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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGGGCCCCGGAATGGAGCCATCCAGTGCTTCATTAAAAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAGgtaagcctttatcctagtattgtgtttgtttttgtactcgctacatggcatgattatttgggggaaattggttctacgacactgaaagatcctgttgtga...

Basic information

species Oryza sativa
transcript LOC_Os12g06630.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g06630.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G001272_T01 (Zea mays), 5'ss of exon 3
CCTGGGCCCCGGAATGGAGCCATCCAGTGCTTCATTAAAAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAGgtaagcctttatcctagtattgtgtt--tgtttttgtactcgctacatggcatgatta--tttgggggaaattggttctacgacactgaaagatcctgttgtga
|||||||| ||  ||| | ||||||| |||||||| ||||||||||||||||| ||||| ||| || | ||||| || |||||| |||||||||| || ||  || ||| |  |  | | |||||||| |||      | | |  |    |    |  ||| ||| |      |||   |      ||    
CCTGGGCCTCGAGATGTAACCATCCAATGCTTCATCAAAAGGGATAAATCTACTCAAACCTACTACTTGTATCTGTGCCTTAGCACAGgtaagcccttttcaaagcattattatactttctttgtacttgctttgattccttacaaagcattacagctattagtttttttgtgctgtttgtagacatt----

upper sequence: LOC_Os12g06630.3 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv12s0055g00460.t01 (Vitis vinifera), 5'ss of exon 4
CCTGGGCCCCGGAATGGAGCCATCCAGTGCTTCATTAAAAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAGgtaagc--ctttatcctagtattgtgtttgtttttgtac-tcgctacatggcatgattatttgggggaaattggttctacgacactgaaagatcctgttgtga
|| ||||| ||  ||||  | ||||| |||||||| |||||||||||||||| |  ||||||| |||| | ||||||||||||| | ||||| |  |||| |  |  | ||  | |    || ||   |   |   |||||   ||||   |      |||  | | |    ||      |  | ||    
CCAGGGCCACGTGATGGGACTATCCAATGCTTCATCAAAAGGGATAAATCTAACTTAACTTACCACCTTTTTCTATGTCTTAGCCCTGgtaatcttcttttttttgctttttcggtaaccttagtttgttaatttttggcagttttataaagttttccttgcatgttcttttctttttctttttcttt---
















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|33381574|gb|CF196917.1|CF196917
EST:     AAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAG                         CTGTGCTCGTTGAAAGTGGCAAGTTCCTTTTATCGGCGAAAAGATACTCCC
genomic: AAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAGgtaagccttt ... tctcatgtagCTGTGCTCGTTGAAAGTGGCAAGTTCCTTTTATCGGCGAAAAGATACTCCC
EST: gi|33810127|gb|CF330953.1|CF330953
EST:     AAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAG                         CTGTGCTCGTTGAAAGTGGCAAGTTCCTTTTATCGGCGAAAAGATACTCCC
genomic: AAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAGgtaagccttt ... tctcatgtagCTGTGCTCGTTGAAAGTGGCAAGTTCCTTTTATCGGCGAAAAGATACTCCC
EST: gi|58672719|gb|CK061405.1|CK061405
EST:     AAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAG                         CTGTGCTCGTTGAAAGTGGCAAGTTCCTTTTATCGGCGAAAAGATACTCCC
genomic: AAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAGgtaagccttt ... tctcatgtagCTGTGCTCGTTGAAAGTGGCAAGTTCCTTTTATCGGCGAAAAGATACTCCC
EST: gi|58656494|gb|CK045174.1|CK045174
EST:     AAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAG                         CTGTGCTCGTTGAAAGTGGCAAGTTCCTTTTATCGGCGAAAAGATACTCCC
genomic: AAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAGgtaagccttt ... tctcatgtagCTGTGCTCGTTGAAAGTGGCAAGTTCCTTTTATCGGCGAAAAGATACTCCC
EST: gi|58680304|gb|CK068991.1|CK068991
EST:     AAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAG                         CTGTGCTCGTTGAAAGTGGCAAGTTCCTTTTATCGGCGAAAAGATACTCCC
genomic: AAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAGgtaagccttt ... tctcatgtagCTGTGCTCGTTGAAAGTGGCAAGTTCCTTTTATCGGCGAAAAGATACTCCC
EST: gi|11170889|gb|AU163519.1|AU163519
EST:     AAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAG                         CTGTGCTCGTTGAAAGTGGCAAGTTCCTTTTATCGGCGAAAAGATACTCCC
genomic: AAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAGgtaagccttt ... tctcatgtagCTGTGCTCGTTGAAAGTGGCAAGTTCCTTTTATCGGCGAAAAGATACTCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGGGCCCCGGAATGGAGCCATCCAGTGCTTCATTAAAAGGGATAAATCTACCCAAACTTACAACCTATATCTATGTCTTAGCTCAGgtaagcctttatcctagtattgtgtttgtttttgtactcgctacatggcatgattatttgggggaaattggttctacgacactgaaagatcctgttgtga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA