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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCCAAAAACCCAGTGGATTTTGTACACAAGCAACGAAGGGCTCTTGAGAGCGAGCATGTATCTGCTCATTTGCATGAATGGATTGATCTCATATTTGGgtaggttttcacccttgaactgatgatatactgtcagcacatttttccataacttagtttctccttttacttagtgtgttcagcaaaatattcacaagtgtctttgtaagccactaaattgttttttcattcag

Basic information

species Arabidopsis thaliana
transcript AT2G45540.2
intron # 27
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G45540.2 (Arabidopsis thaliana), 5'ss of exon 27
lower sequence: LOC_Os02g44380.2 (Oryza sativa), 5'ss of exon 19
GGGCCAAAAACCCAGTGGATTTTGTACACAAGCAACGAAGGGCTCTTGAGAGCGAGCATGTATCTGCTCATTTGCATGAATGGATTGATCTCATATTTGGgtaggttttcacccttgaactgatgatatactgtcagcacatttttccataacttagtttctccttttacttagtgtgttcagcaaaatattcacaagtgtctttgtaagccactaaattgttttttcattcag
||||  | ||||| || |||||  ||   || ||  | | |||||||||||| ||  |||| || |||||||||||||||||||| || || ||||||||||| |||   | |  ||  ||| |  | |  |||   ||| | ||  |   | |  |||     ||||||||| | | |  |  |   |  || ||  | | || |  ||                        
GGGCTGAGAACCCTGTTGATTTCATATGTAAACACAGGAAGGCTCTTGAGAGTGATTATGTCTCCGCTCATTTGCATGAATGGATAGACCTAATATTTGGgtacgtt---atctatgtgctgttccttt-ttgttgccacctcttagctgcattgcgtta----ttttacttaat-tatctactat--tcgtcccatatatgttggccagt-----------------------

upper sequence: AT2G45540.2 (Arabidopsis thaliana), 5'ss of exon 27
lower sequence: GRMZM2G044143_T01 (Zea mays), 5'ss of exon 25
GGGCCAAAAACCCAGTGGATTTTGTACACAAGCAACGAAGGGCTCTTGAGAGCGAGCATGTATCTGCTCATTTGCATGAATGGATTGATCTCATATTTGGgtaggttttcacccttgaactgatgatatactgtcagcacatttttccataacttagtttctccttttacttagtgt-gttcagcaaaatattcacaagtgtctttgtaagccactaaattgttttttcattcag
||||  |||| |  ||||||||||| || || || || | |||||||||||| ||||| || ||||||||||||||||| ||||||||||| || ||||||||   | |      |       |||   ||| ||      ||||| || ||     |     |  | | ||  ||| | |  |||  ||  |    | |  | |||                            
GGGCTGAAAATCATGTGGATTTTGTCCATAAACATCGGAAGGCTCTTGAGAGTGAGCACGTCTCTGCTCATTTGCATGAGTGGATTGATCTAATTTTTGGgtaacctctatattatcctagcttgactcactttct-tgtgtttttgcacaaac--atcctaacaataatttgatgtaggtttgcatcatgct----aataccattg----------------------------

upper sequence: AT2G45540.2 (Arabidopsis thaliana), 5'ss of exon 27
lower sequence: GRMZM2G024245_T01 (Zea mays), 5'ss of exon 4
GGGCCAAAAACCCAGTGGATTTTGTACACAAGCAACGAAGGGCTCTTGAGAGCGAGCATGTATCTGCTCATTTGCATGAATGGATTGATCTCATATTTGGgtaggttttcacccttgaactgatgatatactgtcagcacatttttccataacttagtttctccttttacttagtgtgttcagcaaaatattcacaagtgtctttgtaagccactaaattgttttttcattcag
|||| |||||  | || |||||| |||| | ||| || |  ||||| ||||| || ||||| ||  | | ||||||||||||||| ||||| ||||||||||| |||   |    ||   |  |    | |       | ||   |        ||  || |   | ||  |  | | |||     ||||| ||    | || |                              
GGGCTAAAAATGCTGTTGATTTTATACATATGCATCGGAAAGCTCTCGAGAGTGATCATGTCTCCACACGTTTGCATGAATGGATCGATCTAATATTTGGgtatgtt---agttatgtgttattatgtttccacatatatatgcattttccttctaacttatttatctaacttttttattct-tgcaatat-cattcatatcctc-----------------------------

upper sequence: AT2G45540.2 (Arabidopsis thaliana), 5'ss of exon 27
lower sequence: Vv15s0048g01650.t01 (Vitis vinifera), 5'ss of exon 26
GGGCCAAAAACCCAGTGGATTTTGTACACAAGCAACGAAGGGCTCTTGAGAGCGAGCATGTATCTGCTCATTTGCATGAATGGATTGATCTCATATTTGGgtaggttttcacccttgaactgatgatatactg-tcagcacatttttccataacttagtttctccttttacttagtgtgttcagcaaaatattcacaagtgtctttgtaagccactaaattgtt-ttttcattcag-------------------
||||  | |||||||| |||||| | || ||||| || | |||||||||||| |||||||| ||||| ||||||||||||||||||||||||||||||||||| |||||      |  | ||   | | | |  |   ||| ||  |   ||   | || | | | ||   | | | |  |        |    ||||   |    ||||   |  |   | ||  ||| | |||                    
GGGCTGAGAACCCAGTTGATTTTATTCATAAGCACCGGATGGCTCTTGAGAGTGAGCATGTCTCTGCACATTTGCATGAATGGATTGATCTCATATTTGGgtaagttttattatctttattggacaaaaattaattttcaccttcatttctattcttgtgttttcattctgtgattttccttctttttgttgcaacaatgatagaagtaaaaaatgatggtcttgctttaaatcaactttttgtggaacattcag

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|47828319|gb|CK118003.1|CK118003
EST:     AGCGAGCATGTATCTGCTCATTTGCATGAATGGATTGATCTCATATTTGG                         GTATAAGCAACGTGGCAAAGAAGCTATAATGGCAAATAACGTTTTCTTCTA
genomic: AGCGAGCATGTATCTGCTCATTTGCATGAATGGATTGATCTCATATTTGGgtaggttttc ... tttcattcagGTATAAGCAACGTGGCAAAGAAGCTATAATGGCAAATAACGTTTTCTTCTA