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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGAAGCTTATATATGGCCACTCCAGTTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctatgatcctttgctcttctcaattcattatgtcctgtctgatttccatttctcagaaatgttgatagtgttcttaaattgtcgatctgtag

Basic information

species Arabidopsis thaliana
transcript AT4G20325.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G20325.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA06G08230.3 (Glycine max), 5'ss of exon 5
ATGGAAGCTTATATATGGCCACTCCAGTTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctatgatcctttgctcttctcaattcattatgtcctgtctgat-ttccatttctcagaaatgttgatagtgttcttaaattgtcgatctgtag-----
||||  |  | ||| |  |||| ||| ||||||||||||||||  |||||||||| || || ||||| ||||||||||| | | |    |  | || |  | |  |  || |  |   ||   ||  || | | | ||  || | ||     | |  ||||||  | | ||          
ATGGTCGGATGTATTTATCCACACCAATTGATCCTGTTTTCATCATGTTGCCTATATTTGAGGAAGCTAGAATGAAGgtaattat----ttttatgtttcttttgaaccaatgggagttggaagacatttcttatttccaaagtcttttccatttgtttaaatacttgctcaactattgct

upper sequence: AT4G20325.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA04G08160.1 (Glycine max), 5'ss of exon 1
ATGGAAGCTTATATATGGCCACTCCAGTTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctatgatcctttgctcttctcaattcattatgtcctgtctgatttccatttctcagaaatgttgatagtgttcttaaattgtcgat----ctgtag--
||||  |  | ||| |  |||| ||| ||||||| ||||||||  |||||||||| ||| | ||||| ||||||||||| | |      |  | || || | |  |  |||        |      || | | | |  ||| | ||     | |   |||||  | | |    || | |  
ATGGTCGGCTGTATTTATCCACACCAATTGATCCCGTTTTCATCATGTTGCCTATATTCAAGGAAGCTAGAATGAAGgtaatt----agttatatgttccttttgaaccatgggagttggaagtcatttcttattttggaagtcttttccatttgtgtaaatccttggttcaactattgct

upper sequence: AT4G20325.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv04s0008g03180.t01 (Vitis vinifera), 5'ss of exon 5
ATGGAAGCTTATATATGGCCACTCCAGTTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctatgatcctttgctcttctcaatt-catta-tgtcctgtctgatttccatttctcagaaatgttgatagtgttcttaaattgtcgatctgtag
||||  || ||||||  ||||||  ||||||||||||||||||  ||||||| ||||| || ||||| || ||||||||      ||  || ||     | || | || || || |||  |     |  |     | |       |||    |  |    | ||  |  |   ||||
ATGGGCGCCTATATACTGCCACTATAGTTGATCCTGTTTTCATTATGTTGCCCATTTTTGAGGAAGCTAGGATGAAGgtataataattgtcattcatgatccttattttcactactgtgattggcaacatgggcctttttcttcagttatccgattcaacacatcttaaaatggtag

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|116459190|gb|EG501782.1|EG501782
EST:     TAGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAG                         AAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
genomic: TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctat ... cgatctgtagAAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
EST: gi|116411164|gb|EG453756.1|EG453756
EST:     TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAG                         AAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
genomic: TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctat ... cgatctgtagAAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
EST: gi|116411167|gb|EG453759.1|EG453759
EST:     TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAG                         AAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
genomic: TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctat ... cgatctgtagAAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
EST: gi|116459202|gb|EG501794.1|EG501794
EST:     TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAG                         AAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
genomic: TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctat ... cgatctgtagAAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
EST: gi|116411166|gb|EG453758.1|EG453758
EST:     TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAG                         AAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
genomic: TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctat ... cgatctgtagAAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
EST: gi|116459198|gb|EG501790.1|EG501790
EST:     TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAG                         AAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
genomic: TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctat ... cgatctgtagAAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
EST: gi|116411176|gb|EG453768.1|EG453768
EST:     TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAG                         AAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
genomic: TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctat ... cgatctgtagAAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
EST: gi|116411168|gb|EG453760.1|EG453760
EST:     TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAG                         AAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
genomic: TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctat ... cgatctgtagAAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
EST: gi|116459191|gb|EG501783.1|EG501783
EST:     TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAG                         AAGGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTCGTG
genomic: TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctat ... cgatctgtagAAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
EST: gi|116411162|gb|EG453754.1|EG453754
EST:     TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAG                         AAGGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG
genomic: TTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctat ... cgatctgtagAAAGGTGAAAATTCTGGAAAGTTCAGGCAACTAGATGAGATTTTATTTGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGAAGCTTATATATGGCCACTCCAGTTGATCCTGTTTTCATATTGTTGCCTATTTTCGACGAAGCAAGAATGAAGgtcactctatgatcctttgctcttctcaattcattatgtcctgtctgatttccatttctcagaaatgttgatagtgttcttaaattgtcgatctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA