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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaagaagcctctctagttgttctctgttatttaggattgagaagtcagaaccttaattatctagtgagcttttgttaactattatcggttcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGATTTATTGATCCCAGTACTGGTAAAGTTCGTACAATACCTCTTGAGTTAAT

Basic information

species Oryza sativa
transcript LOC_Os08g29370.2
intron # 4
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 4
lower sequence: GRMZM2G015967_T01 (Zea mays), 3'ss of exon 4
tgaagaagcctctctagttgttctctgttatttaggattgagaagtc--agaaccttaattatctagtgagcttttgttaactattatcggttcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGATTTATTGATCCCAGTACTGGTAAAGTTCGTACAATACCTCTTGAGTTAAT
      |  |  |||||   || |   |  |  | | || ||| | |  ||       |       |||| ||||   | |    | | ||||||| |||||||||||| ||||||||||||||||| ||||| ||||| ||||||||||| ||||| |||||||| || || ||| | |||||  ||||||||||  | ||
--ttacactccatctagccattataaatgttcaatgttttagatgacctagtgtgcctagaggtcggtgaactttctctgaactgtgttggttcttatgcagCTGATGGCTTTGTTGTTCAAACTGGAGATCCAGAGGGGCCAGCTGAGGGCTTTATCGATCCCAGCACCGGCAAAATCCGTACGGTACCTCTTGAAATTAT

upper sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G01260.1 (Glycine max), 3'ss of exon 4
-----tgaagaagcctctctagttgttctctgttatttaggattgagaagtcagaaccttaattatctagtgagcttttgttaactattatcggttcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGATTTATTGATCCCAGTACTGGTAAAGTTCGTACAATACCTCTTGAGTTAAT
       ||   | ||   | ||  | || |  | |||||  ||  |   |||  |   || || |  | |    ||||   |  | ||||    | || |||||| ||||| |||||||| |||||||| |||||||| || || |||||||| ||||||||||| ||||| |  ||| |  | ||||||||  | ||  | | 
atatccaaaatgggcttctttgtactgctttcctctttag--ttatgctttcacgaagatagttttaaattttattttttgaattttttata---ttttgtgcagCGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTTTTATTGATCCAAGTACAGAGAAAATCAGGACAATACCATTAGAAATTAC

upper sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G23850.1 (Glycine max), 3'ss of exon 4
------tgaagaagcctctctagttgttctctgttatttaggattgagaagtcagaaccttaattatctagtgagcttttgttaactattatcggttcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGATTTATTGATCCCAGTACTGGTAAAGTTCGTACAATACCTCTTGAGTTAAT
        ||   || ||||| ||  | || |  | ||||| |        |||  |   || || |  | |    ||||   |  | ||||    | || |||||| ||||| |||||||| |||||||| |||||||| ||||| |||||||| ||||||||||| ||||| |  ||| |  | ||||||||  | ||  | | 
atatccaaaatgggcttctct-gtactgctttcctctttagtaacactt--tcaccaagatagttttaaattttattttttgaattttttata---ttttgtgcagCGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGACCTGCTGAGGGTTTTATTGATCCAAGTACAGAGAAAATCAGGACAATACCATTAGAAATTAC

upper sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0066g01410.t01 (Vitis vinifera), 3'ss of exon 4
tgaagaagcctctctagttgttctctgtta-tttaggattgagaagtcagaaccttaattatctagtgagcttttgttaa--ctattatcggttcttt--tgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGATTTATTGATCCCAGTACTGGTAAAGTTCGTACAATACCTCTTGAGTTAAT
       |||||  |  |  ||   || || |||   ||||       | ||   ||| |   ||||   |||| | |||  ||   ||    | |||  |||||||||||| ||||||||||||||||| ||||||||||| || || ||||| ||||||||||| ||||| |  ||    || ||| |||| |||||  | ||
-actactgcctccatcatgcttagttgataatttcatattgta----tacaatgctaagttgatagttttctttcgataaaactcagatttactttttgttgcagCTGATGGATTTGTTGTTCAAACTGGAGATCCTGAGGGTCCTGCAGAGGGCTTTATTGATCCAAGTACAGAAAAGCCCCGGACAGTACCACTTGAAATCAT

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|51946079|gb|CV152420.1|CV152420
EST:     CTTAGATCTGGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAG                         CTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT
genomic: CTTAGATCTGGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAGgtaaggttgc ... tcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT
EST: gi|25804245|gb|CA760206.1|CA760206
EST:     GGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAG                         CTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGTTGAGGGAT
genomic: GGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAGgtaaggttgc ... tcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT
EST: gi|86500872|gb|CI143505.1|CI143505
EST:     CTTAGATCTGGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAG                         CTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCACCTGAGGGAT
genomic: CTTAGATCTGGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAGgtaaggttgc ... tcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT
EST: gi|29658080|gb|CB654355.1|CB654355
EST:     CTTAGATCTGGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAG                         CTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT
genomic: CTTAGATCTGGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAGgtaaggttgc ... tcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT
EST: gi|29613721|gb|CB618734.1|CB618734
EST:     CTTAGATCTGGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAG                         CTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT
genomic: CTTAGATCTGGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAGgtaaggttgc ... tcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT
EST: gi|29657974|gb|CB654249.1|CB654249
EST:     CTTAGATCTGGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAG                         CTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT
genomic: CTTAGATCTGGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAGgtaaggttgc ... tcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT
EST: gi|86831350|gb|CI297619.1|CI297619
EST:     ACGGAAGTTCTATGATGGCATGGAAATTCAAAGAG                         CTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT
genomic: ACGGAAGTTCTATGATGGCATGGAAATTCAAAGAGgtaaggttgc ... tcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT
EST: gi|29622079|gb|CB627090.1|CB627090
EST:     CTTAGATCTGGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAG                         CTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT
genomic: CTTAGATCTGGTGGAACGGAAGTTCTATGATGGCATGGAAATTCAAAGAGgtaaggttgc ... tcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagaaccttaattatctagtgagcttttgttaactattatcggttcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGATTTATTGATCCCAGTACTGGTAAAGTTCGTACAATACCTCTTGAGTTAAT
                            tgttaac  putative branch site (score: 2)
                                            ttcttttgc  putative PPT
                         ttttgttaactattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaagaagcctctctagttgttctctgttatttaggattgagaagtcagaaccttaattatctagtgagcttttgttaactattatcggttcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGATTTATTGATCCCAGTACTGGTAAAGTTCGTACAATACCTCTTGAGTTAAT

- - - - - - - - -ttgttct