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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTTCCACTACATTGTCTGGACCTGAAGAAACTGAAGAGGATGGTGGAGATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagttcgataataactataggacgtgacttctgtttttactttgctctgagttgatctgaaacttgtgctggtatctatccgtattagtcttca...

Basic information

species Oryza sativa
transcript LOC_Os09g33810.5
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g33810.5 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G800734_T02 (Zea mays), 5'ss of exon 5
TACTTCCACTACATTGTCTGGACCTGAAGAAACTGAAGAGGATGGTGGAGATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagttcgataataactataggacgtgacttct----gtttttactttgct--ctgagttgatctgaaacttgtgctggtatctatccgtattagtcttca
|   ||||||    | |||||||||||||| ||||| ||||| || || ||||| |||||||||||||| ||||| ||||| |||||||| ||||  ||||||||||      | | |  || |   |  ||||||||    |  |  ||  || |  |  |  |||  ||   | |||    |||  ||    |||  ||  | |
TGTGTCCACTGTGCTCTCTGGACCTGAAGAGACTGAGGAGGAAGGAGGGGATGACGATGAGTCCATTGTTCATCACACTGCAAGTGTTGGTGATGAAGAGgtaatgag---taaaagtgtcttttt-atctgacttctaaaggaatgaacagtgttagcatatgtgagttggggcctgtttctgtagatagatttat--gttataa
















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|3768382|gb|AU032409.1|AU032409
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|38482356|gb|CF966398.1|CF966398
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|88844544|gb|CI020391.1|CI020391
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|88723456|gb|CI746966.1|CI746966
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAG
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAG
EST: gi|55411016|gb|CV723392.1|CV723392
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|86854638|gb|CI258931.1|CI258931
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|86823509|gb|CI256446.1|CI256446
EST:     TGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: TGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|33679151|gb|CF307390.1|CF307390
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|29670242|gb|CB666517.1|CB666517
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|86604145|gb|CI114919.1|CI114919
EST:     GGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: GGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|163922657|gb|EG712178.1|EG712178
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTT
EST: gi|14571303|gb|BI118671.1|BI118671
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|88728587|gb|CI752097.1|CI752097
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|88993229|gb|CI108857.1|CI108857
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|163928746|gb|EG714739.1|EG714739
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|29660377|gb|CB656652.1|CB656652
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|89192825|gb|CI050123.1|CI050123
EST:     TGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: TGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|88425700|gb|CI689351.1|CI689351
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|38478876|gb|CF963009.1|CF963009
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|88216131|gb|CI215980.1|CI215980
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|88331324|gb|CI675654.1|CI675654
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|87035310|gb|CI189932.1|CI189932
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGCGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|86256816|gb|CI061579.1|CI061579
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|88219601|gb|CI219161.1|CI219161
EST:     TGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: TGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|569414|gb|D40263.1|D40263
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTNTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|3107410|gb|D43150.1|D43150
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTNTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|29646145|gb|CB651152.1|CB651152
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|29627632|gb|CB632643.1|CB632643
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|29613549|gb|CB618562.1|CB618562
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|88349307|gb|CI678284.1|CI678284
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|88745763|gb|CI769123.1|CI769123
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGAT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGAT
EST: gi|86415415|gb|CI069818.1|CI069818
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTGGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|568989|gb|D39838.1|D39838
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|88216154|gb|CI216003.1|CI216003
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCATTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|86892732|gb|CI312082.1|CI312082
EST:     TGATGAGTCCCATTGTCCATCAATACTGCCAGTGTTGGCGATGCGGGAAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGC
genomic: TGATGAGT-CCATTGTCCATC-ATACTGCCAGTGTTGGCGATGC-GG-AGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGC
EST: gi|29663971|gb|CB660246.1|CB660246
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
EST: gi|88728139|gb|CI751649.1|CI751649
EST:     ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAG                         GGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT
genomic: ATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCT

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: 74 (upstream exon), 75 (downstream exon)
Score: 104

TACTTCCACTACATTGTCTGGACCTGAAGAAACTGAAGAGGATGGTGGAGATGATGATGAGTCCATTGTCCATCATACTGCCAGTGTTGGCGATGCGGAGgtaatgaagt ... gactcaacagGGTCTGAAGAAAGCTTTAGAGGATGGAGCAGACATGGATGAAGAAGACGCTGAGGGAAGAAGGGCCTTACATTTTGCGTGTGGTTACGGTGAG




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