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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttttcaccttgtgcaaggatgatctgttccctagatttagtcgtagaagcaatagtttgaacttggaccacttaaacatggtgtttttgtttt...

Basic information

species Oryza sativa
transcript LOC_Os06g45120.1
intron # 15
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 15
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 16
GGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttttcaccttgtgcaaggatgatctgttccctagatttagtcgtagaagcaa-tagtttgaacttg-gaccacttaaacatggtgtttttgtttt
 ||| |||| |||||| | ||||||| |||||| ||  | ||||| ||||| |||||||||||  | || ||||| || || || ||||||||||||||||| | | || |    ||| | || |||  | || |    | ||     | |     |   ||||  |   ||  ||    || | | |  | |     |   
TGAAACCTTTTATGAGCAATTTGATCCAGATTTTATAAACATTAGGACAAAGGCTCGTGAAGTTCTGCAAAGAGAAGATGACCTGAATGAAATTGTCCAGgtgtgtgttcttttattg-gtaatgattgtttgctaatgaaatgcccccatgctttctcctagtacgggattaagaattgttcagcttcttctgcaaatag-

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 15
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 16
GGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtatttttt--ttcaccttgtgcaaggatgatctgt-----tccctagatt-tagtcgtagaagcaatagtttgaacttggaccacttaaacatggtgtttttgtttt
|||||| |||||||||||||| |||| |||||||||  | || || ||||| ||  | || ||||| ||||| || |||||||| ||||||||||||||||||| | |   ||  ||||||  ||| ||    |||      |  |  | | | |||  || | |  || |   |  ||| |    || |||  | |  | ||     
GGAATCTTTCTATGAGAAGTTCGATCCAGATTTCATCAACATCAGGACAAAGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTGTCCAGgtatgtatcacttatccttgtataagtatctattgtggtgaccaatgaactcttgtctcagcaaccctaatac-attttgaaggggttgaac--gataatctt-----

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 15
lower sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 16
GGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttttcaccttgtgcaaggatgatctgttccctagatttagtcgtagaagcaatagtttgaacttggaccacttaaacatggtgtttttgtttt
|||    ||||||||  | | |||||   | || |||   ||  |||||||||| ||||||||| |||| ||||| ||||||||||| || ||||| ||||||  |      | || |||  ||    ||       |   ||||  |  |   ||                                            
GGAGGGATTCTATGAACATTATGATCCGAACTTTATTTCAATCCGAACAAAAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtg-----aactggtgagag----attcaaagtcagtattttcttttcacag--------------------------------------------

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 15
lower sequence: EFJ33015 (Selaginella moellendorffii), 5'ss of exon 15
GGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttttcaccttgtgcaaggatgatctgttccctagatttagtcgtagaagcaatagtttgaacttggaccacttaaacatggtgtttttgtttt
|||    ||||||||| | | |||||   | || |||   ||  |||||||||| ||||||||| |||| ||||| ||||||||||| || ||||| ||||||  |      | || ||| |  |||     ||        | |  ||  ||                                               
GGAGGGATTCTATGAGCATTATGATCCGAACTTTATTTCAATCCGAACAAAAGCACGTGAAGTGCTACAAAGAGAAGACGATCTAAACGAGATTGTTCAGgtacgtg-----aactggtg-agagattcaaagtcagtactttcttttcacag-----------------------------------------------

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|29618245|gb|CB623257.1|CB623257
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|29625786|gb|CB630797.1|CB630797
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|29613337|gb|CB618350.1|CB618350
EST:     TTACAGAGAGAGGACGATTTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: TTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|33804193|gb|CF327971.1|CF327971
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|38477420|gb|CF961553.1|CF961553
EST:     GAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: GAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|29617006|gb|CB622018.1|CB622018
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|116875538|gb|EC366046.1|EC366046
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|88735905|gb|CI757480.1|CI757480
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|66919084|gb|CX105932.1|CX105932
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGGTAA-GATGCACTGGCAGAATCTGATAAGATTACATTGGAAA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGG-TAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAA
EST: gi|29629621|gb|CB634630.1|CB634630
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|58657888|gb|CK046568.1|CK046568
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGAT
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGAT
EST: gi|4715550|gb|AU056666.1|AU056666
EST:     CGATCCAAATGGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGNATCTGATAAGATTACATTGGAAACA
genomic: CGATCTAAAT-GAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|29667460|gb|CB663735.1|CB663735
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|29658784|gb|CB655059.1|CB655059
EST:     AAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|116875037|gb|EC365545.1|EC365545
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|87039264|gb|CI193886.1|CI193886
EST:     AGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|29630925|gb|CB635934.1|CB635934
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|29656412|gb|CB652687.1|CB652687
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|88337198|gb|CI628284.1|CI628284
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
EST: gi|29626983|gb|CB631994.1|CB631994
EST:     AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAG                         CTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA
genomic: AAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACA

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), 57 (downstream exon)
Score: 92

GGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttt ... caaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAATCCTTCTATGAGAAGTTTGATCAAGATTTCATTGATATTAGAACAAAAGCTCGTGAAGTGTTACAGAGAGAGGACGATCTAAATGAAATTGTCCAGgtattttttttcaccttgtgcaaggatgatctgttccctagatttagtcgtagaagcaatagtttgaacttggaccacttaaacatggtgtttttgtttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA