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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatgagatcctgtagtacgatccgtttcatttttgttcggcttgcttgtctattggggggtttgtggcattgacttgtgccggtcggtgaggtca...

Basic information

species Oryza sativa
transcript LOC_Os03g16980.5
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 2
GCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatgagatcctgtagtacgatccgtttcattt--ttgttcggcttgcttgtctattggggggtttg-tggcattgactt--gtgccggtcggtgaggtca-
|| |||||| ||||||| ||||| || || || ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||   |    || | |  |    |||| ||||||  ||| | |  ||||  |   || |||  ||| |   | ||  | ||   ||  |  ||   || ||  
GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTAGACAAGCTCATGGAGAACGAGAAGCACGAGgtacgtgcg---ccccggacgagatcccgtatcatttcgttgcttgttttgcggg---atcgggctgttgggccgaatccattttgatggtgtccgtctagatcta

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 3
GCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatgagatcctgtagtacgatccgtttcatttt--tgttcggcttgcttgtctattggggggtttg-tggcattgactt--gtgccggtcggtgaggtca-
|| |||||| ||||||| ||||| || || || ||||||||||||||||||||||| |||| |||||||||||||||||| |||||||||||   |       | |  |    |||| ||||||   || | |  ||||  |   || |||  ||| |     ||  | ||   ||  || ||   || ||  
GCTAACCTGCGGATCCTGGTCACTGGTGGGGCGGGCTTCATCGGCTCGCACCTCGTGGACAGGCTCATGGAGAACGAGAAACACGAGgtacgtgcg---ctgcggacgagatcccgtatcatttcgctgcttgttttgcggg---atcgggatgttgggccaaatccattttgatggtggccgtgtagatctc
















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|58654932|gb|CK043612.1|CK043612
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCGTGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|58659240|gb|CK047920.1|CK047920
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|30229035|gb|CB966926.1|CB966926
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|428184|gb|D24332.1|D24332
EST:     GACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAG-NAACNTTTTTCACTGGTTCAAAAGACAACCTGAAGAA
genomic: GACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAAC-TTTTTCACTGGTTCAAAAGACAACCTGAAGAA
EST: gi|30228342|gb|CB966233.1|CB966233
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|313080404|gb|HO213412.1|HO213412
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAATCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|33380802|gb|CF196145.1|CF196145
EST:     AACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: AACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|58656016|gb|CK044696.1|CK044696
EST:     TCATCGGCGCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|58672962|gb|CK061648.1|CK061648
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
EST: gi|58659773|gb|CK048453.1|CK048453
EST:     TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAG                         GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG
genomic: TCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatga ... ttctgttcagGTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGAACCTGAGGATCCTCGTCACCGGCGGAGCTGGCTTCATCGGCTCGCACCTCGTCGACAAGCTCATGGAGAACGAGAAGCACGAGgtacggatgagatcctgtagtacgatccgtttcatttttgttcggcttgcttgtctattggggggtttgtggcattgacttgtgccggtcggtgaggtca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC