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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctatgtgatatagctcttctgattggtcattgtctcatgtgcttatgtacattacccag

Basic information

species Oryza sativa
transcript LOC_Os05g44922.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctatgtgata--tagctcttctgattggtca--ttgtctcatgtgcttatgtacattacccag
|||||||||||| |||||||| ||||||||||| |||||||| |||||||||||||| |||||||||||||| |||||||| ||||||||||| || ||||||||   | |||     |   || | | |  || |||||||||||||  |  ||| || || | ||   |  | ||| ||||
TGACATCCACAAAAGGGGTGGTACAGTTCTTGGAACATCACGCGGTGGCCATGATACCAAAAAGATTGTTGATAACATTCAAGATCGTGGAATCAACCAGgtaaacatgattgcacctattgatataacacataactcttctgattggagaagttgactgatatactagagcgccttatccag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA05G36050.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctat-gtgatatagctcttctgattggtcattgtctcat--gtgcttatgtacattacccag-------------
||| || || ||| | || || ||  | |||||  ||||||||||||| ||||| || |  ||||| |||||||  ||||| ||||| ||||||||||||||   |||  |   ||  |  |||    | |||   ||||   |||    | ||  |||  ||  |    || ||||| ||              
TGATATACATAAGCGTGGGGGAACTATCCTTGGTTCATCACGAGGTGGACATGACACCACTAAGATAGTTGACAGTATTCAAGATCGGGGAATTAATCAGgtc--tgcattgcattctatttattacaacatataacttcattttgtatgtagtaacatcagtagtctaataaattactcaatcaattccaccag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G15170.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctatgtg-atatagctct-tctgattggtcattgtctcatgtgcttatgtacatta--cccag
||| || || ||| | || || || || ||||| |||||||||||||| ||||| || |||||||| |||||||  ||||| ||||| ||||| ||||||||   |||  || |||  |  ||   | |||||  | | | ||    || | |   |||  |   ||| |   | |    |||
TGATATACATAAGCGTGGGGGAACTGTCCTTGGAACATCACGAGGTGGACATGACACCAAAAAGATAGTTGACAGTATTCAAGATCGGGGAATCAATCAGgtc--tgcacttctttcaatgtagcagtatatatttttgtgtgccgtgtaagtacatcagattaatatctctctgaatttcag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G03570.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctat---gtgatatagctc--ttctgattg-------gtcattgtctcatgtgcttatgtacattacccag
|||||| || ||| | || || ||  | |||||  ||||||||||||| |||||||| |  ||||| |||||||  ||||| ||||| ||||||||||||||   |||  ||  ||  |  |||      || || ||   || ||  ||        |||       |    || ||  |  |   ||||
TGACATACATAAGCGTGGGGGAACTATCCTTGGTTCATCACGAGGTGGACATGATACCACTAAGATAGTTGACAGTATTCAAGATCGGGGAATTAATCAGgtc--tgcatttcattctatttattacaacatgtaacttcattttgtatgtataaaaatcagcagtctaataactcattcaattccaccag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G01710.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAGAGG-GGTGGGA--CAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgc--ggttgtttgcacctatgtgatatagctcttctgattggtcattgtctcatgtgcttatgtacattacccag
  || |  |  |  |  | | | |  |||     || |  | |  ||||   |||  |    |  |||| |    ||  |    || |  ||  |||  | |||||| ||      || | | |   | |  |  |   | || |      | |  || |  | |  ||    |||        
-TACGTTAAAGATTGTTGATAGCATCCAGGATCGGGGAATTAATCAGGTTTACATACT-TGGAGGAGATGGAACTCAG-AGAGGGGCTTCTGTGATTTTTGAGgtaattgttaaaatgctggtatgca-gaaagttgatttttttaggcaattaaggttttgt-tatttgcacacag-------

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA06G09320.1 (Glycine max), 5'ss of exon 5
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctatgtgatatagctcttctgattggtcattgtc----tcatgtgcttatgt---acattacccag-----------------------------------------------------------------
||| ||||| ||| | || || ||  ||||||| ||||||||||| || ||||||||    ||||| ||||||| ||| |||||||| ||||||||||||||  |  |   |||  ||     | | ||  || |  |     || | | ||      ||||    |   ||       || |||                                                                  
TGATATCCATAAGCGTGGGGGTACGATTCTTGGGACATCACGAGGGGGGCATGATACTGGCAAGATAGTTGACAGCATCCAGGATCGAGGAATTAATCAGgtttac-catgtgtcagctgtattataatgaagtttctgatgatgatgaatgcgggaatcataaattagagttttgttatatccatgtacttaaaacctaagtaggttattgtcatcgcatgggttttcattgcttgggttatggttacag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA01G00870.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctatgtgatatagctcttctgattggtcattgtctca-tgtgcttatgtacattacccag
||| || || ||| | || || || || || || |||||||||||||| ||||| || |||||||| |||||||  ||||| ||||| ||||| ||||||||   |||  || |||  |  || |   ||  |    |      | | |   ||||  ||   ||  |            
TGATATACATAAGCGTGGGGGAACTGTCCTCGGAACATCACGAGGTGGACATGACACCAAAAAGATAGTTGACAGTATTCAAGATCGGGGAATCAATCAGgtc--tgcatttctttctattta-gcagtagtgtatgtacatcagattaacatctctctgaatttcag------------

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA15G02400.2 (Glycine max), 5'ss of exon 7
------------------TGACATCCACAA--GAGGGGTGGGACAGTT-------CTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCG---TGGAATTAATCAGgtaaatgcggttgtttgcacctatgtgatatagctcttctgat-tggtcattgtctcatgtgcttatg-tacattacccag-------------------------------------------------------------------
                  |  ||| ||  |  | ||  |    ||| |       |||||   ||   ||  |    ||||  ||   | |||| ||||    ||| |  |      | |  || |      | || | |||   |  | || |||  |   | | |  |||| |  | |    || |  || | ||   | ||   | |                                                                    
CACCTCAAAGATTGTTGATAGCATTCAGGACCGGGGAATTAATCAGGTTTATATACTTGGAGGATATGGAACTCAGTATGAAGCAGCTATGATTTTTGAGgtaattaataaatagactaggtttgagtgctgatattcagtttgctataactttgtatt--tgttttaatgatctactgacaaactaacttgatgataacatatgctctaaaagtttggtagatataataattttcactatttaaatttgtactcacaagattaagttatttatgcag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA04G09180.1 (Glycine max), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcggttgtttgcacctatgtgatatagctcttctgattggtcattgtc-tcatgtgctta----tgtacattacccag-----------------------------------------------------------------
||||||||| ||| | || || ||| ||||||| ||||| ||||| || ||||||||    ||||| ||||||| ||| |||||||| ||||||||||||||  |  |   |||   |     | | ||  || |  |     || | | ||   ||||    |||    | |    || |||                                                                  
TGACATCCATAAGCGTGGGGGTACAATTCTTGGGACATCCCGAGGGGGGCATGATACGGGCAAGATAGTTGACAGCATCCAGGATCGAGGAATTAATCAGgtttac-catgtgtcaactgtattataatgaagtttctaatgatgatgaatgcaatcataaatttagagttttgttatatccatgtacttaaaacctaagtaggttattgtcatcgcatgggttttcattgtttgggttatggttacag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G26270.1 (Arabidopsis thaliana), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgta--aatg-----cggttgtttgcaccta--tgtgatatagctcttctgattggtcattgtctcatgtgcttatgtacattacccag
||| ||||| ||| | || |||||  | ||||| || ||||||||||| || ||||| | |||||| ||||||| |||||| ||||| ||||| ||||||||    ||      |   | ||| ||||    | || |  |    | |  |        |   | ||||  || | | |||    |||
TGATATCCATAAGCGTGGAGGGACTATCCTTGGGACCTCACGAGGTGGTCACGATACCACAAAGATAGTTGACAGCATTCAAGATCGAGGAATCAATCAGgttttgataaccatcacctctttacaccgtgttctgttccaagagtacatacaaactcgttcttgatgtagtttttttcatcgttcag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgta---aatgcggttgtttgcacctatgt------gat-atagctcttctgatt-----ggtcattgtctcatgtgcttatgtacattacccag--------------------------------------------------
||||||||| ||  | ||||| || || |||||||||||| |||| |||||||||||   |||||| ||||||| ||||||||||||||| |||||||||||    || |   |  |||     | |||       || || | | || |||||       |     |   ||||||   |||| | | ||  |                                                  
TGACATCCATAAACGTGGTGGTACTGTCCTTGGCACATCAAGAGGAGGCCATGATACCTCAAAGATAGTTGACAGCATTCAGGATCGTGGGATTAATCAGgtgcctaaaggattaatttttcattgtgttccttaaatgatggttattatgatttctgaaattggaattctatgtgcagctgta-actgccagggcatgcaatttccatgcatgatgttgattcattttcttttgatgttccag

upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 5'ss of exon 6
TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgta-------aatgcggttgtttgcac---ctatgtgatatagctcttctgattggtcattgtctcatgtgcttatgtacattacccag--------------------------------------
||| || || ||  | || || ||  | ||||| |||||||||||||||||||||||   |||||| |||||||  ||||||||||||||||| ||||||||        ||| |  ||  |||  |    ||| |||   |    ||| || |  |   | | |  |   | |  | |||   |                                          
TGATATTCATAAACGTGGGGGAACCATACTTGGGACATCACGAGGTGGCCATGATACCTCAAAGATAGTTGACAGTATTCAGGATCGTGGAATCAATCAGgtctgtagacaatactatttcttgtccaagttatctgagtcacactttcggagttttgtgtatttgctacacctgggcacacctcttcaatgcatggacgttagatttatagctttgttgatctcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|569752|gb|D40601.1|D40601
EST:     ATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAG                         GTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTC
genomic: ATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcgg ... cattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTC
EST: gi|571842|gb|D41353.1|D41353
EST:     ATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAG                         GTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATTGAGATCTT
genomic: ATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcgg ... cattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATAT-GAGATCTT

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: 75 (upstream exon), 54 (downstream exon)
Score: 51

TGACATCCACAAGAGGGGTGGGACAGTTCTTGGCACATCACGAGGTGGCCATGATACAAAAAAGATTGTTGACAACATTCAGGATCGTGGAATTAATCAGgtaaatgcgg ... cattacccagGTCTATATCATTGGAGGAGATGGAACACAGAAGGGTGCATATGAGATCTTCAAG




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