCTACTTCTTCACGCGCAACATGTCCTGCTTGATTGCCTTTGCAGTAGGGGAAAAgtaagtcagcgacattggcttctgattatttaacttatcactaagaatctgcaacgaatgtggt--gttcaaataccatttgaaagtcaatgcctttgattt------------------------------------------------------------------------------
   ||||||  || ||| | |||||| ||||  |||| || || |||||||||||||| |||||||||||||| ||||| || || ||  | || || |||| ||    |   | |  ||||   || | |   ||||   |    |||  |||    | | ||  |||         ||||  ||  |  |  |   ||                                                                                
ACATGCTCAACGAAAACAAAGACTGGCACCTCAAGCCCGGCGGGCGCTACTTCTTCACCCGCAACATGTCCTGTTTGATCGCTTTCGCCATCGGAGATAAgtcagctcactttactt-cttcaccttctctcttttatttttctttatcgccaaatgttattgttagtttgttagttttttgttagcgagggattcgaatccctccctcccttctctgtagtatactttgttccgttacggttttgtgctgttttgtttgacgccgttgtttttgcctag

upper sequence: LOC_Os01g73680.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT5G04710.1 (Arabidopsis thaliana), 5'ss of exon 2
CGCTGCTCAGTGAGAACGACGACTGGGACCTGCAGCCTGGTGGCCGCTACTTCTTCACGCGCAACATGTCCTGCTTGATTGCCTTTGCAGTAGGGGAAAAgtaagtcagc-gac---attggcttctgattatttaacttatcactaagaatctgcaacgaatg-tggtgttcaaataccatttgaaagtcaatgcctttgattt------------------------------------------------------------------------------
  || |||||||| ||||| |||||| | ||| | ||||||||||| |||||||| || || ||||||||||| ||| |||| ||||| || || ||||||| ||||  | ||    |||    |   ||  | |||  | |   |  |  |    || ||||  |||   |     |   ||||| | |  | |  ||                                                                                    
ATCTCCTCAGTGAAAACGAAGACTGGAATCTGAAACCTGGTGGCCGTTACTTCTTTACACGAAACATGTCCTGTTTGGTTGCTTTTGCTGTCGGAGAAAAgtgagtcttccgattcaattatgcttccatggtataagatttggtttggctttgataatgaatcctggaactagttcaagctttgataattgaagggttcttcacaaaaatcgttttttttttctttcttagattccttatttgttgggttcagggaacctacatttgttcctcattttgtag

upper sequence: LOC_Os01g73680.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv13s0106g00700.t01 (Vitis vinifera), 5'ss of exon 3
CGCTGCTCAGTGAGAACGACGACTGGGACCTGCAGCCTGGTGGCCGCTACTTCTTCACGCGCAACATGTCCTGCTTGATTGCCTTTGCAGTAGGGGAAAAgtaagtcagcgacattggcttctgattatttaacttatcactaagaatctgcaacgaatgtggtgttcaaataccatttgaaagtcaatgcctttgattt----
 | || | | |||||| || || ||||||||   |||||||||||||||||| |||||||| ||||||||  | ||| ||||||||||  | || ||||||| |||  |  |  |     | |||    | | |   |     || ||||   ||    |  ||  | ||  | |  | || ||  ||       ||       
AGTTGTTAAATGAGAATGATGAATGGGACCTAAGGCCTGGTGGCCGCTACTTATTCACGCGGAACATGTCTAGTTTGGTTGCCTTTGCCATTGGAGAAAAgtgagt--gtaaattaacactttgaactctcagcac-ttgaggaggatctatgacactagatgtactgaagcaac-ctagagagcaaactttcaagagacccac

upper sequence: LOC_Os01g73680.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S2_377V6.1 (Physcomitrella patens), 5'ss of exon 4
CGCTGCTCAGTGAGAACGACGACTGGGACCTGCAGCCTGGTGGCCGCTACTTCTTCACGCGCAACATGTCCTGCTTGATTGCCTTTGCAGTAGGGGAAAAgtaagtc---agcgacattg-gcttct----gattatttaactt-atcactaagaatctgcaacgaatgtggtgt---tcaaataccatttgaaagtcaatgcctttgattt----------------------------------------------------------------------
 ||   | |  ||| |  | || |||    ||||||| |||||||||||||||||||| || |||||||||| | |  |||| |||||  | ||  |||||||||     ||  |||||   |||||    ||| | |||   | |||  |  |||   | ||  | | |   |    |  | || ||      |     | |     ||                                                                        
AGCAATTGAACGAGGAACAGGAGTGGACAGTGCAGCCCGGTGGCCGCTACTTCTTCACTCGGAACATGTCCTCCATCTTTGCATTTGCCATTGGACAAAAgtaagcttgtagtcacatttcacttcttgtggatcagttattgtgatctttgtgaactcggaagtagtatcccgcaaatttagtagcacagtgcaacggttactccaaatccttatgtcatattttagtatttatcaattgttgttttcttgttggacctgtcttgtttatgtgcaacacag

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: 57 (upstream exon), 72 (downstream exon)
Score: 6

CGCTGCTCAGTGAGAACGACGACTGGGACCTGCAGCCTGGTGGCCGCTACTTCTTCACGCGCAACATGTCCTGCTTGATTGCCTTTGCAGTAGGGGAAAAgtaagtcagc ... ttggacgcagGTACAAATTGGGAAATGGGTTCAATATAATTGCGGCTCACACCGATAGCCCATGTCTCAAGCTGAAACCAAGGTCTGCCTCCTTTAAATCTGGGCATCAA




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