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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttatttaatcctagtgttcttttcttacagactgtctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT

Basic information

species Oryza sativa
transcript LOC_Os03g48300.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 12
---gtaatttatttaatcctagtgttcttttcttacagactgtcta---tggaccttaattagttctgaaagatttgcgtaagtttttctatcattca-gGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT
    || ||| |  ||   |  | || | | || | | |   | ||   ||  ||| || |  || ||   |        |  || |  |   | | | |||||||||| ||| |||| ||  |  | || ||||| ||  |||||||||| |||||||||||||||||| | || || ||||   | || ||||||   
actatattttctgcaaatattttattttatactaataaatactatacgttgttcctcaactttttgtgctggtgaaaatcacattctgttgctactgaagGTATTATGATGATTCTGCCTGTGTTCTGCGGAAGATGTTGTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCGCCAACTTTACCATGGAAAGTA

upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 11
-------------------------------------------------------------------gtaatt-tatttaatcctagtgttcttttcttacagactgtctatggaccttaattagttctgaaagatttgcgtaagtttt--tctatcattc----agGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT
                                                                    |  || ||| ||    | |      ||  ||||| ||| | | || |   || |   |   |  | |||| | | | || |  | |   | |     ||||||||||| |||||||| ||  |  | |||||||| ||  |||||||||| |||||||||||||||||| | || || ||||   | || ||||||   
gtaatattttgtgatttattgttttggcactgttatatggttcaaaatgcatcaatagttattcactctgcttgtatctataattggaaaagcttatttaca-actctttttgcataata-tctttatggtgaaattttcatcatttctcgtttgctacttctgaagGTATTATGATGATGCTGCCTGTGTGCTGCGAAAGATGTTCTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCACCAACTTTACCATGGAAAGTA

upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 9
---gtaatttatttaatcctagtgttcttttcttacaga--ctgtctatggaccttaa----ttagttctga-aagatttgcgtaagtttttctatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT
    || ||| |  ||   |  | || | | || | | |  || |  || |  |  ||    || || |||   | | |  | |   | | |   | ||  ||||||||||| ||| |||| ||  |  | || ||||| ||  |||||||||| |||||||||||||||||| | || || ||||   | |||||||||   
actatattttctgcaaatattttcttttatactaataaatactatacattgttcccaacatttttgtgctggtgaaaatcacat---tctgttgctaatgaagGTATTATGATGATTCTGCCTGTGTTCTGCGGAAGATGTTGTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCGCCAACTTTACCTTGGAAAGTA

upper sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 12
---gtaatttatttaatcctagtgttcttttcttacagactg----tctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT
     |   | | | ||| |  | | |  || |   |  ||     | |||  |  |  | |  |  | | | || |    |  | | | | ||  | |||||||| ||||||||||| ||  |  |||| || || ||| | ||||||||||| ||||||||||||||||| || ||||| |  || || ||||||   
gataaacactgtgtcatcgtcatatccacttttggaactctcagtttgtattcatttggagttttaatcagaaatgtcaccagatctctttctctgtaagGTATTACGACGATGCTGCTTGTGTGCTACGGAAAATGTTTTTGGATGCAAAGGCTCCTCATCTTTCTTCAACAATTCCTCCCATTCTGCCATGGAAAATC

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|29674285|gb|CB670560.1|CB670560
EST:     TCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA                         GTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAA
genomic: TCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatt ... tatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAA




















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), 73 (downstream exon)
Score: 12

GTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAAgtaatttatt ... tatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctatggaccttaattagttctgaaagatttgcgtaagtttttctatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT
         ccttaat  putative branch site (score: 12)
                                       tttttctatcattc  putative PPT
           ttaattagtt  TA-rich tract