Sequence
atgc intronic sequence ATGC exonic sequenceGTTTATGCACGAGAGGCTGAACACTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTgtaagtttcttaattgccctagctatagctgctggattttgggtagttatttttgaatcaaagctaccggaagtgaacttggaattgttttatcatttatgtgatgatggtcttttcatgtcaaatgtggcttcacttgtgtgagctttaacatgtctcataggtgaatctgctcttattttatttctctccatggag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39850.2 |
intron # | 18 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39850.2 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA18G02110.1 (Glycine max), 5'ss of exon 19
GTTTATGCACGAGAGGCTGAACACTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTgtaagtttcttaattgccctagctatagctgctggattttgggtagttatttttgaatcaaagctaccggaagtgaacttggaattgttttatcatttatgtgatgatggtcttttcatgtcaaatgtggcttcacttgtgtgagctttaacatgtctcataggtgaatctgctcttattttatttctctccatggag
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GTTCATGCATGAAAGACTCTGTACTCATGCTGAATCTGTTGCTTTCTTTGGAGGTGGAGCTCGAGAAAAAGCTgtgagcatcccatctgtatttaatatcttttctttaagg-gtgtgcttattttagaatgtgcaaactttagaatgaa-----aattacttca-cacttgcttggcac-------------------------------------------------------------------------------------------
upper sequence: AT4G39850.2 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA11G38160.1 (Glycine max), 5'ss of exon 19
GTTTATGCACGAGAGGCTGAACACTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTgtaagtttcttaattgccctagctatagctgctggattttgggtagttatttttgaatca-aagctaccggaagtgaacttggaattgttttatcatttatgtgatgatggtcttttcatgtcaaatgtggcttcacttgtgtgagctttaacatgtctcataggtgaatctgctcttattttatttctctccatggag
||| ||||| || || || |||||||||||||| |||| |||||||||||||||||||||||||| ||||| || || | | | | | || || ||| | | | ||||| | | ||| | | | | | ||| || | || || |
GTTCATGCATGAAAGACTCTGTACTCATGCTGAATCAGTTGCTTTCTTTGGAGGTGGAGCTCGAGAAAAAGCTgtgagcatcccatctaaacaatatttaatatcttttctttaag--ggtgtttttattttagaaggtgcaaactttagaatgaaaatcacttca-cacttgctt------------------------------------------------------------------------------------------------
upper sequence: AT4G39850.2 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA05G31270.1 (Glycine max), 5'ss of exon 17
GTTTATGCACGAGAGGCTGAACACTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTgtaagtttcttaattgccctagctatagctgctggattttgggtagttatttttgaatcaaagctaccggaagtgaacttggaattgttttatcatttatgtgatgatggtcttttcatgtcaaatgtggcttcacttgtgtgagctttaacatgtctcataggtgaatctgctcttattttatttctctccatggag
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GTTCATGCATGAAAGACTTTGTACTCATGCTGAATCTGTTGCTTTCTTTGGAGGTGGTGCTCGAGAAAAAGCTgtgagcatccta---gctct-gcaatatttaatgtattttctttaagtgtgcttgt-ttgaggacatgaaaggtagaaatgaaacc---tgatgcttgtcataataaa------------------------------------------------------------------------------------------
upper sequence: AT4G39850.2 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA08G14480.1 (Glycine max), 5'ss of exon 15
GTTTATGCACGAGAGGCTGAACACTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTgtaagtttcttaattgccctagctatagctgctggattttgggtagttatttttgaatcaaagctaccggaagtgaacttggaattgttttatcatttatgtgatgatggtcttttcatgtcaaatgtggcttcacttgtgtgagctttaacatgtctcataggtgaatctgctcttattttatttctctccatggag
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GTTCATGCATGAAAGACTTTGTACTCATGCTGAATCTGTTGCTTTCTTTGGGGGTGGTGCTCGAGAAAAAGCTgtgagcatcctaact----tagcaatgtttaatgtattttctttaagtgtgtgcttgtttgaggacatgaaaagg----ttgaaatgaaacctgatgcttgtcacaaa------------------------------------------------------------------------------------------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|86054037|gb|DR349794.1|DR349794EST: CTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCT -A--TGGTTGACAAAAAATTCAGGGCCCTACTGGATCATTCTCTCATGCTC
genomic: CTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTgtaagtttct ... ctccatggagCAGATGGTTGACAAAAAATTCAGGGCCCTACTGGATCATTCTCTCATGCTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTTATGCACGAGAGGCTGAACACTCATGCTGAATCTATTGCATTCTTTGGAGGTGGAGCTCGAGAAAAGGCTgtaagtttcttaattgccctagctatagctgctggattttgggtagttatttttgaatcaaagctaccggaagtgaacttggaattgttttatcatttatgtgatgatggtcttttcatgtcaaatgtggcttcacttgtgtgagctttaacatgtctcataggtgaatctgctcttattttatttctctccatggag
- - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT