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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtatagtccaatgtctatgcttgctgaaatatttatgtccatattactagtgtatgtacctctcatttgttttctttgaacatttcag

Basic information

species Oryza sativa
transcript LOC_Os08g42740.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42740.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G100913_T02 (Zea mays), 5'ss of exon 8
CTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtatagtccaatgtctatgcttgctgaaatatttatgtccatattactagtgtatgtacctctcatttgtt-ttctttgaacatttcag
||||||||||||| || ||||| |||||||| ||||||||||||||||||||||||||||||||||| ||||| || ||||| ||||| || || ||||||||| || || |     | ||   ||||| | ||       | |  |  || ||| | | | |   |||   ||||||| ||||| |||
CTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttcact-----tactgcttgaaagaattgcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacattccag

upper sequence: LOC_Os08g42740.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 5'ss of exon 8
CTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtatagtc-caatgtctatgcttgctgaaatatttatgtccatattactagtgtatgtacctctcatttgttttctttgaac-atttcag----------
| ||||| ||||| || |||||||||||||| |||||||||||||||||||| || |||||||| || ||||| ||||| || ||||||||||||||||||||   |   || ||   || ||    |||    |||      |  | |  ||  | ||       | |  || || | | | |  || |          
CAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAGTTCTGCTGgtaagttgataaagtggttgattaaacaaaatgctataatgtcagaagttatgcttttattctctctatacttcctgtaatctaactctgaattggattc

upper sequence: LOC_Os08g42740.2 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 5'ss of exon 9
CTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtata-gtccaatgtctatgcttgctgaaatatttatgtccatattactagtgtatgtacctctcatttgttttctttgaacatttcag---------------------------------------------------------------------------------------------------------
| ||    || || || || ||||| ||| | ||||| || || || || || |||||||| || |||||||| |||||||||||||||||||| ||||||||        ||   |    |||     | | | |||     || |  | |   | |  |  | ||||  |          | || ||                                                                                                         
CGAACAGCAAACCCTGTCCCAAATGTAAAAGGCCAATCGAAAAGAATCAAGGCTGCATGCACATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagtaatggataatttcaattgaatctaaagtcatggatggatcatgattcattcttaccttaattttatagacacagctacttaagtttacgttgcttcactctgagtatgttgacaccagtggttggtaagtctatcacttataagcaaccaaatttattcactcagttttatttatgcgtttttgacag

upper sequence: LOC_Os08g42740.2 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S178_72V6.3 (Physcomitrella patens), 5'ss of exon 8
CTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtatagtccaatgtctatgcttgctgaaat--atttatgtccatattactagtgtatgtacctctcatttgttt---tctttgaacatttcag---------------------------------------------------------------------------
| ||    || || ||||| ||||| ||  |||| || || |||||||| || ||||||||||| |||||||| |||||||||||||||||||| ||||||||   |  ||    ||| ||| ||  | |  | |||     |  | | | |  |  ||||   | || |||     ||      | | | ||                                                                           
CAAACAGCAAACCCTGCCCTAAATGTAAGAGACCGATTGAAAAAAACCAAGGCTGCATGCATATTACTTGCACACCACCTTGCAAATTTGAGTTTTGCTGgtaagttgtaaatattattcttactttagttaaattaaagttacttaattggatttagtactattaatatgtgaaagtcaccatgcttataaggtcatcaactcagctgctgcaattcatgttgcctcattctcaagtgtagcttttgaaccttgacttctttggcag

upper sequence: LOC_Os08g42740.2 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 5'ss of exon 8
CTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgta--tagtccaatgt----------------ctatgcttgctgaaatatttatgtccatattactagtgtatgtacctctcatttgttttctttgaacatttcag-----------------------------------------------------------------------------------------------
| ||    || || ||||| || || ||  | ||||| ||||||||||| || ||||||||||| |||||||||||||||||||||  |||||| ||||||||   | |  |||||                 | |   |  |    |||| | ||  |  ||  ||  | ||| |  ||    ||| |  | || | |   ||||                                                                                               
CAAACAGCAAACCTTGCCCCAAGTGTAAGAGGCCAATTGAGAAAAACCAAGGCTGCATGCATATCACTTGCACTCCACCTTGCAAACATGAGTTTTGCTGgtaaacaatttaatgtaattttaaaaaaatagttttttattttcccttattgaagttaagcttgttaacgaatgaaattcggtcttgct--cattaagctcatcagtgcagctgcggcagtccatgctattgtattttaacgctttgagtgtctggtttggaaatagtgtcacttacaagagttcactgatactataacag

upper sequence: LOC_Os08g42740.2 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 5'ss of exon 8
CTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtatagtccaatg---tctat---gcttgctgaaatatttatgtccatatt-actagtgtatgtacctctcatttgtttt---ctttgaacatttcag---------------------------------------------------------------------
| ||    || || ||||| ||||| ||| | ||||| ||||||||||| || || ||||| || |||||||| || ||||||||||||||||| |||||||| |||| |||    | |||   |  |   | |||   |  ||  | ||| |||     |   | |  | ||   | ||    |||      || ||                                                                     
CAAACAGCAAACCCTGCCCCAAATGTAAAAGGCCAATTGAGAAAAACCAAGGGTGTATGCACATTACTTGCACACCTCCTTGCAAATTTGAGTTTTGCTGgta-agtctaatagattttattgggtctcgaggaatgaatgggtttaaattcactctccaactcatcgataatggttcttaagtttttgttgctttagcctgaatgggttgaaagctggtcattgataagacacttacttatgagcaacccacttttgtttctaaag

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|29635023|gb|CB640032.1|CB640032
EST:     GAAGGGTATTCTTCTGATGTGATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAG
genomic: GAAGGGTATTCTTCTGATGTGATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAG
EST: gi|29643283|gb|CB648290.1|CB648290
EST:     GGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTG                         GTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTA
genomic: GGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtatagtcca ... aacatttcagGTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTA
EST: gi|29671896|gb|CB668171.1|CB668171
EST:     TTGTGGAATATGTTTTGAAGGGTATTCTTCTGATGTGATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAG
genomic: TTGTGGAATATGTTTTGAAGGGTATTCTTCTGATGTGATGAGTTCTGCTGATTGTGATCATTTTTATTGCCATGAATGCTGGGAAG
EST: gi|29643281|gb|CB648288.1|CB648288
EST:     GGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTG                         GTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTA
genomic: GGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtatagtcca ... aacatttcagGTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTA
EST: gi|29677672|gb|CB673947.1|CB673947
EST:     GGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTG                         GTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTA
genomic: GGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAGTTCTGCTGgtatagtcca ... aacatttcagGTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTA