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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctcggtgtaaatcttacatgtggtggtggtgatgatttgcggggggtttggatctcagcggctggggttttgctgtgcag

Basic information

species Oryza sativa
transcript LOC_Os01g52490.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52490.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G151252_T01 (Zea mays), 5'ss of exon 2
GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctcggtgtaaatcttacatgtggtggtggtgatg-atttgcggggggtttggatctcagcg--gctggggttttgct----gtgcag
||||| ||||| ||||||||||||||  ||||||||||||||||||||  ||||      |  |   || |  | |  |   |     ||    ||  |||||||||| |  | |  | || | ||    ||| ||
GTGCTTGAGGTTATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatatcggccccggtactgtgtgcgcggctcatatggcgggagcttctggcctggatctcagggttgttctgcttgttctctttgtgtag

upper sequence: LOC_Os01g52490.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G171426_T01 (Zea mays), 5'ss of exon 2
GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctcggtgtaaatcttacatgtggtggtggtgatg-atttgcggggggtttggatctcagcggctggggttttgctgtgcag
||||| ||||||||||||||||||||  |||||||||||||||||||| ||||||     || |  ||| |    |  ||  |    | |     |  ||||||| || || ||   | |   |||| ||
GTGCTTGAGGTGATCCACCCCGGCCGCGCCAACGTCTCCAAGgtgagatctcggtcattgtcctttatgcgcgtctcatgtggcgggtacttcttgcctggatcttag-ggttgt--tctctgtgtgtag
















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|29685668|gb|CB681943.1|CB681943
EST:     GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|66927289|gb|CX114137.1|CX114137
EST:     GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|286327|gb|D15135.1|D15135
EST:     GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|4716872|gb|AU057988.1|AU057988
EST:     GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|38468914|gb|CF953045.1|CF953045
EST:     GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|86828011|gb|CI274918.1|CI274918
EST:     AGCAATTCGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: AGCAATTCGTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|55436887|gb|CV731621.1|CV731621
EST:     GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|29685667|gb|CB681942.1|CB681942
EST:     GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|8857380|gb|AU094698.1|AU094698
EST:     GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|4716870|gb|AU057986.1|AU057986
EST:     GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|300215673|gb|HO088299.1|HO088299
EST:     CCCCGGCCGGCCC-ACGTCTCC-AG                         GCTGAGCTGAAGGAGAAGCTGGCCTAGCTGTACGAGGTGAAGGACGCGAAC
genomic: CCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|89167241|gb|CI252772.1|CI252772
EST:     GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|87032270|gb|CI264051.1|CI264051
EST:     GATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: GATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|86596339|gb|CI268639.1|CI268639
EST:     ACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: ACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|86824377|gb|CI262919.1|CI262919
EST:     GTGATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: GTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
EST: gi|29659093|gb|CB655368.1|CB655368
EST:     GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAG                         GCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC
genomic: GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAAC

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: 75 (upstream exon), 75 (downstream exon)
Score: 109

GTGCTCGAGGTGATCCACCCCGGCCGGCCCAACGTCTCCAAGgtgagacctc ... tgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGTGGAGGCAAGTCCA




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