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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacccgtcacattttattcactgatatgcttaggctagtgattgaaatttcagaatgaaatctctgaggtttcaggaacattgaaa...

Basic information

species Oryza sativa
transcript LOC_Os02g08090.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08090.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G058252_T03 (Zea mays), 5'ss of exon 1
------------ACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacccgtcacattttattcactgatatgcttaggctagtgattgaaatttcagaatgaaatct--ctgaggtttcaggaacattgaaa-
            || || ||||||||||| || |||||  |||||||||||||||| |||||||| ||||||||||| |||||||||||||| ||||| |||||  ||| ||  |    ||    ||| |   ||    |   || |  |    | |       | |      |||   ||||   ||     |||||   | 
CGTTTTGTGCAGACCGTTCCAGTTAACCCAAAACCTTTTCTGAACAACCTGACAGGAAAGCCTGTTATTGTCAAACTCAAGTGGGGTATGGAGTACAAGGgtaagttat-ctcctttttgttcagtttaa---accagaacattttgttttccaaatactgccgctgctctttatcaaactgaaaattattatacattcccag

upper sequence: LOC_Os02g08090.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G168252_T01 (Zea mays), 5'ss of exon 2
ACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacccgtcacattttattcactgatatgct-taggctagtgattgaaatt--tcagaatgaaatctctgaggtttcag-gaacattgaaa-
||||||||||||||||| || |||||| ||||||||||||| ||||||||||| ||||||||||| |||||||||||||| |||||||||||| |||  | ||        || |||   |    | ||  | |  || ||  | ||    |  ||  | | |||      |  ||| |  | |||||   | 
ACTGTGCCAGTTAACCCAAAACCTTTCCTGAACAACCTGACGGGGAAGCCTGTAATTGTCAAACTCAAGTGGGGTATGGAGTACAAAGgtaatttatcttatttttgtatccagtttgaactggaacattttatttgccagatactgcccctgctcttattcaaactgaaaaaattttattgtacatttccag

upper sequence: LOC_Os02g08090.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G058252_T01 (Zea mays), 5'ss of exon 2
ACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacccgtcacattttattcactgatatgcttaggctagtgattgaaatttcagaatgaaatct--ctgaggtttcaggaacattgaaa-
|| || ||||||||||| || |||||  |||||||||||||||| |||||||| ||||||||||| |||||||||||||| ||||| |||||  ||| ||  |    ||    ||| |   ||    |   || |  |    | |       | |      |||   ||||   ||     |||||   | 
ACCGTTCCAGTTAACCCAAAACCTTTTCTGAACAACCTGACAGGAAAGCCTGTTATTGTCAAACTCAAGTGGGGTATGGAGTACAAGGgtaagttat-ctcctttttgttcagtttaa---accagaacattttgttttccaaatactgccgctgctctttatcaaactgaaaattattatacattcccag

upper sequence: LOC_Os02g08090.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA17G07060.1 (Glycine max), 5'ss of exon 2
ACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgta---atct-atacttttacccgtcacattttattcactgatatgcttaggctagtgattgaaatttcagaatgaaatctctgaggtttcaggaacattgaaa
||| | |||||||| || |||||||||||||||||  |||| ||||||||||| ||||| ||||| |||||||| ||||| ||||| ||||    | | || ||||     |   || ||  |  |||| ||| |  |  ||     ||  | ||      |    | | | |  ||||||           
ACTATACCAGTTAATCCCAAGCCTTTCTTGAACAATTTGACTGGGAAGCCTGTAATTGTGAAACTGAAGTGGGGAATGGAGTACAAGGgtatgagtatgatgctttgctatggatcaattgttctactgttattcc-actcttacactttcatttcgctgttattttgttttatttttcag-----------

upper sequence: LOC_Os02g08090.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G21250.1 (Glycine max), 5'ss of exon 2
ACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgta-atctata---cttttacccgtcacattttattcactgatatgcttaggctagtgattgaaatttcagaatgaaatctctgaggttt-caggaacattgaaa---------------------------------
||| | ||||||||||| |||||||||||||||||  |||| |||||||| || ||||| ||||| |||||||| ||||| ||||| ||||   ||||    ||||     |   || ||  |  |||| |||      | ||   | |   |||||||  |  ||||  |    | | || ||   ||                                     
ACTATTCCAGTTAACCCCAAGCCTTTCTTGAACAATTTGACTGGGAAGCCCGTAATTGTGAAACTCAAGTGGGGAATGGAGTACAAGGgtatgactatgatgctttgtaatgagtcaattgttctactgttatttccctgtta--cactttcatttcagtgtttaatcgttagcttgtgcatgatttttttttatcatgtattcactgtgttattttatttttcag

upper sequence: LOC_Os02g08090.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G30220.1 (Arabidopsis thaliana), 5'ss of exon 2
ACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacccgtcacattttattcactgatatgcttaggctagtgattgaaatttcagaatgaaatctctgaggtttcaggaacattgaaa
||| | || ||||||||||| || |||||||||||| |||| || ||| |||| || ||||| ||||| ||||| ||||||||||||||     |||| ||||   | ||| | |   ||   ||||| |  |   | || | ||  |     |  |      ||   |  |  |||           
ACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAGg-----tatattttt---cttcaaaatgcttttgatgataagtat---ccagagcttatatagctaacagtcttccttctacttcacag-----------

upper sequence: LOC_Os02g08090.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G30220.2 (Arabidopsis thaliana), 5'ss of exon 2
------------ACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacccgtcacattttattcactgatatgcttaggctagtgattgaaatttcagaatgaaatctctgaggtttcaggaacattgaaa
            ||| | || ||||||||||| || |||||||||||| |||| || ||| |||| || ||||| ||||| ||||| ||||||||||||||     |||| ||||   | ||| | |   ||   ||||| |  |   | || | ||  |     |  |      ||   |  |  |||           
TGTGTTTTGCAGACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAGg-----tatattttt---cttcaaaatgcttttgatgataagtat---ccagagcttatatagctaacagtcttccttctacttcacag-----------

upper sequence: LOC_Os02g08090.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv00s0220g00030.t01 (Vitis vinifera), 5'ss of exon 2
ACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacccgtcacattttattcactgatatgcttaggctagtgattgaaatttcagaatgaaatctctgaggtttcaggaacattgaaa
|| || ||| | ||||| ||||| |||||||| ||| |||| ||||||||||||||||||||||| |||||||| ||||| |||||||||||   || ||    |   ||   | |  |||| |   |  ||  |  |  |  ||    | | |  ||    | |||  |||||    |         
ACCGTACCACTGAACCCTAAGCCCTTCTTGAATAACTTGACTGGGAAGCCTGTCATTGTCAAACTCAAGTGGGGAATGGAGTACAAAGgtaa---attctcccgctt-tcgtctgtggttcaattgaaatctatgattttttttt----tcttaacat----tttcttgggtttttttag--------

upper sequence: LOC_Os02g08090.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S46_244V6.1 (Physcomitrella patens), 5'ss of exon 2
ACTGTGCCAGTTAACCCGAAGCCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctatacttttacccgtcacattttattcactgatatgcttaggctagtgattgaaatttcagaatg--aaatctctgaggtttcaggaacattgaaa----------------------------------------------------------------
||  | || || || ||||| || || |||||| || ||||||||||||| || || || ||||| |||||||| |||||||||||||||  ||| |  | || |  ||     ||| |    || | || ||  | |||  ||      ||  |  |      | |   |||  |      | |||||                                                                 
ACCATCCCCGTGAATCCGAAACCCTTTTTGAACGACTTGACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAGgtgctctgttttgtttcttgtatttgtttttattttgctttgtttttgttagcaatatggtcttatggttttcgggttttccaggggttgattcctttgaatacatatgtatttgagggtaatacatttaatcgtggcagttgaatgtctggtgtggtgagaacag

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|88338829|gb|CI677236.1|CI677236
EST:     GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG                         GATATCTTGTTTCTGTCGACTCTTATATGAATCTGCAG
genomic: GACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAGgtaatctata ... cccctttcagGATATCTTGTTTCTGTCGACTCTTATATGAATCTGCAG