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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTATTACCATGTGAAGACCAAGATGTCAGGATTCTTTCAGACAAGTTTCTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctcttctacaccggtagcatgcttaaacccaagaatttgatggtttcaactgataccggttcgaattttggtccag

Basic information

species Oryza sativa
transcript LOC_Os02g34690.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g34690.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 11
TATTATTACCATGTGAAGACCAAGATGTCAGGATTCTTTCAGACAAGTTTCTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctcttctacaccggtagcatgcttaaacccaagaatttgatggtttcaactgataccggttcgaattttggtccag---
||||| ||| | || |||||||||||||| |||||||| |||||||| |||||||| || |||||  | |||||||| || ||  | ||||  || |||||| |||||     |  |  |  | |      | | |    | | || | ||  ||| |  |    |    |     |   |   
TATTACTACTACGTAAAGACCAAGATGTCCGGATTCTTCCAGACAAGCTTCTACTTTGGATACACCATGATGTTCTGTCTTGGCCTTGGAATCCTTTGCGgtgagctcactctcttcactctcttcaaactagcgagtggtgttattgatttgactaaaccttcgttatgtgaaaattttgcag

upper sequence: LOC_Os02g34690.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 11
TATTATTACCATGTGAAGACCAAGATGTCAGGATTCTTTCAGACAAGTTTCTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctcttctacaccggtagcatgcttaaacccaagaatttgatggtttcaactgataccggttcg--aattttggtccag--------------------
||||| ||| |||||||||| ||||||||||| ||||| || || || ||||||||||| ||||| || ||||| ||||| ||||||||||  ||||| ||| || |  |||||   | |   || | |      |  ||||||      | |  |   ||   |||    |||||  |                        
TATTACTACTATGTGAAGACTAAGATGTCAGGCTTCTTCCAAACCAGCTTCTACTTCGGATACACCCTGATGTTTTGCCTTGGTTTAGGAATCCTCTGTGgtgagtt--tctacggtgttctgattcctttttttat-aatttgtgtaccttatttttcacatattcattgatttttatatgaaatttcattttctaaaaaag

upper sequence: LOC_Os02g34690.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 5'ss of exon 11
TATTATTACCATGTGAAGACCAAGATGTCAGGATTCTTTCAGACAAGTTTCTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagc--tcttctacaccggtagcatgcttaaacccaagaatttgatggtttcaactgataccggttcgaattttggtccag-----------------------------------------------------------------------------------------------
||||| ||  || ||||||||||||||||||| ||||| || || || || || || || |||||||| ||||| ||||| ||||| || | ||| || ||||||    | |    | |   |   |  || |||       | |     | ||      |  |  |     | |   ||||                                                                                                
TATTACTATTATATGAAGACCAAGATGTCAGGCTTCTTCCAAACCAGCTTTTATTTTGGTTACACTCTCATGTTATGCCTTGGTTTGGGGATACTGTGTGgtaagtagccattcttagctcaatttttttttaacttctctctctctctctatctctatctctctatctccctatctatccatctatatatctatctccagccgttcttttagacatccttatctgcaattttcttcgggagcattgatggggttttgttattctcttgatactctag

upper sequence: LOC_Os02g34690.1 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S438_29V6.1 (Physcomitrella patens), 5'ss of exon 4
TATTATTACCATGTGAAGACCAAGATGTCAGGATTCTTTCAGACAAGTTTCTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctcttctacaccggta-gcatgcttaaacccaagaatttgatggt-ttcaactgataccggttcgaattttggtccag---------------------------------------------
|| || | | |  ||||||| |||||||| || || || ||||  |||||||||||||| ||||| || ||||||||||| || || || | | |||| ||||||     ||   | ||   |  ||  ||  |    | | |   |  | ||    ||||   || | |      |||  ||                                             
TACTACTTCTACATGAAGACGAAGATGTCCGGGTTTTTCCAGATCAGTTTCTACTTCGGGTACACGCTGATGTTCTGCCTGGGGTTGGGCATATTCTGTGgtaagtgggactgggcaggcgtgggtgggtatcctggggtagtgcgtaatatttggttgat---gggttgtgaggcggttgagtggagtggagggtctgacgggtgtgctgtttgtggcggctggcag

