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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatctcgttcaaagatcttggtagtggacatattagctaaaccagtcacatggattctcagttttttctctactgaaacag

Basic information

species Oryza sativa
transcript LOC_Os09g15750.1
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g15750.1 (Oryza sativa), 5'ss of exon 23
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 5'ss of exon 21
TGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatata----tctcgttcaaagat----cttggtagtggacatattagctaaaccagtcaca--tggattctcagttttttctctactgaaacag-------
||||||| | |||||  || ||||||| ||||||||||||||| | ||||| || ||||||||||||||  |||| ||  |||| |   | || ||||| ||   |     |   || |   | |    | |  |  | |  |  |  | | |||  |  |    | |||  | | |    | | |  | ||| |        
TGCTGGTATAGTGACACTTTTGCATGCATGCCTTGACATGAAACCAATCATACTCGGGAAGTACCATTATGTGCTGTACTTCCTCGTTTTGGCGATGCAAgtgagttcaacttctgtcctgtgtttctccctcttgttagttaggtctgatgaacttgctatgatttgatatttaatcaaattt-tgttaaaaaaatgtatag

upper sequence: LOC_Os09g15750.1 (Oryza sativa), 5'ss of exon 23
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 5'ss of exon 21
TGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatctcgttcaaagatcttggtagtggacatattagctaaaccagtcacatggattctcagttttttctctactgaaacag
||||||| | |||||  |  ||||||| |||||||||||||||||||| || |||||||| || || ||  |||| ||  ||||||   | || ||||||||   |      |||        || |        | |||  | ||| |     ||  | |  ||   |    | |        ||
TGCTGGTATAGTGACATTGTTGCATGCATGCCTTGACATGAAATCCATTATACTGGGGAAATATCACTATGTGCTCTACTTCCTTGTTTTGGCGATGCAGgtgagtgcaattttctg----tctgatgactttttttttaa-tgaactaagtttatctactaacacaatacggtttgagtgtgtag

upper sequence: LOC_Os09g15750.1 (Oryza sativa), 5'ss of exon 23
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 23
TGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatctcgttcaaagatcttggtagtggacatattagctaaaccagtcacatggattctcagttttttctctactgaaacag-------------------
||||||  | || ||  | |||||||| ||||||||||||||  |||||||  ||||||| ||||||||  | |||||| ||||||   | || ||||||||  ||      ||  |  |  |   |  |  |||  ||      |   ||    |||||  |  |||| |||| |||||  |                      
TGCTGGAATAGTAACTTTGCTGCATGCATGCCTTGACATGAAGGCCATCATCTTGGGGAAATACCATTATGTTCTTTATGTCCTTGTTTTGGCCATGCAGgttaattctaaatttgagcacttcatttctctacaatttgtgaccatttgtt-tttggatcttgtgtttattct-tactgttatttatctactttgatgctacag

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|8857666|gb|AU094984.1|AU094984
EST:     TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAG                         CCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
genomic: TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
EST: gi|86592847|gb|CI270404.1|CI270404
EST:     TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAG                         CCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
genomic: TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
EST: gi|86492954|gb|CI135587.1|CI135587
EST:     TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAG                         CCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
genomic: TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
EST: gi|8856938|gb|AU094256.1|AU094256
EST:     TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAG                         CCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
genomic: TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
EST: gi|58591305|gb|CF989613.1|CF989613
EST:     TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAG                         CCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
genomic: TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
EST: gi|86478141|gb|CI120774.1|CI120774
EST:     CCTAGCTATGCAG                         CCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
genomic: CCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
EST: gi|87016283|gb|CI271694.1|CI271694
EST:     TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAG                         CCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
genomic: TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
EST: gi|88249096|gb|CI248945.1|CI248945
EST:     TGCCCTAGCTATGCAG                         CCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
genomic: TGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
EST: gi|29626609|gb|CB631620.1|CB631620
EST:     TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAG                         CCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
genomic: TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
EST: gi|8527826|gb|AU092641.1|AU092641
EST:     TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAG                         CCTCGGATGCTATTGACTGTGGATGAGGATCTNAAGCCCCTCTCTGTTCCG
genomic: TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
EST: gi|29644400|gb|CB649407.1|CB649407
EST:     TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAG                         CCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTG
genomic: TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTG
EST: gi|218478818|gb|FG953673.1|FG953673
EST:     TTCTGGGGAAGTACCATTACATGCTTTATATCCTTACCCTAGCTATGCAG                         CCTAGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
genomic: TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
EST: gi|86479306|gb|CI121939.1|CI121939
EST:     CATGCTTGATATCCTTGCCCTAGCTATGCAG                         CCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
genomic: CATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
EST: gi|27920720|gb|CB096528.1|CB096528
EST:     TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAG                         CCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG
genomic: TTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCG

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: 49 (upstream exon), 65 (downstream exon)
Score: 14

TGCTGGTCTTGTGACGGTTCTGCATGCCTGCCTTGACATGAAATCCATCATTCTGGGGAAGTACCATTACATGCTTTATATCCTTGCCCTAGCTATGCAGgtatatatct ... actgaaacagCCTCGGATGCTATTGACTGTGGATGAGGATCTCAAGCCCCTCTCTGTTCCGGTTTGTGTTGGTCAAGCAGTTGACGTCGTCGGTCAGGCGGGTCGACCCA




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