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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtttcgtttagggtttcgcccgcgtgagggtgaggggagggggagagagcgaggctgatccgctgtattgtgcgcgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGCGGCAAGTCCA

Basic information

species Oryza sativa
transcript LOC_Os06g36160.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36160.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G091383_T01 (Zea mays), 3'ss of exon 1
----gtgcgtttcgtttagggtttcgcccgcgtgagggtgaggggagggggagagagcgaggctgatccgctgtattgtgcgcgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGCGGCAAGTCCA
    ||||| | |      |     |||  ||    |          |       |||||   |||  ||    || |   |  |  |||||||||| || ||||||| |||||| ||| ||||||||||||||||  |||||||||||||||| ||||||||||||||||||||||||||||||||||| |
gtcagtgcggtgcccaagcgtcggagccttcgctgcgagatcctctcgttctattagcgattttgacgcgtgtgatcgcttg-atattgcagGCGGAGCTCAAGGAGAGGCTGGCTAAGATGTACGAGGTGAAGGATCCCAACTGCATCTTCGTCTTCAAGTTCCGCACCCACTTCGGAGGCGGCAAGTCTA

upper sequence: LOC_Os06g36160.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S450_9V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------gtgcgtttcgtttagggtttcgcccgcgtgagggtgaggggagggggagagagcgaggctgatccgctgtattgtgcgcgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGCGGCAAGTCCA
                              ||| | |  ||   ||         | ||   |  || |  ||||       |   | | || | |  ||    ||    |    ||||| || |||||||||||||| ||||||||||||||||||  |||  || |    ||||||||||||  |||| | ||||| || ||||| ||||||||||
gtgagtggcccactggaagctctatgtgttgtgtggtgtgtaatggcacatttttgggtttagtcgaagttagggttttgttggaggacggagctgaggttcgatggttttcactcagGCTGAGCTGAAGGAGAAGCTCGCGAAGCTGTACGAGGTGCGGGATCCCCAGACTATCTTCGTGTTCGGGTTCAGGACCCAGTTTGGAGGTGGCAAGTCCA

upper sequence: LOC_Os06g36160.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------gtgcgtttcgtt--tagggtttcgcccgcgtgagggtgaggggaggg--ggagagagcgaggctgatccgctgtattgtgcgcgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGCGGCAAGTCCA
                             ||| ||| ||||  |  |||   |     ||| ||  |||    |||  |     |   | |          ||  ||||    |    ||||| || |||||||| |||||||| |||||||||||||| |  ||  || |   |||||| ||||||  |||| | || || |||||||| ||||||||||
gtgtgtgtttcattgcaacctggttcactgtgtgttgcgttgtttcggtagagttgttgtgcggtcgagtttcgggttgccccaaaaaaagagagctgagagtcgtgtgttgatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAGACCATCTTTGTGTTCGGGTTCAGAACGCATTTCGGAGGTGGCAAGTCCA

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|88240823|gb|CI238674.1|CI238674
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGGGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|88204674|gb|CI204523.1|CI204523
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|15850357|gb|BI798633.1|BI798633
EST:     ACCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         CCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|88848323|gb|CI086845.1|CI086845
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|8527927|gb|AU092742.1|AU092742
EST:     CAGTTCGTGCTCAAGGTGCTCCACCCGGGGCCGCGCCAACGTCTCCAAG                         GCGGNTCTGAAGGAGAAGCT-GCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: CAGTTCGTGCTCGAGGTGCTCCACCC-GGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|89170709|gb|CI039986.1|CI039986
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|88209028|gb|CI208877.1|CI208877
EST:     AGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|88727341|gb|CI750996.1|CI750996
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|88239271|gb|CI240433.1|CI240433
EST:     CGAGGTGCTCCACCCGGGCCGCGCCAACGTCCCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: CGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|3767255|gb|AU031365.1|AU031365
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAA-CTGTTACGAGGTGAAGGACTCCAA
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGT-ACGAGGTGAAGGACTCCAA
EST: gi|88238593|gb|CI238442.1|CI238442
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|89196939|gb|CI021779.1|CI021779
EST:     GCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: GCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|86595148|gb|CI260387.1|CI260387
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|88482135|gb|CI419406.1|CI419406
EST:     CTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: CTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|30229440|gb|CB967331.1|CB967331
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGNCCGCGCCAACGTCTCCAAG                         NCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|86859457|gb|CI278864.1|CI278864
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
EST: gi|163929010|gb|EG709788.1|EG709788
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAA
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAA-Ggtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAA
EST: gi|38468332|gb|CF952463.1|CF952463
EST:     AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAG                         GCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC
genomic: AGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAAC

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: 78

GGTGACCCTCCGCACCCGCAAGTTCATGACGAACCGCCTCCTCTCCCGCAAGCAGTTCGTGCTCGAGGTGCTCCACCCGGGCCGCGCCAACGTCTCCAAGgtgcgtttcg ... cgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGCGGCAAGTCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaggggagggggagagagcgaggctgatccgctgtattgtgcgcgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGCGGCAAGTCCA
                       ggctgat  putative branch site (score: 78)