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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actacctgcttagagaatcatcctctgctagtgccttactgttttatatacgaaaatacccccataagtattttatttacattcatgtgccctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g18310.2
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18310.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 17
--actacctgcttagagaatcatcctctgctagtgccttactgttttatatacgaaaatacccccataagtattttatttacattcatgtgccctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG
   | ||  ||||  | | |        |    |   ||||    || |  |  |     |||||| ||    |||   |    | || | ||  || |||||||||| || || ||||||||||||||||||||||| |||||||||||||| || || |||||||||||
gttccactagcttgtaaatttgattggagacccttgtttacacaattttccagcaccccccccccacaatccatttgcctcatgttatatacc--ttctcagATCACGAAGAAAAGACAAGCTGAGGTATCGTTATCCGAGAGGAGAATCCTATCTTGACGTCATTCAAAG

upper sequence: LOC_Os03g18310.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 26
actacctgcttagagaatcatcctctgctagtgccttactgttttat-atacgaaaatacccccataagtattttatttacattcatgtgccctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG
                                        |||  |  || |      | | |  ||  |||| | |       |   || | | || ||||||  | |  ||||||||||| ||||||||||||||| | || || || ||| | ||||||||||||||
----------------------------------------gttagaagatgctgtttaaactcagtagttattatttccctcccctcttgtcttattgcagATCGTGCAAGAAGGACAAGCTTAGGTATCGTTATCCTCGTGGTGAGTCATACTTGGATGTCATTCAAAG

upper sequence: LOC_Os03g18310.2 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 20
-----------------------------------------------------actacctgct--tagagaatcatcctctgctagtgccttactgttttata-tacgaaaatac--------ccccataagtattttatttacattcatgtgccctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG
                                                       |  | | |   | |||| ||   | ||  |    |||   |||||    |  ||| || |        | |  ||  |||| | |       |   || | | || |||||| || |  ||||||||||| ||||||||||||||| | || || || ||| | ||||||||||||||
gtatgtttgcagacttgtaatttctctcttatttgcaagttgaatgcaactaatatggcagataacaaagaagcacaatgtga-aacatcttttggttttggggttagaagatgctgtttaaactcagtagttattatttccctcccctattgtcttattgcagATCGCGCAAGAAGGACAAGCTTAGGTATCGTTATCCTCGTGGTGAGTCATACTTGGATGTCATTCAAAG

upper sequence: LOC_Os03g18310.2 (Oryza sativa), 3'ss of exon 18
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 19
----actacctgcttagagaatcatcctctgctagtgccttactgttttatatacgaaaatacccccataagtattttatttacattcatgtgccctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG
    | ||    |  | | ||  ||| | | || | |  |  |  |||| |  | ||   | ||    |   ||   || || ||| |         ||  ||| |||||||  |||||||||||||||||||| |||||| | || ||||| ||||| ||||| || |||||
agttattattaccccaaaaaa--atcatgtacttgggaatctc-atttttttcaggagctttccttgtttcttaggataatttcatcctcacattaattg-cagGTCACGTAAGAAGGACAAGCTGAGGTATCGGTATCCTCGTGGTGAATCTTACCTGGATGTTATCCAAAG

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|29643803|gb|CB648810.1|CB648810
EST:     GATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGA                         ATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTA
genomic: GATGGGATGACGTATGATGAAATAAAGAAAATTAAACCTGAAGAATATGAgtacgcaaat ... cctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatacgaaaatacccccataagtattttatttacattcatgtgccctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG
                                          tgccctttttc  CT-rich tract
                  ataagtattttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actacctgcttagagaatcatcctctgctagtgccttactgttttatatacgaaaatacccccataagtattttatttacattcatgtgccctttttcagATCACGTAGCAAGGACAAGCTGAGGTATCGTTATCCTAGAGGAGAATCCTACCTCGATGTCATTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA