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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGTTAGATGTTAACAACAGCTTTGTTGATGACTCAATCATAATGGATAACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatttcaaattctagcaggactgacttaaaaagtttgatacagtattttttccctagatattcaacttcatagttaaatccttggtttaaagat...

Basic information

species Oryza sativa
transcript LOC_Os03g17980.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G107867_T01 (Zea mays), 5'ss of exon 10
TATGTTAGATGTTAACAACAGCTTTGTTGATGACTCAATCATAATGGATAACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatttcaaattctagcaggactgacttaaaaagtttgatacagtattttttccctagatattcaacttcatagttaaatccttggtttaaagat-
 | ||||||||  | |||||||||| ||| |||||| | ||| |||||||| | |||||  ||||||||||||||| ||||||||||||||||| |||||||||| | |  |   ||  |  |    | |     |   | | |  || |||| ||    |    ||   |  |  |   | | |  ||||  |   ||  
CACGTTAGATGCCAGCAACAGCTTTCTTGGTGACTCTACCATCATGGATAATGATGATGCTAATGGGAGGCTACCTACTGTGATCAAGTTTGAATTCCAGgtgtgtagtagctcgttacactaaatttcatcatcatgatataacccattattgttgatttgtccatcacatgttttgaatta-ttgttggagtggtgaca
















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|89186738|gb|CI052151.1|CI052151
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|86510847|gb|CI153480.1|CI153480
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|29672696|gb|CB668971.1|CB668971
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29672696|gb|CB668971.1|CB668971
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29672696|gb|CB668971.1|CB668971
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29672696|gb|CB668971.1|CB668971
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29672696|gb|CB668971.1|CB668971
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|86427605|gb|CI072702.1|CI072702
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|86426169|gb|CI071266.1|CI071266
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|2317410|gb|C22464.1|C22464
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|2317410|gb|C22464.1|C22464
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|2317410|gb|C22464.1|C22464
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|2317410|gb|C22464.1|C22464
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|2317410|gb|C22464.1|C22464
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|218504457|gb|FG953019.1|FG953019
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|218504457|gb|FG953019.1|FG953019
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|218504457|gb|FG953019.1|FG953019
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|218504457|gb|FG953019.1|FG953019
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|218504457|gb|FG953019.1|FG953019
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|88833351|gb|CI076832.1|CI076832
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|88902528|gb|CI088066.1|CI088066
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|86491677|gb|CI134310.1|CI134310
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|86432280|gb|CI085891.1|CI085891
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|29673828|gb|CB670103.1|CB670103
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29673828|gb|CB670103.1|CB670103
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29673828|gb|CB670103.1|CB670103
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29673828|gb|CB670103.1|CB670103
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29673828|gb|CB670103.1|CB670103
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|86489325|gb|CI131958.1|CI131958
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|29663427|gb|CB659702.1|CB659702
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29663427|gb|CB659702.1|CB659702
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29663427|gb|CB659702.1|CB659702
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29663427|gb|CB659702.1|CB659702
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29663427|gb|CB659702.1|CB659702
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|86492611|gb|CI135244.1|CI135244
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|86491517|gb|CI134150.1|CI134150
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|86526185|gb|CI166391.1|CI166391
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|88967880|gb|CI098122.1|CI098122
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|89182206|gb|CI113575.1|CI113575
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|86845257|gb|CI340365.1|CI340365
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         ACCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACGGGGCCTCAG
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaagACCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACGGGGCCTCAG
EST: gi|29627234|gb|CB632245.1|CB632245
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|29614996|gb|CB620009.1|CB620009
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29614996|gb|CB620009.1|CB620009
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29614996|gb|CB620009.1|CB620009
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29614996|gb|CB620009.1|CB620009
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29614996|gb|CB620009.1|CB620009
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|88831211|gb|CI082021.1|CI082021
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|29672731|gb|CB669006.1|CB669006
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29672731|gb|CB669006.1|CB669006
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29672731|gb|CB669006.1|CB669006
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29672731|gb|CB669006.1|CB669006
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29672731|gb|CB669006.1|CB669006
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|86490455|gb|CI133088.1|CI133088
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGCTTTACAAG                 
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAAT----C----C-AGgtgtgcaatt ... gc
EST: gi|29616520|gb|CB621532.1|CB621532
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29616520|gb|CB621532.1|CB621532
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29616520|gb|CB621532.1|CB621532
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29616520|gb|CB621532.1|CB621532
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-
EST: gi|29616520|gb|CB621532.1|CB621532
EST:     ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAG                         C
genomic: ACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaag-

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: 73 (upstream exon), 74 (downstream exon)
Score: 7

TATGTTAGATGTTAACAACAGCTTTGTTGATGACTCAATCATAATGGATAACGGTGATGTAAATGGGAGGCTACCTGCTGTGATCAAGTTTGAAATCCAGgtgtgcaatt ... gctttacaagACCAGAGACGAGAAGTATCTGCTGGATATGCAGAGAGTTACGGGGCCTCAGCTCCTTTTCCTGGACTTCTGTGCAGACTTCCTTACCAAGCTGAGGGTTC




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