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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACAgtatgtgttattgcttttcttacatgaacttgccaaagtacaaatacagaataatcaactaaggtttcctttccacaatctcaccatgttatgaatttgtctggaag

Basic information

species Oryza sativa
transcript LOC_Os01g56630.2
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G079389_T01 (Zea mays), 5'ss of exon 14
GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACAgtatgtgttattgcttttcttacatgaacttgccaaagtacaaatacagaataatcaactaaggtttcctttccacaatctcaccatgttatgaatttgtctggaag
|| ||||||||| | ||||||||||||||||| ||| ||||||| ||||||||||| || |||| |||| |||||||||| || ||||||||||||  ||  | || |||  | ||| ||| |  |||||||    ||     ||   | |     | ||   |||| | |    ||| || || |  || ||  ||
GTTGTGTATGCTGTATTGCATCGACAAGAGGTGTTTGAGCCATTTAAAAACCATCCACGTTTCAGTGAACTGCTTGAGAACATATACACAgtatgt--taccgattatctctcgtgatctttcagaagtaca----caattctattttccaga---ttctcatcacattgt----atgctacgagt--gtttgatag

upper sequence: LOC_Os01g56630.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G078576_T04 (Zea mays), 5'ss of exon 14
GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACAgtatgtgttattgcttttcttacatgaacttgccaaagtacaaatacagaataatcaactaaggtttcctttccacaatctcaccatgttatgaatttgtctggaag
|| || |||||| | ||||||||||||||||| ||| ||||||| ||||| ||||| || || |||||| |||||||||| || ||||| |||||||||||||  ||| || |   |||||       || || |||| | ||||| | |     ||||        |||  |  || || |||   ||||||  ||
GTTGTATATGCTGTATTGCATCGACAAGAGGTTTTTGAGCCATTTAAAAATCATCCACGTTTTAATGAACTGCTTGAGAACATATACACTgtatgtgttattg--tttattgc---aacttt------tataagtacacattaatctatt-----ttccagattctcatcatattatattctgag--tgtctgatag

upper sequence: LOC_Os01g56630.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA20G28880.1 (Glycine max), 5'ss of exon 13
GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACAgtatgtgttat---tgcttttcttacatgaacttgccaaagtaca--aatacagaataatcaactaaggtttc----------ctttccacaatctc--accatgtta-tgaa-tttgtctggaag------------------------------------------------------
|| |||||||| ||  ||||  | || || || |||||||||||||| || ||||| || ||||||||| || |||| || ||||| || |||||||| ||   || |||  ||| |||||  | ||||| ||     |  |     ||||   |||  |||            |||   | ||||     ||  ||| ||||  ||||||                                                           
GTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAATCATCCACGTTTCAATGAACTGATTGATAACATTTATACTgtatgtgtcatatatgttttatttaaatgaaagtaccaaaatatgctgaccctttgcaatcttgtaacttttaaaggagcaagttttgtgctatctttagtcacattaatgaagcttgtctttgtataataaatcatgtttctcaagtgtgtgcaaaatgtatctattaaatatttacag

upper sequence: LOC_Os01g56630.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA10G38920.2 (Glycine max), 5'ss of exon 14
GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACAgtatgtgttat-tgcttttcttacatgaacttgccaaagtacaaatacagaataatcaacta-aggtttcctttccaca-atctcaccatgttatgaatttgtctggaag
|| |||||||| ||  ||||  | || || || |||||||||||||| || ||||| |||||||||||| || |||| || ||||| || |||||||| || |   ||| |||  |  |  |||  || |   | | |   ||  | || || ||   |    ||| || || | |  ||  ||| | |||         
GTAGTGTATGCAATAATGCACAGGCAGGAAGTCTTTCAGCCATTCAAGAATCATCCACGCTTCAATGAACTGATTGATAACATTTATACTgtatgtgtcatatatattttttaggtttaaatgc--aattttgattcccttattttaaaatagagacatttagtcctcatattttaatat-ctataattttag-------

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|426809|gb|D22882.1|D22882
EST:     CATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACA                         GTGTTGGATTTCTTCAATAGTCGAATGGNCATGCAGCAGTTAGATGGNGAA
genomic: CATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACAgtatgtgtta ... tgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
EST: gi|58678344|gb|CK067031.1|CK067031
EST:     CATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACA                         GTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
genomic: CATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACAgtatgtgtta ... tgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
EST: gi|5004229|gb|AU069378.1|AU069378
EST:     GAGAATATTTACACA                         GTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
genomic: GAGAATATTTACACAgtatgtgtta ... tgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
EST: gi|29639051|gb|CB644060.1|CB644060
EST:     CATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACA                         GTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
genomic: CATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACAgtatgtgtta ... tgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
EST: gi|5004218|gb|AU069367.1|AU069367
EST:     GAGAATATTTACACA                         GTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
genomic: GAGAATATTTACACAgtatgtgtta ... tgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
EST: gi|86497820|gb|CI140453.1|CI140453
EST:     TCAATGAATTGCTTGAGAATATTTACACA                         GTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
genomic: TCAATGAATTGCTTGAGAATATTTACACAgtatgtgtta ... tgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA

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: 50 (upstream exon), 72 (downstream exon)
Score: 7

GTCGTGTATGCTATCTTGCATCGACAAGAGGTATTTCAGCCATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACAgtatgtgtta ... tgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAATGGTCTGTAGATAAGGTTCTTGAGGTTATTAACAAAAACTGCCGTTCAT




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