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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACGGTACTTATCCTCCAGTTGTTGAAGCTTTCCGACAGAAGATTCTTGAAGCTGATAGTATCTTGTTTGCTTCTCCTGAGTATAACTTCTCTGTTTCAGgtttgtgtaataaagattcttcttattgcaaagttctttagtgagtttcacttttattgtttggtcttaagaggtttcttgatttgctacaagaacatat...

Basic information

species Arabidopsis thaliana
transcript AT3G27890.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G27890.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA13G26630.2 (Glycine max), 5'ss of exon 1
AACGGTACTTATCCTCCAGTTGTTGAAGCTTTCCGACAGAAGATTCTTGAAGCTGATAGTATCTTGTTTGCTTCTCCTGAGTATAACTTCTCTGTTTCAGgtttgtgtaataaagattcttcttattgcaaagttctttagtgagtttcacttttattgtttggtcttaagaggtttcttgatttgctacaagaacatat----------
|| || || || || ||| | ||||||||||| || || ||||||||| |||||||||||||  | |||||||||||||| ||||| | ||||||  |||||          |  ||| |||||       |  |   |  || ||||  ||| ||  |  |  || |    |    ||  |      | || ||| | |          
AATGGGACCTACCCACCAATAGTTGAAGCTTTTCGTCAAAAGATTCTTCAAGCTGATAGTATTCTCTTTGCTTCTCCTGAATATAATTACTCTGTCACAGgt----------accatttttcttgaacttcatctgggttttgtgtttttcttatacagggtattcattcatgaaaactccaaaaaaaaaaaaaacgtttaatttgattc

upper sequence: AT3G27890.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA11G21260.1 (Glycine max), 5'ss of exon 2
AACGGTACTTATCCTCCAGTTGTTGAAGCTTTCCGACAGAAGATTCTTGAAGCTGATAGTATCTTGTTTGCTTCTCCTGAGTATAACTTCTCTGTTTCAGgtttgtgtaataaagattcttcttattgcaaagttctttagtgagttt-cacttttattgtttggtcttaagaggtttcttgatttgctacaagaacatat
|| || || || || |||   |||||||| || || ||||||||||| | ||||||||||||| | |||||||| |||||||| || | ||||||  || || ||     |  |   |||  || |||     || |||| |  |||   |  |||     | || | | |     |  |  | |    | || | |||||
AATGGGACCTACCCCCCACAAGTTGAAGCCTTTCGCCAGAAGATTCTCGCAGCTGATAGTATCCTCTTTGCTTCCCCTGAGTACAATTACTCTGTCGCAAgtatgctggctccactatctgtttcttgttttcttttttaatttgttgatatctttggaaataggacattaactactgatatagtcaaaataata-catat
















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|124709183|gb|EH800585.1|EH800585
EST:     AGCTGATAGTATCTTGTTTGCTTCTCCTGAGTATAACTTCTCTGTTTCAG                         CTCCACTTAAGAA
genomic: AGCTGATAGTATCTTGTTTGCTTCTCCTGAGTATAACTTCTCTGTTTCAGgtttgtgtaa ... attgtaccagCTCCACTTAAGAA
EST: gi|86076957|gb|DR372714.1|DR372714
EST:     AGCTGATAGTATCTTGTTTGCTTCTCCTGAGTATAACTTCTCTGTTTCAG                         CTCCACTTAAGAATGCTCTTGACTGGGCTTCAAGACCACCTAATGTTTGGG
genomic: AGCTGATAGTATCTTGTTTGCTTCTCCTGAGTATAACTTCTCTGTTTCAGgtttgtgtaa ... attgtaccagCTCCACTTAAGAATGCTCTTGACTGGGCTTCAAGACCACCTAATGTTTGGG
EST: gi|125019879|gb|EL092148.1|EL092148
EST:     AGCTGATAGTATCTTGTTTGCTTCTCCTGAGTATAACTTCTCTGTTTCAG                         CTCCACTTAAGAATGCTCTTGACTGGGCTTCAAGACCACCTAATG
genomic: AGCTGATAGTATCTTGTTTGCTTCTCCTGAGTATAACTTCTCTGTTTCAGgtttgtgtaa ... attgtaccagCTCCACTTAAGAATGCTCTTGACTGGGCTTCAAGACCACCTAATG
EST: gi|125322449|gb|EL336534.1|EL336534
EST:     AGCTGATAGTATCTTGTTTGCTTCTCCTGAGTATAACTTCTCTGTTTCAG                         CTCCACTTAAGAA
genomic: AGCTGATAGTATCTTGTTTGCTTCTCCTGAGTATAACTTCTCTGTTTCAGgtttgtgtaa ... attgtaccagCTCCACTTAAGAA
EST: gi|125306286|gb|EL320371.1|EL320371
EST:     AGTATAACTTCTCTGTTTCAG                         CTCCACTTAAGAATGCTCTTGACTGGGCTTCAAGACCACCTAATGTTTGGG
genomic: AGTATAACTTCTCTGTTTCAGgtttgtgtaa ... attgtaccagCTCCACTTAAGAATGCTCTTGACTGGGCTTCAAGACCACCTAATGTTTGGG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACGGTACTTATCCTCCAGTTGTTGAAGCTTTCCGACAGAAGATTCTTGAAGCTGATAGTATCTTGTTTGCTTCTCCTGAGTATAACTTCTCTGTTTCAGgtttgtgtaataaagattcttcttattgcaaagttctttagtgagtttcacttttattgtttggtcttaagaggtttcttgatttgctacaagaacatat

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagaaca