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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaagacctttgttgacacttctgttactctgctcacttttagctcttctagtttacatgatttctgatgtactttacactcag

Basic information

species Oryza sativa
transcript LOC_Os02g04490.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g04490.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G470556_T01 (Zea mays), 5'ss of exon 10
GTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaagacctttgttgacacttctgttactctgctcacttttagctcttctagtttacatgatttctgatgtactt-tacactcag
||||||||||||| ||||||||||| || |||||||||||||| || || ||||||||||||||||| |||||||| ||||| |||||| || | |||||||||| |||| | ||    | |  ||  |||  |  ||||||| || || |   |   | || |||  |   ||| | ||| |||
GTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGACAAACTGCGTGAGTGgtaag-ccttaggtg----tccaattggtcttgttgcttttagatcctccaccatttctaatgtcttttactcttatccacccag

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G139977_T02 (Zea mays), 5'ss of exon 4
GTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaagacctttgttgacacttctgttactctgctcacttttagctcttctagtttacatgatttctgatgtactttacactcag
||||||||||||| || |||||||| || |||||||||||||| || || ||||||||||||||||| |||||||| ||||| || ||| || | ||||||||||  | ||   |||||     ||  |||  |  ||||||| || ||       ||  | |||| ||||  ||||||| |||
GTTACATATGGGCTTGTCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATCCTGAGATTCAAAAGACTCCGAAATCTGATAAACTGCGTGAGTGgtaag--ccttagagacaca---attgatcttgttgcttttagatcctc-------caccagttctaatgtcttttacacccag

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA07G00230.1 (Glycine max), 5'ss of exon 11
GTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaag-------acctttgttgacact---tctgttactctgctcacttttagctcttctagttta-catgatt---tctgatgtactttacactcag-----------------------
| || || ||||| || || || ||||| || |||||||| ||||| || |||||||| || |||||||| || ||||||||||| ||  |  | || |||| ||        | |  ||  | ||    |  |  |      |  || ||   | | || ||  |   |||||   | |  |   || ||   ||||                       
GCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATCCAGAAATTCAGAAAACCCCAAAATCCGATAAGCTACGTGAATGgtgagcgtaatagcttcagtatatacaaaatgagaaaaaaacttgtctatttattttccttgtacaatgtgattaggtttattcatctctaacttcagcatttgtcaacatgtttctgcag

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA08G24290.1 (Glycine max), 5'ss of exon 13
GTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaagacctttgttgacacttctgttactctg--------ctcacttttagctcttctagttta-catgatttc-tgatgta-ctttacactcag-----------------------
| || || ||||| || || || ||||| || |||||||| ||||| || |||||||| || |||||||| || ||||||||||| ||  |  | || |||| || |   |     || |   |  |   ||         |  || ||   | | || ||  |   |||||   | || || || ||   ||||                       
GCTATATCTGGGCCTGTCCTCCATTAAAGGGAGAAGATTATATTTTATATTGCCATCCAGAAATTCAGAAAACACCAAAATCCGATAAGCTACGTGAATGgtgagcctaatagcttcagtatagacaaaatgaaaaaaagttgtctatttattttccttgtacaatgtgattaggttatttatctctaacttcagcatttgtaaacatgtttcttcag

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA15G00250.1 (Glycine max), 5'ss of exon 11
GTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaag------accttt--gttgacacttctgttactctgctcacttttagctcttcta-gtttacatgatttctgatgtactttacactcag-------------------------------
| ||||||||||| || || || ||||| ||||||||||| ||||| || || ||||| || |||||||| ||||||||||| || ||  | ||||| |||||||      | |||   | | |   |  ||  |   ||        ||  | || ||  | ||||  ||     | |||||     || |                                
GCTACATATGGGCATGTCCTCCATTAAAGGGTGAAGATTATATTTTATATTGTCATCCGGAAATTCAGAAAACTCCAAAATCTGATAAGCTTAGGGAATGgtaagtttaaaagcttcaggataaacataatgagaaagtgaagttgcctaattgttttacatgtacaaaatgctcaaggtactcatttctaactatagtttgtttcatgaacaatttccaacag

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G55970.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaagacctt-tgttgacacttctgttactc--tgctcacttttagctcttctagtttaca-tgatttctgatgtactttacactcag
| || |||||||| || || ||  | || ||||| ||||||||| | ||||| |||||||| || ||||||||||||||  |||||||| | ||||| ||||| ||  |   |      ||  | |||||   |  ||| | |||  |    | |||  || | ||  |     ||| ||    ||||
GCTATATATGGGCATGTCCTCCACTTAAGGGTGACGATTACATTCTTTACTGTCATCCTGAAATCCAGAAGACTCCAAAGACCGACAAACTAAGGGAATGgtatgagatcgcgactgttctgtttttacttgtttgtcagtgttatgtacatttgttggcactaatcacattcctacctt---ttcag

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT3G12980.1 (Arabidopsis thaliana), 5'ss of exon 11
GTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaagacctttgttgacacttctgttactc--tgctcactttta---gctcttctagtttaca-tgatttctgatgtactttacact-cag
| || |||||||| ||||| ||| | || ||||||||||| ||||| || ||||||||||| |||||||| || |||||  | || ||| | ||||| ||||| |   | | |     | | |  ||||   |  |||| | ||   |    | | |  || | ||||   | ||   | || |  | |||
GCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATCCTGAAATTCAGAAAACGCCAAAGACTGATAAACTAAGGGAATGgtatggaatatatactttcctgtaatacttgtttttcacgtgtaagagagaatattgcatataatgatgcataatactccttccttttcag

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 5'ss of exon 10
GTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaaga----cctttgtt--------gacacttctgttactctgctcacttttagctcttctagtttacatgatttctgatgta--ctttacactcag------------------------
| || |||||||| || || ||||| || |||||||| || || ||||| ||||||||||| |||||||| || |||||||| || ||| | || || |||| |||       | |||        ||   ||   | | | | ||   ||  |  || |  | |     |   |||     ||  | ||    |  |                        
GCTATATATGGGCTTGTCCTCCTTTGAAGGGTGAAGACTATATATTGTATTGCCATCCTGAAATTCAGAAAACACCAAAATCTGATAAACTCAGAGAATGgtgagagtagttatcgttagaaaatagaagtttgaatcattttactagtttcaatttcctgaaataagtttttattcctccctaatccttctggttggtgtgcacaaaattttctatttcag

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|58693977|gb|CK082664.1|CK082664
EST:     TGCCATCCTGAGCTTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTG                         GTACTTATCTATGCTTCGAAAAGCTACCAAGGAGGAGATTGTTGTTGAGCT
genomic: TGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaagacctt ... ttacactcagGTACTTATCTATGCTTCGAAAAGCTACCAAGGAGGAGATTGTTGTTGAGCT
EST: gi|58667783|gb|CK056469.1|CK056469
EST:     TGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTG                         GTACTTATCTATGCTTCGAAAAGCTACCAAGGAGGAGATTGTTGTTGAGCT
genomic: TGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaagacctt ... ttacactcagGTACTTATCTATGCTTCGAAAAGCTACCAAGGAGGAGATTGTTGTTGAGCT
EST: gi|29635246|gb|CB640255.1|CB640255
EST:     TGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTG                         GTACTTATCTATGCTTCGAAAAGCTACCAAGGAGGAGATTGTTGTTGAGCT
genomic: TGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaagacctt ... ttacactcagGTACTTATCTATGCTTCGAAAAGCTACCAAGGAGGAGATTGTTGTTGAGCT
EST: gi|29622743|gb|CB627754.1|CB627754
EST:     TGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTG                         GTACTTATCTATGCTTCGAAAAGCTACCAAGGAGGAGATTGTTGTTGAGCT
genomic: TGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaagacctt ... ttacactcagGTACTTATCTATGCTTCGAAAAGCTACCAAGGAGGAGATTGTTGTTGAGCT
EST: gi|58665449|gb|CK054135.1|CK054135
EST:     TGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTG                         GTACTTATCTATGCTTCGAAAAGCTACCAAGGAGGAGATTGTTGTTGAGCT
genomic: TGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaagacctt ... ttacactcagGTACTTATCTATGCTTCGAAAAGCTACCAAGGAGGAGATTGTTGTTGAGCT

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), 75 (downstream exon)
Score: 37

GTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATCCTGAGATTCAGAAGACTCCAAAATCCGACAAATTGAGGGAGTGgtaagacctt ... ttacactcagGTACTTATCTATGCTTCGAAAAGCTACCAAGGAGGAGATTGTTGTTGAGCTGACAAATCTATATGACCATTTCTTCATTACTATGGGGGAGTGCAAGGCT




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