upper sequence: LOC_Os02g34690.1 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ15096 (Selaginella moellendorffii), 5'ss of exon 12
TATTATTACCATGTGAAGACCAAGATGTCAGGATTCTTTCAGACAAGTTTCTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctct-tctacaccggtagcatgcttaaacccaagaatttgatggtttcaactgataccggttcgaattttggtccag
|| || |||    |||||||||||||||| || || || || || ||||||||||||||||||||||| ||| ||||| | ||  | || |  ||||| ||| ||  |  |  || ||| | |  | |||   |  | | ||| |||   ||  |  | |   | | || |           
TACTACTACTTCATGAAGACCAAGATGTCCGGGTTTTTCCAAACGAGTTTCTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagtaccatacactccgattgttttcttggtcggatggatt-gataactttgatggtt--tgatgcgcag----------

upper sequence: LOC_Os02g34690.1 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ37593 (Selaginella moellendorffii), 5'ss of exon 12
TATTATTACCATGTGAAGACCAAGATGTCAGGATTCTTTCAGACAAGTTTCTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctct-tctacaccggtagcatgcttaaacccaagaatttgatggtttcaactgataccggttcgaattttggtccag
|| || |||    |||||||||||||||| || || || || || ||||||||||||||||||||||| ||| ||||| | ||  | || |  ||||| ||| ||  |  |  || ||| | |  | |||   |  | | ||| ||||  ||  | || |   | | || |           
TACTACTACTTCATGAAGACCAAGATGTCCGGGTTTTTCCAAACGAGTTTCTACTTCGGCTACACTCTGATGCTCTGCGTTGGACTGGGGAGCCTCTGTGgtgagtaccatacactccgattgttttcttggtcggatggatt-gatgactttga-tggttttgatgcgcag----------

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|40724719|gb|CK431287.1|CK431287
EST:     CTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCG                         GTGCTGTCGGGTATCTTGGA
genomic: CTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctctt ... tttggtccagGTGCTGTCGGGTATCTTGGA
EST: gi|88989366|gb|CI043865.1|CI043865
EST:     CTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCG                         GTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA
genomic: CTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctctt ... tttggtccagGTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA
EST: gi|88273264|gb|CI388720.1|CI388720
EST:     TCTGCCTAGGTTTAGGAACACTCTGCG                         GTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA
genomic: TCTGCCTAGGTTTAGGAACACTCTGCGgtaagctctt ... tttggtccagGTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA
EST: gi|86492725|gb|CI135358.1|CI135358
EST:     CTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCG                         GTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA
genomic: CTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctctt ... tttggtccagGTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA
EST: gi|89182373|gb|CI113742.1|CI113742
EST:     CTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCG                         GTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA
genomic: CTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctctt ... tttggtccagGTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA
EST: gi|29642291|gb|CB647298.1|CB647298
EST:     CTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCG                         GTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA
genomic: CTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctctt ... tttggtccagGTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA
EST: gi|163920596|gb|EG709603.1|EG709603
EST:     CTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCG                         GTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA
genomic: CTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctctt ... tttggtccagGTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA
EST: gi|18388900|gb|BM422098.1|BM422098
EST:     TACTTCGGCTACACTCTTATGGTTCTGCCTAGGTTTAGGAACACTCTGCG                         GTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA
genomic: TACTTCGGCTACACTCTTAT-GTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctctt ... tttggtccagGTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGA

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: 72 (upstream exon), 53 (downstream exon)
Score: 14

TATTATTACCATGTGAAGACCAAGATGTCAGGATTCTTTCAGACAAGTTTCTACTTCGGCTACACTCTTATGTTCTGCCTAGGTTTAGGAACACTCTGCGgtaagctctt ... tttggtccagGTGCTGTCGGGTATCTTGGATCGACACTGTTTGTGAGAAGGATCTACAGGAACATAAAGTGTGACTAAAAATTGACCCCGGTTTAGACAGATGGGGCGAA




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