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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgacctggtaaaaattaatctcatatctgtcaaagaacaatggtactgatttgttcctgccactggtggcacttctctttgtttttagGAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATCTTCATTTCCTTCCTGTTG

Basic information

species Oryza sativa
transcript LOC_Os01g63060.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63060.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G169293_T01 (Zea mays), 3'ss of exon 3
gtatgtgacctggtaaaaattaatctcatatctgtcaaagaacaatggtactgatttgttcctgccactggtggcacttctctttgtttttagGAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATCTTCATTTCCTTCCTGTTG
|||||| | |||     | | | | |||| |   | ||| |   |    | | |||||||                 || | | ||     |||| ||||| || || ||||| ||| ||||||| ||||| ||||| ||||||||||||||||| ||||||
gtatgtcatctgcctttattcagtttcatgttcataaaatac--acaacattaatttgtt-----------------ttgtgtatggc---agGAGCTTGGCCAAGAGAAAGGTTATCTTAGTGAAAGCGTTTTCACTTTCATCTTCATTTCCTTTCTGTTG

upper sequence: LOC_Os01g63060.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G004949_T01 (Zea mays), 3'ss of exon 1
gtatgtgacctggtaaaaattaatctcatatctgtcaaagaaca-atggtactgatttgt-tcctgccactggtggcacttctctttgtttttagGAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATCTTCATTTCCTTCCTGTTG
||| || | ||      |   | | |||| |   | ||| || | |    | | |||| | |  ||||||||||| |||  |||  |||    |||| ||||| || || ||||| ||| ||||||||||| | ||||| |||||||||||||||||  |  ||
gtaagtcatcttcctttatacagtttcatgttcataaaataatacagaacattaatttttgttgtgccactggtgacacacctccatgtgc--agGAGCTTGGCCAAGAGAAAGGTTATCTTAGTGAGAGCTTATTCACTTTCATCTTCATTTCCTTTTTTCTG
















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|33675715|gb|CF303954.1|CF303954
EST:     TGCATCGACCTGGGCCACTGCTCCAGGACTTGGGATTCATGGCTCTTCCG                         GAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATC
genomic: TGCATCGACCTGGGCCACTGCTCCAGGACTTGGGATTCATGGCTCTTCCGgtatgtgacc ... ttgtttttagGAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATC
EST: gi|2312423|gb|C28578.1|C28578
EST:     TGCATCGNCCNGGGCCACTGCTCCAGGACTTGGGATTCATGGCTCTTCCG                         GAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATC
genomic: TGCATCGACCTGGGCCACTGCTCCAGGACTTGGGATTCATGGCTCTTCCGgtatgtgacc ... ttgtttttagGAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATC
EST: gi|29646376|gb|CB651383.1|CB651383
EST:     TGCATCGACCTGGGCCACTGCTCCAGGACTTGGGATTCATGGCTCTTCCG                         GAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATC
genomic: TGCATCGACCTGGGCCACTGCTCCAGGACTTGGGATTCATGGCTCTTCCGgtatgtgacc ... ttgtttttagGAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATC
EST: gi|300215948|gb|HO088574.1|HO088574
EST:     TGCATCGACCTGGGCCACTGCTCCAGGACTTGGGATTCATGGCTCTTCCG                         GAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATC
genomic: TGCATCGACCTGGGCCACTGCTCCAGGACTTGGGATTCATGGCTCTTCCGgtatgtgacc ... ttgtttttagGAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATC
EST: gi|117231357|gb|CT842216.1|CT842216
EST:     TGCATCGACCTGGGCCACTGCTCCAGGACTTGGGATTCATGGCTCTTCCG                         GAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATC
genomic: TGCATCGACCTGGGCCACTGCTCCAGGACTTGGGATTCATGGCTCTTCCGgtatgtgacc ... ttgtttttagGAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATC

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: 70 (upstream exon), 49 (downstream exon)
Score: 8

TACATTCATGGACTGGCTGCTCGAGGAGTACATTACTTGCATCGACCTGGGCCACTGCTCCAGGACTTGGGATTCATGGCTCTTCCGgtatgtgacc ... ttgtttttagGAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATCTTCATTTCCTTCCTGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaacaatggtactgatttgttcctgccactggtggcacttctctttgtttttagGAACTTGGACAGGACAAAGGATATGTTAGTGAGAGCGTGTTCACATTCATCTTCATTTCCTTCCTGTTG
          tactgat  putative branch site (score: 8)
                                    cacttctctttgtttt  putative PPT
                                            tttgttttta  TA-rich tract