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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTATTGGGGAGTTGATCCTGACAGCCGTCTTGTGGTTTCTGATGATGACGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatgataagcttaatcaaccaatcaacaatatcacatcaattctcaaggcctggaactatgcctcttttatcaacacctgacgtgtaatggcttcatcag

Basic information

species Oryza sativa
transcript LOC_Os03g58170.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58170.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G22850.1 (Arabidopsis thaliana), 5'ss of exon 3
TTTTATTGGGGAGTTGATCCTGACAGCCGTCTTGTGGTTTCTGATGATGACGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatgataagcttaatcaaccaatcaacaatatcacatcaattctcaaggcctggaactatgcctcttttatcaacacctgac-gtgtaatggcttcat-cag
 | || ||||||   ||| ||||  | | |||||| |||||||||||||  || | ||| || |||| |||||| ||||||| ||| ||||||||||||||||   |   |   | ||          |  |  | ||| ||    |  |   |  || |  | |       |  || |  |  ||   ||||    || | || |||
CTCTACTGGGGAACCGATGCTGAAGGACATCTTGTTGTTTCTGATGATGTTGAGACTGTCAAGAAGGGTTGTGGTAAATCCTTTGCGCCATTCCCTAAAGgtatgtagcaagccgtttttcgggtt--ttgaagacatctcactgttcttt--gatctagtgcaaa----tatgaattaggatgtggttgtgtgtatgcataatgcag
















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|88509169|gb|CI436675.1|CI436675
EST:     CTTGTGGGGAATCCTGTGCACCATTCCCTAAA-                         GTNTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATG
genomic: CTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGT-TTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATG
EST: gi|218500531|gb|FG947081.1|FG947081
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|88212890|gb|CI210741.1|CI210741
EST:     TAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: TAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|89189322|gb|CI048861.1|CI048861
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|66947208|gb|AU312052.1|AU312052
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|86523413|gb|CI163619.1|CI163619
EST:     ATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: ATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|88213677|gb|CI213526.1|CI213526
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|218487274|gb|FG955015.1|FG955015
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|88536373|gb|CI466120.1|CI466120
EST:     TGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: TGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|87013143|gb|CI281657.1|CI281657
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|88228300|gb|CI227780.1|CI227780
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|86530561|gb|CI170767.1|CI170767
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|25806294|gb|CA762255.1|CA762255
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|87023502|gb|CI284649.1|CI284649
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|218491081|gb|FG953110.1|FG953110
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|88226560|gb|CI226476.1|CI226476
EST:     CCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|218483502|gb|FG948236.1|FG948236
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|86892718|gb|CI312075.1|CI312075
EST:     TGCACCATTTCCNTAAAG                         GTTTNTTNTTCACCCACATCCGGAGGACTGCAAGAGCTACGAACCACCCTA
genomic: TGCACCA-TTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCA-CCACATCCGGAGGACTGC-AGAGCTACGAA-CACCCTA
EST: gi|86495647|gb|CI138280.1|CI138280
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|218478490|gb|FG961155.1|FG961155
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|86533207|gb|CI173413.1|CI173413
EST:     CGAAATTGTGAATGAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|86543657|gb|CI183863.1|CI183863
EST:     CACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|86498551|gb|CI141184.1|CI141184
EST:     CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
EST: gi|15854665|gb|BI807477.1|BI807477
EST:     CATTCCCTAAAG                         GTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA
genomic: CATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGA

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: 71 (upstream exon), 75 (downstream exon)
Score: 92

TTTTATTGGGGAGTTGATCCTGACAGCCGTCTTGTGGTTTCTGATGATGACGAAATTGTGAATAAGGCTTGTGGAAAATCCTCTGCACCATTCCCTAAAGgtaatgaatg ... gcttcatcagGTTTCTTCTTCACCACATCCGGAGGACTGCAGAGCTACGAACACCCTATGAATGAGGTGAAACCAGTGCCGAGGCTCGACAGCAAGGGGGAGGTATGCGG




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