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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatcttctagtgaattccaacctgcttttacaacacatggaaccctaaattctagtaaaaattttggccctgcacttttaacagctagttcttttgcagATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG

Basic information

species Oryza sativa
transcript LOC_Os01g62810.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62810.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 6
----atatcttctagtga-attccaacct---gcttttacaacacatggaaccctaaattctagtaaaaattttggccctgcacttttaacagctagttct-tttgcagATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG
          | ||||   |||  ||  |   | |||| ||| | ||    |     ||| || | |||||||  |||||    ||| |    | ||||||  ||||||||||||||||||| ||||||||||||||||| ||||| ||||||
tgtagcggggtttagtttcattttaagttttagtttttccaatagatatgcc-----attttattcaaaattt--gccctta--tttaactctcaagttctgcttgcagATTCAGGAGCACTTCTTACATTTGGATGGGGGCTGTATGGACAG

upper sequence: LOC_Os01g62810.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G302245_T01 (Zea mays), 3'ss of exon 4
atatcttctagtgaattccaacctgcttttacaacacatggaaccctaaattcta-gtaaaaattttggccctgcactt--ttaacagctagttctt--ttgcagATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG
     || ||| ||  |  |   | | |||| | |  | |     | ||    || |  |   | ||     | | |||  |||||    |  || |  |||||||||||||||| || ||||||||||| ||||| ||||| ||||||
----attgtagcgaggtttagttt-catttaaagctgaagtttttccaatagatatgccattttgttcaaatttctcttatttaacgctgaagtcctgcttgcagATTCAGGAGCTCTTCTTACATTTGGGTGGGGGCTGTATGGACAG
















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|29617734|gb|CB622746.1|CB622746
EST:     TTGCGTGAAGGCCATTGCATGTGGGGGTCGCCACAGTGCTGTAGTAACAG                         ATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG
genomic: TTGCGTGAAGGCCATTGCATGTGGGGGTCGCCACAGTGCTGTAGTAACAGgtaagccctt ... tcttttgcagATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG
EST: gi|29617735|gb|CB622747.1|CB622747
EST:     TTGCGTGAAGGCCATTGCATGTGGGGGTCGCCACAGTGCTGTAGTAACAG                         ATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG
genomic: TTGCGTGAAGGCCATTGCATGTGGGGGTCGCCACAGTGCTGTAGTAACAGgtaagccctt ... tcttttgcagATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG
EST: gi|29664301|gb|CB660576.1|CB660576
EST:     TTGCGTGAAGGCCATTGCATGTGGGGGTCGCCACAGTGCTGTAGTAACAG                         ATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG
genomic: TTGCGTGAAGGCCATTGCATGTGGGGGTCGCCACAGTGCTGTAGTAACAGgtaagccctt ... tcttttgcagATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG
EST: gi|29677605|gb|CB673880.1|CB673880
EST:     CAGTGCTGTAGTAACAG                         ATTCAGGACCACTACTTACATTTGGATGGGGACTGTACGGACAG
genomic: CAGTGCTGTAGTAACAGgtaagccctt ... tcttttgcagATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG
EST: gi|29670637|gb|CB666912.1|CB666912
EST:     TTGCGTGAAGGCCATTGCATGTGGGGGTCGCCACAGTGCTGTAGTAACAG                         ATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG
genomic: TTGCGTGAAGGCCATTGCATGTGGGGGTCGCCACAGTGCTGTAGTAACAGgtaagccctt ... tcttttgcagATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG
EST: gi|86900111|gb|CI300166.1|CI300166
EST:     TTGCGTGAAGGCCATTGCATGTGGGGGTCGCCACAGTGCTGTAGTAACAG                         ATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG
genomic: TTGCGTGAAGGCCATTGCATGTGGGGGTCGCCACAGTGCTGTAGTAACAGgtaagccctt ... tcttttgcagATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaattctagtaaaaattttggccctgcacttttaacagctagttcttttgcagATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG
                               ttttaac  putative branch site (score: 2)
                                            ttcttttgc  putative PPT
     ttctagtaaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatcttctagtgaattccaacctgcttttacaacacatggaaccctaaattctagtaaaaattttggccctgcacttttaacagctagttcttttgcagATTCAGGAGCACTACTTACATTTGGATGGGGACTGTACGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA