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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaactcactctcttctccccttaaaccatttctttgctcagagtgttctcaatatttatggtttttcactgcgatcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCGCTGCGTGGGAA

Basic information

species Oryza sativa
transcript LOC_Os01g64660.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64660.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G836250_T01 (Zea mays), 3'ss of exon 2
gtacgaactcactctcttctcccctta-aaccatt-----tctttgctcagagtgttctcaatatttatggtttttcact-gcgatcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCGCTGCGTGGGAA--------------------------------------
|||||||    |   ||| ||| | |   |  |||     | |  | || ||| ||  ||    ||| ||  |   | |  ||    | ||||||||||| ||||| |||||||||||||||||||| |||||||||||||||  ||||||||| |                                       
gtacgaatatccctccttgtccacctgcgattattgtccgtttgagttccgagagtgttctgc-tttctgactcggcgcccgccgcggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAGGTGAGCAGACTGAACTTGTTAATTATTGACCTGCCCGT

upper sequence: LOC_Os01g64660.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G836250_T02 (Zea mays), 3'ss of exon 2
gtacgaactcactctcttctcccctta-aaccatt-----tctttgctcagagtgttctcaatatttatggtttttcact-gcgatcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCGCTGCGTGGGAA
|||||||    |   ||| ||| | |   |  |||     | |  | || ||| ||  ||    ||| ||  |   | |  ||    | ||||||||||| ||||| |||||||||||||||||||| |||||||||||||||  ||||||||| | 
gtacgaatatccctccttgtccacctgcgattattgtccgtttgagttccgagagtgttctgc-tttctgactcggcgcccgccgcggtgtgcagTGCGTCCTTGTGTCCGAGGAGGACGAGGAAGCAACGTTCGTGGACCCTAAGCTGCGTGGAAG
















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|29682613|gb|CB678888.1|CB678888
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
EST: gi|88346774|gb|CI657325.1|CI657325
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGA
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGA
EST: gi|88575674|gb|CI669819.1|CI669819
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTG
EST: gi|88448534|gb|CI693922.1|CI693922
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCG
EST: gi|88340388|gb|CI659594.1|CI659594
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCT
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCT
EST: gi|88320093|gb|CI639421.1|CI639421
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACC
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACC
EST: gi|88321676|gb|CI672817.1|CI672817
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAA
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAA
EST: gi|58590217|gb|CF988525.1|CF988525
EST:     GGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
genomic: GGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
EST: gi|218478896|gb|FG959665.1|FG959665
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
EST: gi|33663175|gb|CF294142.1|CF294142
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
EST: gi|88331152|gb|CI639563.1|CI639563
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACG
EST: gi|88338555|gb|CI645809.1|CI645809
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTT
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTT
EST: gi|44676478|gb|CR289912.1|CR289912
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
EST: gi|88329187|gb|CI653094.1|CI653094
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
EST: gi|88381754|gb|CI682426.1|CI682426
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
EST: gi|88370994|gb|CI595106.1|CI595106
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
EST: gi|88341640|gb|CI641392.1|CI641392
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGAC
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGAC
EST: gi|88576289|gb|CI670434.1|CI670434
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
EST: gi|88408548|gb|CI686045.1|CI686045
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGG
EST: gi|88570906|gb|CI662279.1|CI662279
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACG
EST: gi|88359332|gb|CI679859.1|CI679859
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGT
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGT
EST: gi|88326670|gb|CI658392.1|CI658392
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGA
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGA
EST: gi|88343123|gb|CI641649.1|CI641649
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAG
EST: gi|88390100|gb|CI590613.1|CI590613
EST:     TGCTGTCCAAGGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGAC
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGAC
EST: gi|88336728|gb|CI643903.1|CI643903
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGT
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGT
EST: gi|88430397|gb|CI567416.1|CI567416
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
EST: gi|88388836|gb|CI592724.1|CI592724
EST:     TGCTGTC-AACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCAC-                         TGCGTTCTTGTCTCC-AGGAGGA
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGA
EST: gi|88347733|gb|CI655086.1|CI655086
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCG
EST: gi|86848574|gb|CI293902.1|CI293902
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCG
EST: gi|38481229|gb|CF965318.1|CF965318
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTG
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTG
EST: gi|86829513|gb|CI286720.1|CI286720
EST:     TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACC                         TGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCT
genomic: TGCTGTCCAACGAGGTGTTCGTCAAGGCTCTCGTCAGCAGCGGCCGCACCgtacgaactc ... tcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttgctcagagtgttctcaatatttatggtttttcactgcgatcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCGCTGCGTGGGAA
                     aatatttatggttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgaactcactctcttctccccttaaaccatttctttgctcagagtgttctcaatatttatggtttttcactgcgatcgcgtgcagTGCGTTCTTGTCTCCGAGGAGGACGAGGAAGCGACGTTCGTGGACCCTGCGCTGCGTGGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA