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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaaagtgttcttactgaatctcatgattctaatctgttgatttccttcaaaaataacatttttttctgtgaattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC

Basic information

species Oryza sativa
transcript LOC_Os03g02380.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02380.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G051189_T01 (Zea mays), 3'ss of exon 1
-------------------gtaagtgaaagtgttcttactgaatctcatgattctaatc-tgttgatttcctt---caaaaataacatttttttc-----tgtgaattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC
                      |   |   ||||||   |   | |  ||     |||  | | ||  |       || || ||||  |||  |        ||   ||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| || ||| ||||||||||| | ||||||             
gtaaggagccattccctctcccaactactatgttctctttagttgtgctggcaagaattatatagaaatatcagcacacaagtaacggtttgcttgtggacatggtctttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGGATGTGTTCTATCTTCCTCTTCATGGCAGCCATCTTGCAGAGACGGTTGATGGTT-------------

upper sequence: LOC_Os03g02380.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G13760.1 (Glycine max), 3'ss of exon 6
---------------------gtaagtgaaagtgttcttactgaatctcatgattctaatctgttgatttccttcaaaaataacatttttttctgtgaattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC
                      | | || || || |    || |         |  || | | ||   |    |    | |||   | | || | |  |   |||||||  ||||||||||||||||||| |||||||||||||| || || ||||| ||  ||||    ||| |||| || || || |||||  |||| ||    |
gtatgttacacaatctactacttcaatgcaa-tgcttgagcttaccaatgcagtagtattttcttatctctggttttgactaattgtgtattttctcga---tgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC

upper sequence: LOC_Os03g02380.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 6
----gtaagtgaaagtgtt--cttactgaatctcatgattctaatc------tgttgatttccttcaaaaataacatttttttctgtgaatttt------gcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC
    || |   ||  |  |   | | |  |   |  |||  |||        |  |  |||| |       |    |   |   |||| |||||      ||||||  ||||||||||||||||||| |||||||||||||| || || ||||| ||  ||||    ||| |||| || || || |||||  |||| ||    |
gtatgttacacaatctactacttcaatacaatgcgcgatcttaacagtgtagtagtattttcttatgcgtgtgctttgactaattgtgtattttcttggtgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCGGATAAGC

upper sequence: LOC_Os03g02380.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagtg-----aaagtgttcttactgaatctca-----tga---ttctaatctgttgatttccttcaaaaataacatttttttctgtgaattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC
||||||      ||  |  | || ||| | |  |     |||   |||   ||   ||  |   |       ||     |  || | ||   | || |||| ||||||||||||||||| ||||||||||| ||||| || |||||||||||  | ||     |||| || || ||||| ||| |  ||  ||||  ||
gtaagtccccccaacattctttttctgcaccatagtagctgagatttcgtgtcccatgtctctgtgttgtggtactgactagttttatgtgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC

upper sequence: LOC_Os03g02380.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 6
---------gtaagtgaaagtgttcttactgaatctcatgattctaatctgttgatttccttcaaa-----aataacatttttttctgtgaattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC
          |||  |    |  |||||   |     || |||    ||| |    | |  || ||     ||||    ||| ||||     ||||| |||| |||||||| || ||||||||||||||||||||||| || || ||||||||  ||||  || |  |||| ||  |||| ||| |  |||| ||    |
tgtactgttttaatggtttcttctcttaaccatagggataatttatctctctctgctcctctctaacactaaatattggtttgttcttccctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC

upper sequence: LOC_Os03g02380.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6
-------gtaagtgaaagtgttcttactgaatct-catgattctaatctgttgat--ttccttcaaaaa--taacatttttttctgtgaa--ttttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC
        |   |  |     | | |     |||   || | ||  |||| ||||  |||||||       ||| | || ||| ||  |   ||||| |||| ||||||||||| ||||||||||||||||||||||| || || ||||||||  ||||  | ||| |||| || ||||| |||||  || |||||    
ccttattttggatatagaccatgtgaagacttctatgtgctccttctctggtgatcgttccttctgtttcttaatagttgtttttggtatgtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT

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|58667325|gb|CK056011.1|CK056011
EST:     ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAAT                         GTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAATgtaagtgaaa ... aattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
EST: gi|396941243|gb|HO188452.1|HO188452
EST:     ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAAT                         GTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAATgtaagtgaaa ... aattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
EST: gi|89181048|gb|CI045131.1|CI045131
EST:     TTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAAT                         GTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
genomic: TTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAATgtaagtgaaa ... aattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
EST: gi|29623150|gb|CB628161.1|CB628161
EST:     ATTTTTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAAT                         GTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAATgtaagtgaaa ... aattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
EST: gi|9865094|gb|AU100844.1|AU100844
EST:     ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAAT                         GTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAATgtaagtgaaa ... aattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
EST: gi|87030160|gb|CI111856.1|CI111856
EST:     ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAAT                         GTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAATgtaagtgaaa ... aattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
EST: gi|29614296|gb|CB619309.1|CB619309
EST:     ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAAT                         GTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAATgtaagtgaaa ... aattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
EST: gi|29628548|gb|CB633559.1|CB633559
EST:     ATTTTTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAAT                         GTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAATgtaagtgaaa ... aattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
EST: gi|88904241|gb|CI001974.1|CI001974
EST:     TCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAAT                         GTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATGTTCCTC
genomic: TCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAATgtaagtgaaa ... aattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
EST: gi|88993057|gb|CI108685.1|CI108685
EST:     ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTAGTGCTTTACAAT                         GTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAATgtaagtgaaa ... aattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
EST: gi|25798678|gb|CA754639.1|CA754639
EST:     ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACNAT                         GTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC
genomic: ATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAATgtaagtgaaa ... aattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTC

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: 71 (upstream exon), 63 (downstream exon)
Score: 18

GAAGATGAGATCTCAATATATTCCTGAGGAGGCAAGAAGCACAATCATGAATTTCTTCCGCATACCACTGAACTTGTTTGTTTGTGTGGTGCTTTACAATgtaagtgaaa ... aattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctaatctgttgatttccttcaaaaataacatttttttctgtgaattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC
                         aaataac  putative branch site (score: 18)
                       aaaaataacatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaaagtgttcttactgaatctcatgattctaatctgttgatttccttcaaaaataacatttttttctgtgaattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG