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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaagattaggtgttcataaaaatgttcaagtctataaaaatgttgtagacacttttgtttttctatagcacaagctaatcttgccacatgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGACACCTGAATTCTTGGATTTGTTTGAACTCAAACCATCAGAAGAATGCTC

Basic information

species Oryza sativa
transcript LOC_Os12g40510.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 8
----aaaaaagattaggtgttcataaaaatgttcaa-gtctataaaaatgttgtagacacttttgtttttctatagcacaagctaatcttgccacatgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGACACCTGAA-TTCTTGGATTTGTTTGAACTCAAACCATCAGAAGAATGCTC
     | |   |     || |         |||||| || || |  | | ||||     ||||| || |  |||  |||||| |    |||| | || ||  |||||||||||||||||||||||||||||||||||| || || ||||| ||||| | ||||| ||  |||  ||  ||  |    || ||| |||||| |  ||
ctgtgagaggcaacgcatgatatgctgtcagttcaaagtatagatgactattgt-----cttttcttgtgatatctcacaagtttgcattgctatatttggacagGGACATCACCACTACATTTCCAAGCTTTGTCTTTCACTCTCAGGTTGATGATAACTGAAATTGATGGGGTTACTTTGAAAAGAAACATTAGAAGA-TATTC

upper sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 8
aaaaaagattaggtgttcataaaaa--tgttcaagtctataaaaatgttgtagacacttttgtttttctatagcacaagctaatcttgccacatgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGACACCTGAATTCTTGGATTTGTTTGAACTCAAACCATCAGAAGAATGCTC
 |   ||||  |  | ||||| ||   | |   |    | |    | ||      | || | |  |  | |   | |  ||  | ||      |  | |||||||||||||||| ||||| || |||||||| |||||||| || || || || || ||||         |  | ||   ||   |  |  |  | |||  |
cagtgagatgtgtagatcatagaacattatatgaactaacatctttttttcctgtatttctctggtcttttctgatatcct--ttttaatgtgtacgagcagGGACATCACCACAACATTCCCGAGCTTTGTATTCCATTCACAAGTAGACGATACTTGAAGATAATTTCTCCTATGGCTTCTTCCTTTGGGCTGCATGGCC

upper sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT4G26560.1 (Arabidopsis thaliana), 3'ss of exon 6
aaaaaagattaggtgttcataaaaatgttcaagtctataaaaatgttgtagacacttttgtttttctatagcacaagctaatcttgccaca-----------tgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGACACCTGAATTCTTGGATTTGTTTGAACTCAAACCATCAGAAGAATGCTC
         |  |     | |  || |   ||  | |     |     |  |   |    |||||||  | |||    || |    |||             |||||||||||| ||||| ||||||||||| |||||||| || || || || || || || ||||||                                          
--------gtgagctcctaaaccaaagactaacccgaggtttagccaatgcaacttcaaatttttctgcatcacgtattattaacaccatgatatctgatattgtgtgcagGGATATCACAACTACATTTCCGAGCTTTGTGTTACACTCGCAAGTGGAAGATACCTGA------------------------------------------

upper sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 9
---------------------------aaaaaagattaggtgttcataaaaatgttcaagtctataaaaatgttgtagacacttttgtttttctatagcacaagc--taatcttgccacatg-----tgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGACACCTGAATTCTTGGATTTGTTTGAACTCAAACCATCAGAAGAATGCTC--
                           ||  | ||||   | |    ||  |  |||             | ||      | | |   |  | | ||  | | |   | ||| ||     ||     | |||||||| ||||| ||||| |||||||||||||| |||||||| ||||| || || |||||||       |   |    | |    | |  ||  | |    |   
gtgagttccaaatctttctatttatataaccaggattgaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcagGGATATCACGACTACGTTTCCAAGCTTTGTGTTCCATTCTCAGGTTGAAGATACCTGAAAAAGCAAAA--GCAAAAGCAAGCAGCGGCAAGACATCATTGTA

upper sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 8
aaaaaagattaggtgttcataaaaatgttcaagtctataaaaatgttgtagacacttttgttttt-ctatagcacaagctaatcttgccacatgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGACACCTGA---ATTCTTGGATTTGTTTGAACTCAAACCATCAGAAGAATGCTC
      || |   |   |  | |  | | | ||  |     ||||       || |||| | | |  |||     |  |  ||||       |||||||||||| || || ||||||||||| |||||||| ||||| || ||||| || || ||||||   |  |       | || | |    |  ||      ||||    
----gtgagttcctaaaccaagacttatccgaggtttaggcaatgcaacttccaattttttctgtgttattattaacaccgatctctgatattgtgtgcagGGATATAACAACTACATTTCCGAGCTTTGTGTTCCACTCGCAGGTGGAAGATACCTGAGAAAAACAATAGCATATTAGCAGAGGAGACAATTTGGGAATT---

upper sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 7
-aaaaaagattaggtgttcataaaaatgttcaagtctataaaaatgttgtagacacttttgtttttcta--tagcacaagctaatcttgccacatgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGACACCTGAATTCTTGGATTTGTTTG--AACTCAAACCATCAGAAGAATGCTC
     |  |||      | ||  | |     || |  |     ||| | |   |   |          |  |         |  | ||    | | ||  ||||||||||||||| ||||| |||||||||||||| ||||| || || || |||||||||| ||    |  ||   |   |||           |  | |||  
cttttatcattgtacacttatggacaaa---aaatgcaattggatgctatgagcttctcaaaccactcaactgatgttgatttgttttatttcctttgaacagGGACATCACCACCACATTCCCAAGCTTTGTCTTTCATTCTCAAGTTGACGACACCTGAAGTCCCATACATGAAAGTTGACTGGTTTTTGTTAATAATTGC--

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|88382022|gb|CI530828.1|CI530828
EST:     TTCGTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCANTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
genomic: TTC-TTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAAgtaagatatg ... atgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
EST: gi|29675928|gb|CB672203.1|CB672203
EST:     GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
genomic: GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAAgtaagatatg ... atgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
EST: gi|86865739|gb|CI335441.1|CI335441
EST:     TTGCTGAAGAACATGACTCTCCAGTACCTC-A                         GGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
genomic: TTGCTGAAGAACATGACTCTCCAGTACCTCAAgtaagatatg ... atgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
EST: gi|300215900|gb|HO088526.1|HO088526
EST:     GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
genomic: GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAAgtaagatatg ... atgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
EST: gi|25800868|gb|CA756829.1|CA756829
EST:     GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
genomic: GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAAgtaagatatg ... atgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
EST: gi|29680333|gb|CB676608.1|CB676608
EST:     GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
genomic: GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAAgtaagatatg ... atgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
EST: gi|86487223|gb|CI129856.1|CI129856
EST:     GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
genomic: GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAAgtaagatatg ... atgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
EST: gi|86434583|gb|CI105816.1|CI105816
EST:     GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
genomic: GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAAgtaagatatg ... atgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
EST: gi|29673880|gb|CB670155.1|CB670155
EST:     GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
genomic: GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAAgtaagatatg ... atgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
EST: gi|86489252|gb|CI131885.1|CI131885
EST:     GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAA                         GGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA
genomic: GTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAAgtaagatatg ... atgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGA

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: 74 (upstream exon), 71 (downstream exon)
Score: 37

CAGACACAAAGCATGATGGAAGAATTGATAAAGAAGAGTGGCGCAATCTGGTTCTTCGTCATCCCTCTTTGCTGAAGAACATGACTCTCCAGTACCTCAAgtaagatatg ... atgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGACACCTGAATTCTTGGATTTGTTTGAACTCAAACCATCAGAAGAATGCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtagacacttttgtttttctatagcacaagctaatcttgccacatgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGACACCTGAATTCTTGGATTTGTTTGAACTCAAACCATCAGAAGAATGCTC
                              agctaat  putative branch site (score: 37)
          ttttgtttttctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaagattaggtgttcataaaaatgttcaagtctataaaaatgttgtagacacttttgtttttctatagcacaagctaatcttgccacatgtgtgcagGGACATCACCACTACATTTCCAAGCTTTGTCTTCCATTCCCAGGTCGATGACACCTGAATTCTTGGATTTGTTTGAACTCAAACCATCAGAAGAATGCTC

aaaaaag
- - - - - - - - - ataaaaa
- - - - - - - - - - - - - - - - - - - - - atgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgccac