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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaaaacttatcaccagatttcacttacgagtaattgtgttccttgagctactcaataagcttgcttttcaatctgtttcag

Basic information

species Arabidopsis thaliana
transcript AT1G17720.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 5'ss of exon 3
CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAG---GCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaaaacttatcaccagatttcacttacgagtaattgtgttccttgagctactcaataagcttgcttttcaatctgtttcag
      |  |  || || ||   |||| |    |||||  | |||||   ||||||||| ||||| || ||||| || ||||| || ||||||||||||||| |||  |    |  | | | ||  | | |  ||||  |||  |   ||   |  | ||  |  |||  ||   ||  | ||   
---AATGCCTGTAGAAAAGAGGCTGAGAAAGTTGATTATTCCGTTAGCAGGCATCCTGAATTTCGCTACAAAACTGAGTTTCAAAGCCATGAACCAGAGgtatattgtacaagactaactgctt--agtga--agtacctgtaatttctg--ttgtttaactaatttgtcttgtcatgcgattag-

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 3
CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTT---AGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaaaacttatcaccagatttcacttacgagtaattgtgttccttgagctactcaataagcttgcttttcaatctgtttcag---------------------
 |  |   |||  |||  || ||||||      ||||||||  ||   ||||||||||| || || || || || |||||||||||||||||||| ||||||  |  |||||||  |   | ||| | |||        ||| | || ||  | |   |  |   |  | | |  |||||   |||                     
-AGCGCCAGTC--GGAGTGAACTTGAGAGACAAGATTACCCGATTGCCAGGCATCCTGAATTCCGTTACAAGACTGAATTTCAGAGTCATGAACCTGAGgtatgt-gaaacttaaaat--ggttttaattatag-----tgtctcccctggtccatgaatcagagtgacatatatatctgccacagttggactgtataattttgata

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 3
CATGGAGGGTCCAGGAAGGATCTTGAG-CAGACGGATTACCCAGTTAGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaaaacttatcaccagattt-----cacttacgagtaattgtg--ttccttgagct---actcaataagcttgcttttcaatctg----tttcag
 |  |   |||   ||   ||   ||| ||    | |        ||| || || |||||||| || ||||  |||||||||||||||||||| ||||||  || | | |    |   | | |     ||| ||  | ||  |||   |||| |||  |   || ||  |       ||  ||| |||    | | | 
-AATGCCAGTCGGAGAGAAATGGAGAGACAAGATGCTCCGATTACTAGACACCCAGAGTTTCGCTACAAAAGTGAATTTCAGAGTCATGAACCTGAGgtatgttgataatctggattggctgttgtagcacatagtattatctgttatttccatgaagttggacgcataagatcaaattaacaagctggcattctta-

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 3
CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTT---AGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaa----aacttatcaccagattt-cacttacgagtaatt-----gtgttccttgagctactc--aataagcttgcttttca-atctgtttcag
 |  |   ||| ||||  || ||||||  |   || || |  |||   |||||||||||||| || || || || |||||||||||||||||||| ||||||| |       || ||  |   |||     | | || | |  ||     ||||   ||||  |  |   | | ||         || ||||   |  |
-AATGCTTGTCGAGGA--GAACTTGAGAGGCAAGAATATCTTGTTTCTAGGCATCCTGAGTTCCGTTACAAGACCGAATTTCAGAGTCATGAACCTGAGgtacgtgggtcttaaattggcgatagaccgatagtaacaatttgttcatgagtgtcaattgacttcttgtgactgaggcactgagccatatctagcttgg

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G142334_T02 (Zea mays), 5'ss of exon 3
CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTT---AGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacatta--aaacttatcaccagatttcacttacgagtaattgtgttccttgagctactcaataagcttgcttttcaatctgtttcag
      |  || || || |||  |||| |  | |||||  |  |    ||||||||||||||||| || ||||| || ||||| || ||||| ||||||||| |||     |   ||       |   | |          ||  || |||||   | |  | ||  |    ||   ||    |    
---CATGCCTCTAGAAAAGATGCTGAGAAAGCTGATTATTCTATCAGCAGGCATCCTGAGTTTCGCTACAAAACTGAGTTTCAAAGCCATGAGCCAGAGgtatattctcgcaagcattgtttagtggtattatttgtcttatgaattacttgaa--atttgacaaagtgatgttattattgaatag--

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 3
CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTT---AGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaaaactta-tcaccag-atttcacttacgagtaattgtgttccttgagctactcaataagcttgcttttcaatc--tgtttcag
||||| || || || | |||| | |||  |  ||| ||  |  ||   |||||||||||||| || || |||||||| ||||||||||| |||||||||||| || |  | ||  |||  |   || |||  ||     ||  | |   |      | ||||||    |  | |   |||  ||||||||
CATGGTGGATCAAGTAGGGATTTGGAGAGGGTGGACTATTCTATTGGTAGGCATCCTGAGTTCCGTTACAAAACAGAGTTTCAGAGTCACGAACCAGAGgta-atcatcatttggtcagtaatgttgcaccaac-----atcctatgggtcagaagagtcaatatttataatgtatgatcattgtttcag

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 3
CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTT---AGGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaaaactta-tcaccag-atttcacttacgagtaattgtgttccttgagctactcaataagcttgcttttcaatctgtttcag
||||| || || || | |||| | |||  || ||| ||  |  ||   |||||||||||||| || || |||||||| |||||||||||||| ||||||||| || |  | ||  |||  |   || |||  ||     || | ||     |||  | |   ||    ||  |    || ||||||||
CATGGTGGATCAAGAAGGGATTTGGAGAGGATGGACTATTCTATTGGTAGGCATCCTGAGTTCCGTTACAAAACAGAGTTTCAGAGTCATGAGCCAGAGgta-atcatcatttggtcagtaatgttgcaccaacatcctatgg-gtcagaagagtcaatatttataaatgtatgatcat-tgtttcag

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 3
CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAG---GCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaaaacttatcaccagatttcacttacgagtaattgtgttccttgagctactcaataagcttgcttttcaat--ctgtttcag
|||   || || || | |||  | |||  || ||| ||  |  ||||    ||||||||||| || ||||||||||| |||||||||||||| || |||||| |||   | | |       ||    |     | |  |||||   |   |    || || |    ||  ||   ||   ||||||||
CATCACGGATCAAGAAGGGACTTGGAGAGGATGGACTATTCTATTAGTAGACATCCTGAGTTCCGTTATAAAACAGAGTTTCAGAGTCATGAGCCTGAGgta-attttcagtcactggttaatgctgcccg-aaatgcttgtggagcagaaat--cttaacatttatgacttgtgattgttgtttcag

upper sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 3
CATGGAGGGTCCAGGAAGGATCTTGAGCAGACGGATTACCCAGTTAG---GCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaaaacttatcaccagatttcacttacgagtaattgtgttccttgagctactcaataagcttgcttttcaat--ctgtttcag
||| | || || || | |||  | |||  || ||| ||  |  ||||    ||||||||||| || ||||||||||| |||||||||||||| || |||||| |||   | | |       ||    | |   | |  |||||   |   |     | || |    ||   |   ||   ||||||||
CATTGCGGATCAAGAAGGGACTTGGAGAGGATGGACTATTCTATTAGTAGACATCCTGAGTTCCGTTATAAAACAGAGTTTCAGAGTCATGAGCCTGAGgta-attttcagtcactggttaatgctgcctg-aaatgcttgtggagcagaaatg--ttaacatttatgacatgtgattgttgtttcag

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|164173855|gb|ES058098.1|ES058098
EST:     TAAAACAGAATTTCAGAGTCATGAACCAGAG                         TTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGA
genomic: TAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaaa ... tctgtttcagTTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGA
EST: gi|116411283|gb|EG453875.1|EG453875
EST:     GGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAG                         TTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGA
genomic: GGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaaa ... tctgtttcagTTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGA
EST: gi|116432328|gb|EG474920.1|EG474920
EST:     GGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAG                         TTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGA
genomic: GGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaaa ... tctgtttcagTTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGA
EST: gi|116478422|gb|EG521014.1|EG521014
EST:     GGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAG                         TTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGA
genomic: GGCATCCTGAGTTTCGATATAAAACAGAATTTCAGAGTCATGAACCAGAGgtacattaaa ... tctgtttcagTTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGA