Sequence
atgc intronic sequence ATGC exonic sequencegtacctaatttatctacagtattcttgagatattcacttagtctaccgcagaaacttaagcattgtaaaggaaactatatctgtgtaaatatattgtaagaacacgactacctattaaatggagattccagaaacttcccttgtcatgtttgctgttaaaaagaaaatataacataggaacttgtattgtagGATGCTGTTGATTGTCCTGAATGGATTGTGCCCTTTAACGTCTTCAAGTCTTTAGCGGAGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G20650.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G20650.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G22390.1 (Glycine max), 3'ss of exon 9
gtacctaatttatctacagtattcttgagatattcacttagtctaccgcagaaacttaagcattgtaaaggaaactatatctgtgtaaatat-attgtaagaacacgactacctattaaatggagattccagaaacttcccttgtcatgtttgctgttaaaaagaaaatataacataggaacttgtattgtagGATGCTGTTGATTGTCCTGAATGGATTGTGCCCTTTAACGTCTTCAAGTCTTTAGCGGAGGAG
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---------------------------------------------------------------------------------tatgatgttatcattcaaagaacatgtctct--------tagagccttttgaaacttgcatactgttgatacctgt----gctatcatttaagacgcgatgtcttgtttcagGATGCTGTTGATTGTCCTGAATGGATTGTCCCCTTCCACATATTCAAGTCATTAGCTGAAGAG
upper sequence: AT3G20650.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G41190.1 (Glycine max), 3'ss of exon 9
gtacctaatttatctacagtattcttgagatattcacttagtctaccgcagaaacttaagcattgtaaaggaaactatatctgtgtaaatatattgtaagaacacgactacctattaaatggagattccagaaacttcccttgtcatgtttgctgttaaaaagaaaatataacataggaacttgtattgtagGATGCTGTTGATTGTCCTGAATGGATTGTGCCCTTTAACGTCTTCAAGTCTTTAGCGGAGGAG
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------------------------------------------------------------------------------------atgaagttatcattcaaagactgct-cttatttag----ggccctgtaaagctggcatactgt---taatacctatgcttccatttaagacacgatgtcttgtttcagGACGCTGTTGATTGTCCTGAATGGATTGTCCCCTTCCATGTATTCAAGTCATTAGCTGAAGAG
upper sequence: AT3G20650.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 9
gtacctaatttatctacagtattcttgagatattcacttagtctaccgcagaaacttaagcattgtaaaggaaactatatctgtgtaaatatattgtaagaacacgactaccta-ttaaatggagattccagaaacttcc---cttgtcatgtttgctgttaaaaagaaaatataacataggaacttgtattgtagGATGCTGTTGATTGTCCTGAATGGATTGTGCCCTTTAACGTCTTCAAGTCTTTAGCGGAGGAG
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------------------------------------------------------------------------------------------------ttatgatcctgctgctcagctctaccttgattccttaagttacagaaccacacaatcctacccataaaataatattgagaagaaagagcttttgttgcagGATGCTGTTGATTGTCCTGAATGGATTGTCCCATTTCATGTCTTCAAATCATTGGCAGAAGAGMapped 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|86084647|gb|DR380406.1|DR380406EST: TTCAAATCTAGCAGCCCATTTGGTATCGAATACGTGTTTCATCTCGAG GATGCTGTTGATTGTCCTGAATGGATTGTGCCCTTTAACGTCTTCAAGTCT
genomic: TTCAAATCTAGCAGCCCATTTGGTATCGAATACGTGTTTCATCTCGAGgtacctaatt ... tgtattgtagGATGCTGTTGATTGTCCTGAATGGATTGTGCCCTTTAACGTCTTCAAGTCT
EST:
gi|125017436|gb|EL089705.1|EL089705EST: TCAAATCTAGCAGCCCATTTGGTATCGAATACGTGTTTCATCTCGAG GATGCTGTTGATTGTCCTGAATGGATTGTGCCCTTTAACGTCTTCAAGTCT
genomic: TCAAATCTAGCAGCCCATTTGGTATCGAATACGTGTTTCATCTCGAGgtacctaatt ... tgtattgtagGATGCTGTTGATTGTCCTGAATGGATTGTGCCCTTTAACGTCTTCAAGTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccttgtcatgtttgctgttaaaaagaaaatataacataggaacttgtattgtagGATGCTGTTGATTGTCCTGAATGGATTGTGCCCTTTAACGTCTTCAAGTCTTTAGCGGAGGAG
atataac putative branch site (score: 3)
tgttaaaaagaaaata TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacctaatttatctacagtattcttgagatattcacttagtctaccgcagaaacttaagcattgtaaaggaaactatatctgtgtaaatatattgtaagaacacgactacctattaaatggagattccagaaacttcccttgtcatgtttgctgttaaaaagaaaatataacataggaacttgtattgtagGATGCTGTTGATTGTCCTGAATGGATTGTGCCCTTTAACGTCTTCAAGTCTTTAGCGGAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG