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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCCTGATGGACGTGAAGAGTCTGTCATGAAAAGAACTACACTTGTTGCTAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacatatatactgattactgatgtttttaatttcgcattccactagtatagtactacatgaatgtgtttcgatcttctgaagttcattttctctag...

Basic information

species Oryza sativa
transcript LOC_Os06g45120.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
TTGCCTGATGGACGTGAAGAGTCTGTCATGAAAAGAACTACACTTGTTGCTAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaa-tacatatatactgattact--gatgtttttaatttcgcattccactagtatagtactacatgaatgtgtttcgatcttc---tgaagttcattttctctag
|| |||||||| |||||||| |||||||||||  | || ||||| || |||||||| || |||||||| || |||||||||||||| || |||||||||||| | |   ||| |  ||| | ||  ||| | | || ||    |||        ||| || |  |  ||    || | ||   |   || | || | ||    |  
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctattt----attgttgagaaataatatt-tactaactctttcctattgccaattgtaatttaattggcttg-

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 12
TTGCCTGATGGACGTGAAGAGTCTGTCATGAAAAGAACTACACTTGTTGCTAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaa-tacatatatactgattactgatgtttttaatttcgcattccactagtatagtactacatgaatgtgtttcgatcttctgaagttcattttctctag------
|| |||||||| |||||||| |||||||||||  | || ||||| || |||||||| || |||||||| || |||||||||||||| || |||||||||||| | |   ||  |  ||| | || || | |||| | |        | || |||  ||||| ||   |  || | | ||  ||| | || ||||    |        
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGCACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtagctcttgaattct-atttatttattgttaaga---attaatatt-tacta-attctttcgtattg-tcaactgtaatttatttggcttgtgaaagt

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 12
TTGCCTGATGGACGTGAAGAGTCTGTCATGAAAAGAACTACACTTGTTGCTAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacatatatactgattactgat-gtttttaatttcgcattccactagtatagtactacatgaatgtgtttcgatcttctgaagttcattttctctag
||||||||||| ||||| || |||||||||||| | || ||||||||||||||||| || ||||||||||| ||||||||||||||||| ||||| |||||||||    |   ||  |    | || ||| || ||   | || ||| | |  ||    | |     | | |||   | || | | ||  |||        
TTGCCTGATGGCCGTGAGGAATCTGTCATGAAACGTACCACACTTGTTGCTAACACCTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAGgtaatgttcaggcacacagatttaatagttattgat---gaatcccatt-gccta----tgctcattttttttttttttttttaatgtgaattccag----

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 12
TTGCCTGATGGACGTGAAGAGTCTGTCATGAAAAGAACTACACTTGTTGCTAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacatatatactgattactgatgtttttaatttcg--cattccactagtatagta-ctaca-tgaatgtgtttcgatcttctgaagttcattttctctag
 ||||||||||  | ||||| ||||||||||| |||||||| || || |||||||| || ||||||||||| |||||  | || || || ||||||||||||||| | |  ||  | |||  |  |||| | ||||  |    ||      || ||||  ||||  |  || | ||||      || || ||  |||   |   
CTGCCTGATGGGAGAGAAGAATCTGTCATGAAGAGAACTACGCTCGTAGCTAACACTTCTAACATGCCTGTGGCTGCAAGGGAGGCTTCAATTTATACAGgtaatgctttgatcttcattgttt-tgttatgaattgggattcttttgtatgtgtagtttctacccttcatttttttcatagggctaaactttgtttgagc---

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 12
TTGCCTGATGGACGTGAAGAGTCTGTCATGAAAAGAACTACACTTGTTGCTAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaa-tacatata----tactgattactgatgtttttaatttcgcattccactagtatagtactacatgaatgtgtttcgatcttctgaagttcattttctctag
 |||||||||| |||||||| |||||||||||  ||||||||||||| || ||||| || || |||||||| ||||||||||| || || |||||||||||||| || || ||    || | ||||||      |  |||  |    |  |  | | | | | |  ||  ||  | ||| ||||| || | ||| | |    |  
CTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGCCTGTGGCTGCTCGTGAGGCTTCAATTTATACAGgtaaatatatttacttctattcattactagcacatgaaatggctgggtgaaaaaattttgaagtcaat--attagcttc-atcttttgcaattcttgtgtgtt--

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 12
TTGCCTGATGGACGTGAAGAGTCTGTCATGAAAAGAACTACACTTGTTGCTAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacatatatactgattactgatgttt-----ttaatttc----gcattccactagtatagtactacatgaatgtgtttcgatcttctgaagttcattttctctag-----------------------------------------------
|| || || || || || ||||| ||||||||  | ||||| ||||| || |||||||| ||||||||||| |||||||||||||| || ||||||||||||        | |  |  |  || | ||||     || ||| |    |||   ||     ||| |    ||    | |   ||| |    || | ||  |    | ||                                                
TTACCCGACGGTCGGGAGGAGTCCGTCATGAAGCGTACTACGCTTGTGGCCAACACATCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATTTATACAGgtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattt-tcgcatataattgcgtcctttctacatttgctctgaagattctgttttctgttgcag

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 12
TTGCCTGATGGACGTGAAGAGTCTGTCATGAAAAGAACTACACTTGTTGCTAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacatatatactgattactgatgtttttaattt---cgcattccactagtatagtactacat---gaatgtgtttcgatcttctgaagttcattttctctag---
|||||||| ||||| || |||||||| |||||  | || || || || || || ||||| || |||||||| |||||||||||||| ||||| |||||||||    ||| |  | | ||| |||| | ||    |||   |||| |       || |||   | ||   ||| |  |||   |       | ||  || ||| | |   
TTGCCTGACGGACGAGAGGAGTCTGTTATGAAGCGGACCACTCTCGTGGCCAATACATCAAATATGCCTGTGGCTGCTCGTGAAGCTTCCATCTATACAGgtt-cccatcttgagttatt-ctgaagcttaacttttgatcgcaatgtgaccttaaagtttgaaatcttgaaggattttacgttcatcacattttgttatctgttgcag

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 12
TTGCCTGATGGACGTGAAGAGTCTGTCATGAAAAGAACTACACTTGTTGCTAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaata--catatatactgattactgatgtttttaatttcgcattccactagtatagtactacatgaatgtgttt--cgatcttctgaa-gttcattttctctag--------------------------------
|| |||||||| |||||||||||||| |||||  | || || || || || ||||| || ||||||||||| |||||||||||||| || || || |||||| ||   | | | | ||||      |  || |   |   | ||   || | | |  | ||   || |||| |     | | | ||| | | ||   | ||   |                                
TTACCTGATGGTCGTGAAGAGTCTGTTATGAAGCGTACCACTCTCGTGGCCAACACCTCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATCTACACAGgttattttcttttcttctgagactctactttctaggtgctgtatgaaacca-tttcatcctctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcag

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 12
TTGCCTGATGGACGTGAAGAGTCTGTCATGAAAAGAACTACACTTGTTGCTAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacatatatactgattactgatgtttttaatttcgcattccactagtatagtactacatgaatgtgtttcgatcttctgaagttcattttctctag
 | ||||||||||| |||||||||||||||||  | || || || || ||||| || || || |||||||| || || || ||||| || ||||| || ||||   | |    | | |      | | |  |  | ||| ||      ||                                                  
CTCCCTGATGGACGCGAAGAGTCTGTCATGAAGCGTACAACTCTCGTCGCTAATACTTCAAATATGCCTGTGGCGGCACGAGAAGCTTCAATTTACACGGgtatgtccttccaattcaggctcaacgctgattttatcg-atggtttcag--------------------------------------------------

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 11
lower sequence: EFJ33015 (Selaginella moellendorffii), 5'ss of exon 11
TTGCCTGATGGACGTGAAGAGTCTGTCATGAAAAGAACTACACTTGTTGCTAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacatatatactga---ttactgatgtttttaatttcgcattccactagtatagtactacatgaatgtgtttcgatcttctgaagttcattttctctag
 | ||||||||||| |||||||||||||||||  | || || || || ||||| || || || |||||||| || || || ||||| || ||||| || ||||   | |    | | |   | |  | || |||||     |  |||                                                        
CTTCCTGATGGACGCGAAGAGTCTGTCATGAAGCGTACAACTCTCGTCGCTAATACTTCAAATATGCCTGTGGCGGCACGAGAAGCTTCAATTTACACGGgtatgtccttccaattcaggctcagcgctgattttatcgatggtttcag------------------------------------------------------

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|58692820|gb|CK081507.1|CK081507
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|58611693|gb|CK039405.1|CK039405
EST:     TAACACATCCAACATGCCTGTGGCGGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|58601223|gb|CK011751.1|CK011751
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTA
EST: gi|58659487|gb|CK048167.1|CK048167
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|116875037|gb|EC365545.1|EC365545
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|116875538|gb|EC366046.1|EC366046
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|58657888|gb|CK046568.1|CK046568
EST:     TAACACATCCAACATGCCTGTGGGTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|29617005|gb|CB622017.1|CB622017
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|27578142|gb|CB000837.1|CB000837
EST:     TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
EST: gi|58594482|gb|CF992790.1|CF992790
EST:     TAACACATCCAACATGCCTGGGGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA
genomic: TAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacata ... tgcccaccagGAATTACAATTGCTGAATACTTCCGTGACATGGGCTATAATGTCAGTATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCCTGATGGACGTGAAGAGTCTGTCATGAAAAGAACTACACTTGTTGCTAACACATCCAACATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaatacatatatactgattactgatgtttttaatttcgcattccactagtatagtactacatgaatgtgtttcgatcttctgaagttcattttctctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC