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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaatctttggcctccctgacaatttgtttaaacatgcccgtagaaagtgctgttcctggtctaacatctactgacaaaatgtggtgacatttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG

Basic information

species Oryza sativa
transcript LOC_Os01g62810.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62810.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 9
-----gttaatctttggcctccctgacaatttgtttaaacatgcccgtagaaagtgctgttcctggtctaacatctactgacaaaatgtggtgacatttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG--------------------------------------------------------
     ||  |           ||  | || | |        |  |  |  | | | |   |   | | |  |||   |||||||   ||      | |  |||||||||||| ||||| ||||||||||||||||||||||| || |||                                                        
aggtggtggaaaaaaatgtgtccatagaaatggaaaggggttaactatctatattaccaataa-gtttttccat---ctgacaagg-gttacacaactattgcagATGAAGGTGAGGTATTCTGCTGGGGATGGAACAAGTATGGCCAGGTGGGTGCCCCTTAACATACCTTTTGCATAAACATATTGGATTGTAAAATTAGCTG

upper sequence: LOC_Os01g62810.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G337819_T01 (Zea mays), 3'ss of exon 9
-----gttaatctttggcctccctgacaatttgtttaaacatgcccgtagaaagtgctgttcctggtctaacatctactgacaaaatgtggtgacatttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
     ||  |           ||  | || | |        |  |  |  | | | |   |   | | |  |||   |||||||   ||      | |  |||||||||||| ||||| ||||||||||||||||||||||| || |||
aggtggtggaaaaaaatgtgtccatagaaatggaaaggggttaactatctatattaccaataa-gtttttccat---ctgacaagg-gttacacaactattgcagATGAAGGTGAGGTATTCTGCTGGGGATGGAACAAGTATGGCCAG

upper sequence: LOC_Os01g62810.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G302245_T01 (Zea mays), 3'ss of exon 7
gttaatctttggcc-tccctgacaatttgtttaaacatgcccgtagaaagtgctgt-tcct---ggtctaacatctactgacaaaatgtggtgacatttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
    | ||  |||  |     | ||| | | || | |   |   ||      || | ||||   |   |    ||  ||||||||  ||      | |  |||||||||||||||||| |||||||||||||||||||||||||| |||
----aactaaggcggtgaacaaaaatgtatctagagaaatcgaaaggggtaactatatcctcaggaagtcttctcatctgacaaag-gttacacaactattgcagATGAAGGCGAGGTATTCTGCTGGGGATGGAACAAGTACGGCCAG

upper sequence: LOC_Os01g62810.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 9
---gttaatctttggcctccctgacaatttgtttaaacatgcccgtagaaagtgctgttcctggtctaacatctactgacaaaatgtggtgacatttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
   ||| | ||     |        | ||||||  |           |    |  | ||  | |  |   ||   ||  |    | |  |  | ||| |  |||| | ||  | |||||||||||||||||||||||||| ||||||
catgttgagctc--atcgatgctgtattttgttagatggaaatttgcgtgtctattattaatagattcttattagctctccctttttttttcccttt-tcaagATAATGGAAAAGTCTTCTGCTGGGGATGGAACAAGTATGGACAG

upper sequence: LOC_Os01g62810.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 9
gttaatctttggcctccctgacaatttgtttaaacatgcccgtagaaagtgctgttcctggt-ctaacatctactgacaaaatgtggtgacatttatgc-----agATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
        |||  | |  |||   | | |||     |     | |||| |    |  ||  |  ||| |  | || |  |  | |  |    |||         |||| | ||  | |||||||||||||||||||||||||| ||||||
----tgtgttgagcacattgatgctgtattttttatta--gatggaaatttgcatgtctattattaatagattcttattagctctccttttttttccctcttcaagATAATGGAAAAGTCTTCTGCTGGGGATGGAACAAGTATGGACAG

upper sequence: LOC_Os01g62810.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 9
gttaatc-tttggcctccctgacaatttgtttaaacatgcccgtagaaagtgctgttcctggtctaacatctactgacaaaa-tgtggtgacatttat-gcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
|| |  | |||  ||         |||   ||  |  |   |   |||||||   ||| |  |  ||| |  |   ||     |||| |    ||| | | |||||||||    || |||||||||||||||||||| |||||||||
gtaacccatttaaccaaagactagattcagtttcatgttagctaggaaagtg--attcatcttaaaacttaaaaaaactgctctgtgtttttgtttgttgtagATGAAGGGAGAGTATTCTGCTGGGGATGGAACAAATACGGACAG

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|29617354|gb|CB622366.1|CB622366
EST:     GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTG                         ATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
genomic: GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTGgtacctttga ... atttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
EST: gi|29617734|gb|CB622746.1|CB622746
EST:     GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTG                         ATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
genomic: GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTGgtacctttga ... atttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
EST: gi|88228786|gb|CI228266.1|CI228266
EST:     GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTG                         ATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
genomic: GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTGgtacctttga ... atttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
EST: gi|88217463|gb|CI217312.1|CI217312
EST:     GTATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTG                         ATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
genomic: GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTGgtacctttga ... atttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
EST: gi|29617735|gb|CB622747.1|CB622747
EST:     GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTG                         ATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
genomic: GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTGgtacctttga ... atttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
EST: gi|29664301|gb|CB660576.1|CB660576
EST:     GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTG                         ATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
genomic: GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTGgtacctttga ... atttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
EST: gi|38473651|gb|CF957783.1|CF957783
EST:     GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTG                         ATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
genomic: GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTGgtacctttga ... atttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
EST: gi|88998355|gb|CI038240.1|CI038240
EST:     GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTG                         ATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
genomic: GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTGgtacctttga ... atttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
EST: gi|29677605|gb|CB673880.1|CB673880
EST:     GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTG                         ATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
genomic: GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTGgtacctttga ... atttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
EST: gi|86496172|gb|CI138805.1|CI138805
EST:     GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTG                         ATGAAGGCGAGGTCTTCTGCTGGGGACGGAACAAGTACGGACAG
genomic: GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTGgtacctttga ... atttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
EST: gi|29670637|gb|CB666912.1|CB666912
EST:     GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTG                         ATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
genomic: GAATGCACGAGCTGTTTCTTGTGGAGCTCGTCATAGTGCAATAATAACTGgtacctttga ... atttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtgctgttcctggtctaacatctactgacaaaatgtggtgacatttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG
                         tactgac  putative branch site (score: 1)
                                           acatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatctttggcctccctgacaatttgtttaaacatgcccgtagaaagtgctgttcctggtctaacatctactgacaaaatgtggtgacatttatgcagATGAAGGCGAGGTCTTCTGCTGGGGATGGAACAAGTACGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA