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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcatgatactgcttcagtgtaatgtatcaagcatctgcagatatgggcatgcttcagcattttctaacattaaacgtttgaatatcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAGAGTGAGCTAACACCAAGCAATGCCAATATACTGGATGGGCGGTATGCCG

Basic information

species Oryza sativa
transcript LOC_Os08g29370.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G015967_T01 (Zea mays), 3'ss of exon 6
gtaagtatcatgatactgcttcagtgtaatgtatcaagcatctgcagat-atgggcatgct--tcagcattttctaacattaaacgtttgaatatcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAGAGTGAGCTAACACCAAGCAATGCCAATATACTGGATGGGCGGTATGCCG
    |||  |      |||   | || |   ||||| |||| ||||||  ||  ||||  |    |   | ||||||| | | |    |  |   |||| ||||||||||||||||||||||||||||||||| | |||||| | || |||||||||||||||||||||||||||||||||||| |||| |||||||| || |
----gtaagagagacatgcaagattgca-catatca-gcatatgcagacgatctgcatcgtatctaatgtattctaacctgagataacttcactgcatgacagGAATTTGATGACAATTCTGCTTCTAGCCAAGTATTTTGGCTCTTGAAAGAGAGTGAGCTAACACCAAGCAATGCCAATATATTGGACGGGCGGTACGCAG

upper sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G23850.1 (Glycine max), 3'ss of exon 6
gtaagtatcatgatactgcttcagtgtaatgtatcaagcatctgcagatatgggcatgcttcagcattttctaacattaaacgtttgaatatcat---ggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAGAGTGAGCTAACACCAAGCAATGCCAATATACTGGATGGGCGGTATGCCG
          |||      |  | | |     ||      |||  |   |||   ||  ||      || ||   ||| |    ||  || |  |      |||||||||| ||||| ||||| || ||||| || |||||| | || ||||| ||||||||||| || || |||||||||||| ||||||| || ||||| |
---------gtgaggagaatctattctttgacattgctgttctttaagcatgctaatcttttttttcttgcttctatttactccttttatgttgtttgaatagGAATTTGAGGACAACTCTGCCTCCAGCCAGATATTTTGGCTATTGAAAGAAAGTGAGCTAACTCCCAGTAATGCCAATATATTGGATGGTCGATATGCAG

upper sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G01260.1 (Glycine max), 3'ss of exon 6
gtaagtatcatgatactgcttcagtgtaatgtatcaagcatctgcagatatgggcatgcttcagcattttctaacattaaacgtttgaatatcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAGAGTGAGCTAACACCAAGCAATGCCAATATACTGGATGGGCGGTATGCCG
|| || |  ||        | || ||   |   | ||||||  |   || |     |  |   || |||  | ||        ||    | |      |||||||||| ||||| ||||| |||||||| || |||||| | || ||||| ||||||||||| || || |||||||||||| ||||||| || |||||||
gtgaggagaatctattctttgcattgctgttctttaagcat--gataatcttttttttttcttgcttttatttactcc---ttttatgttgtttgaatagGAATTTGAGGACAACTCTGCCTCTAGCCAGATATTTTGGCTATTGAAAGAAAGTGAGCTAACTCCTAGTAATGCCAATATATTGGATGGTCGATATGCCG

upper sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G01480.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagtatcatgatactgcttcagtgtaatgtatcaagcatctgcagatatgggcatgcttcagcattttctaacattaaacgtttgaatatcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAGAGTGAGCTAACACCAAGCAATGCCAATATACTGGATGGGCGGTATGCCG
|| |||  | |  | || ||||    |  | |    ||  | |     |||  |  |  |  | ||| | ||   ||| |       || ||     ||||| |||||  |  | || |  || |||||| | |||||| || |||||||||||||||| |||||||||||| |||| ||  ||||||| || || || |
gtgagt-cctttcttcttcttcttcttctttttcatagtttatattattat--gtcttatgaaacatatact--tattgagt-----aacatataaacagGAGTTTGAGAATGACTCAGGATCAAGCCAAGTGTTTTGGCTGCTAAAAGAGAGTGAGCTGACACCAAGCAATTCCAACATCTTGGATGGTCGTTACGCTG

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|86848897|gb|CI295714.1|CI295714
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|88221803|gb|CI221759.1|CI221759
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|313084044|gb|HO213827.1|HO213827
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|25804245|gb|CA760206.1|CA760206
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|86500872|gb|CI143505.1|CI143505
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAATTCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|29658080|gb|CB654355.1|CB654355
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|29613721|gb|CB618734.1|CB618734
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|29657974|gb|CB654249.1|CB654249
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|86831350|gb|CI297619.1|CI297619
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|86257246|gb|CI004064.1|CI004064
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
EST: gi|29622079|gb|CB627090.1|CB627090
EST:     AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT                         GAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG
genomic: AAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGATgtaagtatca ... atcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatatgggcatgcttcagcattttctaacattaaacgtttgaatatcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAGAGTGAGCTAACACCAAGCAATGCCAATATACTGGATGGGCGGTATGCCG
                       ttctaac  putative branch site (score: 1)
                    attttctaacattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatcatgatactgcttcagtgtaatgtatcaagcatctgcagatatgggcatgcttcagcattttctaacattaaacgtttgaatatcatggcagGAATTTGATGACAATTCTGCTTCTAGCCAAATCTTTTGGTTGTTAAAAGAGAGTGAGCTAACACCAAGCAATGCCAATATACTGGATGGGCGGTATGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA