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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaacttcttttttagagaaatggccagtgaagtttcctgtcatgcaggccaatattttttgcatactgtattcaatttgcaactacaaaggttgag...

Basic information

species Oryza sativa
transcript LOC_Os04g23890.2
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G032351_T01 (Zea mays), 5'ss of exon 19
TGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaa-cttcttttttagagaaatggccagtgaagtttcctgtcatgcaggccaatattttttgcatac-tgtattcaa--tttgcaactacaaaggttgag------------------------------------------------------------------------------
||| ||| ||||||| ||||||||||| ||||||||||||||||||| ||||||| |||| || ||||||||||||||||||||||| |||||||||||||||||||  ||| |  |||      |  ||  |  | || | ||| |  | || |||  ||   ||  |   || | | ||  ||||    || | |  |                                                                                  
TGAAATGTTGTATGGACGTACACCTTTTCGAGGAAAGAACAGGAAAAGGACATTTCATAATATCCTGCACAAAGACCTTACATTTCCAAGTAGCATTCCGgtaagaaatttcatccttatttttgttacc--tacaattgcatgtaaatctggtcaaatttgcctgtgtttgtgcagttaacatttgatggtatagaaataagttttgaaactatctacaatgttttgtaccacatacaacgttgtttattctgttcacctattaacaaatgtttactccag

upper sequence: LOC_Os04g23890.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GLYMA08G33520.1 (Glycine max), 5'ss of exon 3
TGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaacttcttttttagagaaatggccagtgaagt--ttcctgtcat--gcaggccaatattttttgcatactgtattcaatttgcaactacaaaggttgag
||||||||| ||||| |||||||| ||| |||||||||| ||  | ||||||||||  || ||  | ||||| || ||||| ||||| || |||||||||||||  |      | ||||  |  ||  |  | || |  ||   ||  |  ||   |||||   |||| || |  |        || | | | || | |||   
TGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAATATTTTACACAAGGATCTTACCTTTCCAAGCAGCATTCCGgtaaataacaaaatattagt-agttgaactttaaaatatttatagttgtttgccatccaattcattttccaaagagag---gggttcctatttcagaagttttt

upper sequence: LOC_Os04g23890.1 (Oryza sativa), 5'ss of exon 20
lower sequence: Vv03s0038g04210.t01 (Vitis vinifera), 5'ss of exon 20
TGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaacttcttttttagagaaatggccagtgaagtttcctgtcatgcaggccaatattt-tttgcatactgtattcaatttgcaactacaaaggttgag
||||||||| ||||| ||||| |||||| |||||||||| ||| | ||||||||||  |||||  |||||||||| || || |||||||||||||||||||||| | | ||  |||   |   ||  ||| ||   |    |    |       |  |||   ||   ||||  |     ||    | ||||   |  || 
TGAGATGCTTTATGGCCGTACTCCTTTCAGAGGAAAGAATAGGCAGAAGACATTTTCCAACATCTTGCACAAAGATCTGACTTTTCCCAGTAGCATTCCGgtaaaatcatcactttctaatgcattaccactgtcttaagataatttctctttgatcattcacttatgtacttaaaagtgttgagcagtacagcagagga-

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|29685192|gb|CB681467.1|CB681467
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29618297|gb|CB623309.1|CB623309
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29619193|gb|CB624205.1|CB624205
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29679663|gb|CB675938.1|CB675938
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|86870343|gb|CI319449.1|CI319449
EST:     CACAAA-ACC-TACATTTCCCAGTA-CAGTCC-                         GTTAGTC-TGCAGCAAAGCAATTAATCCATGAATTACTTCAGAGAGATCCT
genomic: CACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29680790|gb|CB677065.1|CB677065
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29626656|gb|CB631667.1|CB631667
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|86861209|gb|CI326647.1|CI326647
EST:     CATTTTATAACATAC-GCACAAAGACC-TACATTTCCCAGTAGCATTCCGG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCC
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCC-Ggtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCC
EST: gi|29615866|gb|CB620878.1|CB620878
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29685421|gb|CB681696.1|CB681696
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|25806004|gb|CA761965.1|CA761965
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCTGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29612811|gb|CB617824.1|CB617824
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29630592|gb|CB635601.1|CB635601
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29620201|gb|CB625213.1|CB625213
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29619194|gb|CB624206.1|CB624206
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29613428|gb|CB618441.1|CB618441
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|86481914|gb|CI124547.1|CI124547
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29618974|gb|CB623986.1|CB623986
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|29646470|gb|CB651477.1|CB651477
EST:     CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|38478618|gb|CF962751.1|CF962751
EST:     TTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCG                         GTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
genomic: TTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCT
EST: gi|33381050|gb|CF196393.1|CF196393
EST:     CATTTTATAACATACTGCACNNNGACCTTACATTTCCCAGTAGCATTCCG                         GNNAGTCTTGCAGCAAAG
genomic: CATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAG

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: 58 (upstream exon), 68 (downstream exon)
Score: 16

TGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCCCAGTAGCATTCCGgtaagaactt ... gattctccagGTTAGTCTTGCAGCAAAGCAATTAATCCATGGATTACTTCAGAGAGATCCTTCAAATCGTATAGGTTCAAATGCTGGTGCAAATGACATCAAGCAACATT




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