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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcctgaacaacaagaagctattgcctctattcagttcaacaatcctattcttttttccccaatgagcactggcatttcacctaaatggctacatgatatgctgcctatattctgtttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACATCAAGTGCTTAACAATGAGGAAAAGAAGACATTATTGGAGCGGTACACTC

Basic information

species Oryza sativa
transcript LOC_Os01g59140.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G476009_T01 (Zea mays), 3'ss of exon 2
gttagtcctg-----aacaacaagaagctattgcctctattcagttcaacaatcctattcttttttccccaatgagcac-tggcatttcacctaaatggctacatgatatgctgcctat----attctgtttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACATCAAGTGCTTAACAATGAGGAAAAGAAGACATTATTGGAGCGGTACACTC
|| |||  |      | ||| ||||||||| | |  | |||  |  |  ||   |  ||  ||  ||| |   | |||  ||   ||   |    ||  ||   || | || |   | |    | |       |    |||| |||||  |||||||||| |||||||||||||| || |||||||| ||||| ||||| |  || ||||| ||||||||  |  |||||||||||||  
gtcagttttttgcacaccaagaagaagctactactccaattt-gaccggcagcaccgttgcttggtccgcg-cgcgcatatgctgttgtgcaatgatctct-tgtgttttgttatttctgataactgaagcaatcgacagGAGGCCGAGATGCTTATAAACATCAAGGAACATGTCCTTGTTCCTGAGCATCAGGTGCTCACAAACGAGGAGAAGAAGACGCTTCTGGAGCGGTACACCT

upper sequence: LOC_Os01g59140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0016g03530.t01 (Vitis vinifera), 3'ss of exon 3
gttagtcctgaacaacaagaagctattgcctctattcagttcaacaatcctattcttttttccccaatgagcactggcatttcacctaaatggctacatgatatgctgcctatattctgtttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACATCAAGTGCTTAACAATGAGGAAAAGAAGACATTATTGGAGCGGTACACTC
                    || | | | |  | |   |   || | ||  |||  |   | | |  | | |    | | |     |||| ||| |  ||   |       | ||| | |   |||  |||| || |||||| |  | || ||||| ||||||||||| |||||||| ||||| ||||| | || |||||| |||||||| ||  ||||| |||| ||  
-------------------tagttgtggtccttgt--gggagaaaactctcattactcactactcttttatcttctgaaat-----taaaaggcgaggtggagtata----acattttttggctttacagGAGGCAGAATTGTTGGTCAACATCAAAGAACATGTTCTTGTTCCTGAGCATCAGGTGCTGACCAGTGAGGAGAAGAAGACTTTGCTGGAGAGGTATACCG
















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|29685048|gb|CB681323.1|CB681323
EST:     GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAG                         GAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
genomic: GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAGgttagtcctg ... ttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
EST: gi|29684984|gb|CB681259.1|CB681259
EST:     GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAG                         GAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
genomic: GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAGgttagtcctg ... ttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
EST: gi|89190351|gb|CI015316.1|CI015316
EST:     GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAG                         GAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
genomic: GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAGgttagtcctg ... ttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
EST: gi|87019557|gb|CI282058.1|CI282058
EST:     CCACTTGG-AATTTTCCAG                         GAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
genomic: CCACTTGGAAATTTTCCAGgttagtcctg ... ttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
EST: gi|58611563|gb|CK039275.1|CK039275
EST:     GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTGGGAAATTTTCCAG                         GAAGCCGAATGGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
genomic: GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAGgttagtcctg ... ttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
EST: gi|33683092|gb|CF311331.1|CF311331
EST:     GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAG                         GAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
genomic: GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAGgttagtcctg ... ttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
EST: gi|29685049|gb|CB681324.1|CB681324
EST:     GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAG                         GAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
genomic: GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAGgttagtcctg ... ttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
EST: gi|86498512|gb|CI141145.1|CI141145
EST:     GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAG                         GAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
genomic: GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAGgttagtcctg ... ttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
EST: gi|88843734|gb|CI010992.1|CI010992
EST:     GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAG                         GAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
genomic: GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAGgttagtcctg ... ttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
EST: gi|58669435|gb|CK058121.1|CK058121
EST:     GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAG                         GAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT
genomic: GGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAGgttagtcctg ... ttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACAT

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: 69 (upstream exon), 68 (downstream exon)
Score: 17

CGTCTCCAGAGCGGTATTGGTTCTTCAACAGAACCTCACTCCATTTGCAAGGTCATTTCTTCAAGAATTAGAGCCAAAGATCCACTTGGAAATTTTCCAGgttagtcctg ... ttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACATCAAGTGCTTAACAATGAGGAAAAGAAGACATTATTGGAGCGGTACACTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcatttcacctaaatggctacatgatatgctgcctatattctgtttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACATCAAGTGCTTAACAATGAGGAAAAGAAGACATTATTGGAGCGGTACACTC
        acctaaa  putative branch site (score: 17)
                                     tattctgttttttttt  putative PPT
                                   tatattctgttttttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtcctgaacaacaagaagctattgcctctattcagttcaacaatcctattcttttttccccaatgagcactggcatttcacctaaatggctacatgatatgctgcctatattctgtttttttttagGAAGCCGAATTGCTTATAAATATCAAGGAACATGTTCTCGTTCCTGAACATCAAGTGCTTAACAATGAGGAAAAGAAGACATTATTGGAGCGGTACACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG