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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttccaccttgcttaattagtgtgtgtccatgtaattgttcagagctacaagagaaaactgcagacgttttcagtacttgcagacgaagaacctgaatgggattatgcataaaaaaatacttacttttcagtttcatgctgttcttggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAGGCCATCGATTGCCCCTACCCCTGTGACAAAACATGCCACAACATCATAT

Basic information

species Oryza sativa
transcript LOC_Os01g21630.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g21630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G066500_T01 (Zea mays), 3'ss of exon 7
gtactttccaccttgcttaattagtgtgtgtccatgtaattgttcagagctacaagagaaaactgcagacgttttcagtacttgcagacgaagaacctgaatgggattatgcataaaaaa-atacttacttttcagtttcatgctgttcttggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAGGCCATCGATTGCCCCTACCCCTGTGACAAAACATGCCACAACATCATAT
                                                                                          || || |  |         |||||   |   |||| ||  ||    || |         ||     ||||||| ||||| ||||| || || ||||||||||| ||||||||| | || ||||| ||||| |||||||||||||| |||  |||||||| |||||||||||
----------------------------------------------------------------------------------------gtaataaaccaaccaaaccgttgcattgcagccatacatatattagtattacgaaagcaaattatgaatgcagGGGATTGCCAAGTCAGTGGGCGACTGGTACTTCGGTCGAGCTCAAGTCAAGGCGATCGACTGCCCCTACCCCTGCGACGGAACATGCCGCAACATCATAT

upper sequence: LOC_Os01g21630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G164134_T01 (Zea mays), 3'ss of exon 10
gtactttccaccttgcttaattagtgtgtgtccatgtaattgttcagagctacaagagaaaactgcagacgttttcagtacttgcagacgaagaacctgaatgggattatgcataaaaaaatacttacttttca-gtttcatgctgttcttggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAGGCCATCGATTGCCCCTACCCCTGTGACAAAACATGCCACAACATCATAT
                                                                                   | | |  || || |   |    |    | | |  ||| |  |   |  ||| || |  || |||||     ||  ||||| ||| |||| || ||||| ||||||||||||| ||||||||||||||||||  |||| |||| ||| ||||| ||||| || |||||| |||| ||||
-----------------------------------------------------------------------------------gtaaa-aaacaatccacaacacacctggaacatcaaactgttggatactcatgtgttctgatgttc----gtgcacagGGGATTTCAAAATCCGTTGGCGACTGGTACTTTGATCGAGCTGAGGTGAAGGCGGTCGACTGCCGCTATCCCTGCGACAACACTTGCCACCACATTATAT

upper sequence: LOC_Os01g21630.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 11
gtactttccaccttgcttaattagtgtgtgtccatgtaattgttcagagctacaagagaaaactgcagacgttttcagtacttgcagacgaagaacctgaatgg-gattatgcataaaaaaatacttacttttcagtttcatgctgttcttggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAGGCCATCGATTGCCCCTACCCCTGTGACAAAACATGCCACAACATCATAT
                                                           | | |||||    ||    |   ||  |       |   |  |   | || || | |||||     |||  |      ||  | |  ||  || || ||||||| |||||     ||||||| ||||||||||| |  ||| |||   | || |||||||| ||||||||||| |||||||| || ||||||||  |  |||
-----------------------------------------------------------agattgcagg-acttgtgatttgtgttgttatttgataggtgtattgtttttgtaaaaaaagggttttaaatactgaattttttcaattgatg-atatgcagGGGATTGCTTTAGCTGTTGGAGACTGGTACTTCGACCGATCTGGCATTAAAGCCATCGACTGCCCCTACCCTTGTGACAAGACCTGCCACAATCTAGTAT

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|88221512|gb|CI221468.1|CI221468
EST:     CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAG                         GGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG
genomic: CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAGgtactttcca ... ggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG
EST: gi|86504593|gb|CI147226.1|CI147226
EST:     CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAG                         GGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG
genomic: CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAGgtactttcca ... ggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG
EST: gi|86505451|gb|CI148084.1|CI148084
EST:     CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAG                         GGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG
genomic: CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAGgtactttcca ... ggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG
EST: gi|86501446|gb|CI144079.1|CI144079
EST:     CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAG                         GGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG
genomic: CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAGgtactttcca ... ggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG
EST: gi|87020132|gb|CI277864.1|CI277864
EST:     CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAG                         GGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG
genomic: CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAGgtactttcca ... ggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG
EST: gi|89162351|gb|CI104679.1|CI104679
EST:     CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAG                         GGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG
genomic: CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAGgtactttcca ... ggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG
EST: gi|86504646|gb|CI147279.1|CI147279
EST:     CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAG                         GGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG
genomic: CCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAGgtactttcca ... ggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAG

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: 36 (upstream exon), 40 (downstream exon)
Score: 2

GTCGAGGAGCAACGGGCTGTTCATCAACTCGTGCTTCGCTCACTGCCAGTCCGAGCTGACGGCCACCTGGAATGGTGGCTCTCCTGCTCTCCAGAACAAGgtactttcca ... ggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAGGCCATCGATTGCCCCTACCCCTGTGACAAAACATGCCACAACATCATAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatgcataaaaaaatacttacttttcagtttcatgctgttcttggatgtgcagGGAATTGCAAAGTCTGTTGGTGACTGGTACTTTGGTCGAGCTGAGGTGAAGGCCATCGATTGCCCCTACCCCTGTGACAAAACATGCCACAACATCATAT
                tacttac  putative branch site (score: 2)
       ataaaaaaatacttac  TA-rich tract