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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgttttaatgtggttgtctgtgttcttatctgttgtatagtgtgttcatgatttgaagatgatgctagcaatcctttaataccctgttggtttgcttcatgaaactatag

Basic information

species Arabidopsis thaliana
transcript AT5G39740.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G39740.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 6
TTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgttttaatgtggttgtctgtgttcttatctgttgta-tagtgtgttcatgatttgaagatgatgct-agcaatccttt----aatacc-ctgttggtttgcttcatgaaactatag--------------------------------------------
 | ||| |||||| |||||   || || ||||||||||||||  | |||||||| || || ||||| ||||||||||||||||| |||||||| ||||||||   ||||| |  | || |      ||||     ||||  || ||||   ||  | | ||||| || |   | | ||   ||||    || ||  | ||   | |      || |    |                                              
CTATGTTGAACCAGCTGATGAAAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgt---gtgttgtgctttgatctcaactgttggctgctgtaataatagttgatttgtcacttgaacatcaaattcatcagctcttttagaaacacaaccgtcaatataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttcttctgcag

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g67134.1 (Oryza sativa), 5'ss of exon 6
TTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgttttaatgtggttgtctgtgttcttatctgttgta-tagtgtgttcatgatttgaagat--gatgctagcaatccttta-ataccctgttggtttgct--tcatgaaactatag-----------------------------------------------
 | ||| |||||| |||||   ||  | ||||||||||||||  | |||||||| || || ||||| ||||||||||||||||| |||||||| ||||||||   ||||| |  | || | |    ||||     ||||  || ||||   || || | ||||| ||   || |      || |||| | || |    | |  | |   | |   | | | |                                               
CTATGTTGAACCAGCTGATGAAAGGCGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTCATTAGGACAACCACTGGAAACCGTGTCTTTGGTGCCCTCAAGgt---gtgttgtgctttgatcgcaactgttggctgctgtaataatagttgatttatcacttgaacatcaaattcctcagctcttttagaaacacaaccgttacgataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttttcttctgcag

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G163081_T04 (Zea mays), 5'ss of exon 6
TTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtat--------tgtgtttta----------atgtggttgtctgtgttcttatctgttgtat--agtgtgttcatgatttgaagatgatgct--agcaatcctttaataccctgttggtttgcttcatgaaactatag------------------------
 ||||| || ||| |||||   || || ||||||||||||||  | |||||||| |||||||||||||| || || |||||||| |||||||| ||||||||||        ||| | |||          || | | ||||  ||||  ||| |     ||  ||  |  ||||  ||| | |    ||||  |  | || | |  |    || ||      |||      || |||                        
CTCTGTTGAGCCAGCTGATGAGAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTTATCAGGACTACAACAGGGAACCGTGTCTTTGGTGCCCTCAAGgtatatatcttctgtttgttaccatgatattatattggtgtcattgtttgtatttagcccatcaagaataatcattttttcatgtgcttgctgtaagagtcatctcttgttgtggtgaacgatttcccatctctctagcccctttaacgtttgttgccgcag

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM5G815894_T03 (Zea mays), 5'ss of exon 6
TTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgttttaatgtggttgtc-tgtgttcttatctgttgtata-gtgtgttcatgatttgaagatgatgctagcaatcctttaatac---cctgttg------gtttgcttcatga-aactatag-----------------------------------------------
 ||||| || ||| |||||   || || ||||||||||||||  | |||||||| ||||| |||||||| ||||| |||||||| |||||||| |||||||||   ||| ||  | | | |||| ||   |  ||| ||  || |  || |||   |   |     ||  |  ||  |||  |||   |    | |||||      |  |  || |||   |||                                                   
CTCTGTTGAGCCAGCTGATGAGAGGAGGCCTTTCCGTGCTCTCTTGGATGTTGGCCTTATTAGGACTACAACTGGGAACCGTGTCTTTGGTGCCCTCAAGgtac-atgtcttccttttgatgtcatgatgttatatttggggtgtttgtttgtagttagctcattaatagtaataataatttttttgcatgaacttgttgtacaaggcatcttttatggtgactggttttccatctctgtagttttttaacgtttgttgcattatgttgctgcag

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 6
TTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgttttaatgtggttgtctgtgttcttatctgttgtatagtgtgttcatgatttgaagatgatgctagcaatcctttaataccctgttggtttgcttcatgaaactatag
 ||||| || ||| | ||    || || ||||||||||| ||  | ||||| || ||||| |||||||| |||||||||||||| |||||||| ||||||||||  |  ||   | |  | |  ||  |   ||  | |  || | | |  |  || ||||  | ||  | | ||    |   || ||  | ||        |             
CTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTCCGTGCCCTCTTAGATGTCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtatattccttctttatcat-gaatgattgtatacatatgatacattttccttgtgttttg--gttgtaggtggcttatcaagaaaacttttttatacgatct-------------

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA16G03170.1 (Glycine max), 5'ss of exon 6
TTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgttttaatgtggttgtctgtgttcttatctgttgtatagtgtgttcatgatttgaagatgatgctagcaatcctttaataccctgttggtttgcttcatgaaactatag
||| ||||||||  ||||   ||| || || ||||||||||| ||||||||||| ||||| |||||||| ||||| |||||||| |||||||| || |||||| | | |  || ||   |  |   || | | || |  | |  |  ||| |||  | |||||  | ||  |    ||  ||||                                
TTCAGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACTGGCAACCGTGTCTTTGGTGCCCTTAAGgtaatctatcatactgcaatgctaattggtgtgattttgttttaatggtgatca--aattgaa--taatttt--ttattgtttacag-----------------------------

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA07G06580.1 (Glycine max), 5'ss of exon 6
TTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgttttaatgtggttgtctgtgttcttatctgttgtatagtgtgttcatgatttgaagatgatgctagcaatcctttaataccctgttggtttgcttcatgaaactatag
||| ||||||||  ||||   ||| || || ||||||||||| ||||||||||| ||||| |||||||| || || ||||||||||||||||| || |||||| | | |  |  |||  |  |      | | || | || ||  |  || |||  | ||||| |        |  ||  ||||                                
TTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACCGGTAACCGTGTGTTTGGTGCCCTTAAGgtaatctatcatgctgtaatgttaatcagtgtgattttttttaatggttgatca--aattgaata----atctgtgattgtttacag-----------------------------

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA07G06590.1 (Glycine max), 5'ss of exon 6
TTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgttttaatgtggttgtctgtgttcttatctgttgtatagtgtgttcatgatttgaagatgatgctagcaatcctttaataccctgttggtttgcttcatgaaactatag
||| ||||||||  ||||   ||| || || ||||||||||| ||||||||||| ||||| |||||||| || || ||||||||||||||||| || |||||| | | |  || |||  |           | ||| ||   ||  ||| || ||| ||    ||| |   |    |  || | ||    |   |                     
TTCCGTGGAACCTGCTGAGAGCAGGAGGCCATTCCGTGCTCTCCTTGATGTTGGTCTTATTAGGACTACAACCGGTAACCGTGTGTTTGGTGCCCTTAAGgtaatctatcatactgtaatg---------ttaatcagtgtgattttgttttaatggtt----gatcaaattgaataatctgtgattgtttacag---------------------

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv05s0094g00870.t01 (Vitis vinifera), 5'ss of exon 6
TTCTGTGGAACCAACTGATTCCAGAAGACCTTTCCGTGCTCTTCTTGATGTTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgttttaatgtggttgtctgtgttcttatctgttgtatagtgtgttcatgatttgaagatgatgctagcaatcctttaataccctgttggtttgcttcatgaaactatag
 ||||| ||||| || |||  ||| || || |||||||| |||||||||||||| ||| | || || || ||||| |||||||| |||||||| || |||||||| | |||||      | |      | || |  | || |   ||    | |   |  |    |     | |||  | |  ||||   ||    |     |             
CTCTGTTGAACCCACAGATAGCAGGAGGCCATTCCGTGCCCTTCTTGATGTTGGGCTTGTGAGAACAACAACTGGCAACCGTGTTTTTGGTGCTCTGAAGgtattatattttacaagcctcgctcagttgctcactttttttgc-gtacagttaaagtccgtctttttattttgca--cttgaaataatatgactatacatct-------------

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|164049117|gb|ES187432.1|ES187432
EST:     TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGT
genomic: TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGT
EST: gi|164090744|gb|ES125769.1|ES125769
EST:     CCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAAGAGATTTGC
genomic: CCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAA-GAGATTTGC
EST: gi|125017746|gb|EL090015.1|EL090015
EST:     CTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGA
genomic: CTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGA
EST: gi|163980490|gb|ES071119.1|ES071119
EST:     GGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCT
genomic: GGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCT
EST: gi|125297938|gb|EL312023.1|EL312023
EST:     TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGG
genomic: TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGG
EST: gi|164121875|gb|ES155835.1|ES155835
EST:     TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATT
genomic: TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATT
EST: gi|116398433|gb|EG441025.1|EG441025
EST:     TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGC
genomic: TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGC
EST: gi|124707921|gb|EH799323.1|EH799323
EST:     TACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAAGGTCTTGATATCCCTCACAGTGACAA
genomic: TACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGA-GGTCTTGATATCCCTCACAGTGACAA
EST: gi|125188113|gb|EL203067.1|EL203067
EST:     TTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCT
genomic: TTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCT
EST: gi|164056865|gb|ES093947.1|ES093947
EST:     TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGTTACAAGAGATT
genomic: TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTG--ACAAGAGATT
EST: gi|116398349|gb|EG440941.1|EG440941
EST:     TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCT
genomic: TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCT