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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGAAGCCTGGTACTACACAGACTAGCGTTCCCGGAGTTTTCGCTGCGGGTGATGTTCAGGATAAGAAGTATAGGCAAGCCATCACTGCTGCAGGAACTGgttagttctctactttctctgaaagaaactgctttagttagctattttagttatgttgcctagaactacttgactttgtgtgcaatatatgattttggaa...

Basic information

species Arabidopsis thaliana
transcript AT4G35460.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G35460.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA01G36070.1 (Glycine max), 5'ss of exon 1
ACGAAGCCTGGTACTACACAGACTAGCGTTCCCGGAGTTTTCGCTGCGGGTGATGTTCAGGATAAGAAGTATAGGCAAGCCATCACTGCTGCAGGAACTGgttagttctctactt-tctctgaaagaaactgct-ttagttagctattttagttatgt-tgcctagaactacttga-ctttgtgtgcaatatatgattttggaa
|||||||| || || || |||| || ||| ||||| || ||||| || ||||||||||| ||||||||||||||||| || |||||||| || |||||| |||| | || ||| ||| | | ||| | || | ||| || |||| | || || | || | | || | ||
ACGAAGCCGGGGACGACGAAGACCAGTGTTGAGGGAGTGTTTGCTGCTGGGGATGTTCAGGACAAGAAGTATAGGCAAGCTATTACTGCTGCTGGCACTGgtaagttacagatttgtctatgatgcatagagctgcttattggacattggtgt-atgtacatgtgtgtgtataagatccctggttttgaagcatagtagtg---

upper sequence: AT4G35460.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA11G09350.1 (Glycine max), 5'ss of exon 1
ACGAAGCCTGGTACTACACAGACTAGCGTTCCCGGAGTTTTCGCTGCGGGTGATGTTCAGGATAAGAAGTATAGGCAAGCCATCACTGCTGCAGGAACTGgttagttctctactt-tctctgaaagaaactgctttagttagctattttagttatgt-tgcctagaactacttgactttgtgtgcaatatatgattttggaa
|||||||| || || || |||| || || ||||| || ||||| || ||||||||||| ||||||||||||||||| || |||||||| || |||||| ||| | | || ||| || | | ||| || | ||| || |||| || || | || | || | | | | |||| ||| |
ACGAAGCCGGGGACGACGAAGACCAGTGTGGAGGGAGTGTTTGCTGCTGGGGATGTTCAGGACAAGAAGTATAGGCAAGCTATTACTGCTGCTGGCACTGgtacgttgtagatttatctaagatgcgtagagtttttattggacattgctgt-atgtgtgtatatgatccctggttttgaagcgtagt-tatgttttgtcca

upper sequence: AT4G35460.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA16G21630.1 (Glycine max), 5'ss of exon 1
ACGAAGCCTGGTACTACACAGACTAGCGTTCCCGGAGTTTTCGCTGCGGGTGATGTTCAGGATAAGAAGTATAGGCAAGCCATCACTGCTGCAGGAACTGgtta-----gttctctactttctctg---aaagaaactgctttagttagctattttagttatgttgcctagaactacttgactttgtgtgcaatatatgattttggaa
|| || ||||| || ||| ||||||| ||| |||||||| ||||| ||||||||||| ||||| |||||||||||||| || || ||||| || |||||| | ||| || | | | | ||| ||| | || | | | | ||||| || | | || |||| | | || | | |||||
ACCAAACCTGGCACCACAAAGACTAGTGTTGATGGAGTTTTTGCTGCTGGTGATGTTCAAGATAAAAAGTATAGGCAAGCTATTACAGCTGCTGGCACTGgtaattcttgtttcataatctttgtattcaaataaattagattgttgtgttgtgatagttgtg--gattcatgttatttgattattcctg--gttttgaatttt----

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|301501483|gb|HO207023.1|HO207023
EST:     TGATGTTCAGGATAAGAAGTATAGGCAAGCCATCACTGCTGCAGGAACTG                         GGTGCATGGCAGCTTTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC
genomic: TGATGTTCAGGATAAGAAGTATAGGCAAGCCATCACTGCTGCAGGAACTGgttagttctc ... gattgtgtagGGTGCATGGCAGCTTTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC
EST: gi|125322390|gb|EL336475.1|EL336475
EST:     TCACTGCTGCAGGAACTG                         GGTGCATGGCAGCTTTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC
genomic: TCACTGCTGCAGGAACTGgttagttctc ... gattgtgtagGGTGCATGGCAGCTTTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC
EST: gi|125133107|gb|EL174772.1|EL174772
EST:     AAGCCATCACTGCTGCAGGAACTG                         GGTGCATGGCAGCTTTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC
genomic: AAGCCATCACTGCTGCAGGAACTGgttagttctc ... gattgtgtagGGTGCATGGCAGCTTTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC
EST: gi|86079310|gb|DR375067.1|DR375067
EST:     TGATGTTCAGGATAAGAAGTATAGGCAAGCCATCACTGCTGCAGGAACTG                         GGTGCATGGCAGCTTTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC
genomic: TGATGTTCAGGATAAGAAGTATAGGCAAGCCATCACTGCTGCAGGAACTGgttagttctc ... gattgtgtagGGTGCATGGCAGCTTTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC
EST: gi|86083823|gb|DR379582.1|DR379582
EST:     TCAGGATAAGAAGTATAGGCAAGCCATCACTGCTGCAGGAACTG                         GGTGCATGGCAGCTTTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC
genomic: TCAGGATAAGAAGTATAGGCAAGCCATCACTGCTGCAGGAACTGgttagttctc ... gattgtgtagGGTGCATGGCAGCTTTGGATGCAGAGCATTACTTACAAGAGATTGGATCTC

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGAAGCCTGGTACTACACAGACTAGCGTTCCCGGAGTTTTCGCTGCGGGTGATGTTCAGGATAAGAAGTATAGGCAAGCCATCACTGCTGCAGGAACTGgttagttctctactttctctgaaagaaactgctttagttagctattttagttatgttgcctagaactacttgactttgtgtgcaatatatgattttggaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa