Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctgctgatctttaccaaaccattccacatatgaaatcttatgtcgctttttccatgaacaatggagctatggttaacagggtactaaaggcgtcgagtatatagaggaattgtaacttatgtcttatgatggtatagaatttgatcaaaaatcagtattgttattttattgaacagGTGAGATATCCAGTTTTACTTACACCTGCTGAGAAACAAATGGCGAGAGAAGTTTGCATTGCATTTAGGCAAGCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G15070.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 9
gtaagtctgctgatctttaccaaaccattccacatatgaaatcttatgtcgctttttccatgaacaatggagctatggttaacagggtactaaaggcgtcgagtatatagaggaattg-taacttatgtcttatgatggtatagaatttgatcaaaaatcagtattgttattttattgaacagGTGAGATATCCAGTTTTACTTACACCTGCTGAGAAACAAATGGCGAGAGAAGTTTGCATTGCATTTAGGCAAGCG
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----------------------------------------------------------------------------aagaaacaaa-tatttaatat-tcaaaagcaggctggagttgctggctggtgtgcaacaataattttt--cttgttgaaaaat--gt-ctacaatttcatttggcagGTTAGGTATCCAGTCCTCCTGACTCCTGCTGAGAAAGAAATGGCAAGAGAAGTTTGCATTGCATTCAGGCAAGCG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 7
gtaagtctgctgatctttaccaaaccattccacatatgaaatcttatgtcgctttttccatgaacaatggagctatggttaacagggtactaaaggcgtcgagtatatagaggaattg-taacttatgtcttatgatggtatagaatttgatcaaaaatcagtattgttattttattgaacagGTGAGATATCCAGTTTTACTTACACCTGCTGAGAAACAAATGGCGAGAGAAGTTTGCATTGCATTTAGGCAAGCG
|| || | | || | | | ||| || | || ||| | || | || ||| | || | | |||| ||| ||||| || |||||||| | || || |||||||||||| ||||||| |||||||||||||||||||| |||||||||
-------------------------------------------------------------------------------gaaacaaatatttat----tcaaaaacaggctggagtttctggctggtgtgcaacaataatttaatttttcttgttgaaaaatgcctacaatttcatttggcagGTTAGGTATCCAGTCCTCCTGACTCCTGCTGAGAAAGAAATGGCAAGAGAAGTTTGCATTGCATTCAGGCAAGCG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 7
gtaagtctgctgatctttaccaaaccattccacatatgaaatcttatgtcgctttttccatgaacaatggagctatggttaacagggtactaaaggcgtcgagtatatagaggaattgtaacttatgtcttatgatggta--tagaatttgatcaaaaatcagtattgttattttattgaacagGTGAGATATCCAGTTTTACTTACACCTGCTGAGAAACAAATGGCGAGAGAAGTTTGCATTGCATTTAGGCAAGCG
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-----------------------------------------------------------------------------------aaggaacaaacatgtaccattgcaaagcaggccag-aattgcttgcttgaaacagtaatttaacttctgtattgaagcatgtttatcatctcatctgacagGTTAGGTATCCAGTGTTACTGACTCCTGCTGAGAAGGAAATGGCAAGAGATGTTTGCATTGCATTCAGTCAAGCG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 10
gtaagtctgctgatctttaccaaaccattccacatatgaaatcttatgtcgctttttccatgaacaatggagctatggttaacagggt-actaaaggcgt-cgagtatatagagga--attgtaacttatgtcttatgatggtatagaatttgatcaaaaatcagtattgttattttattgaacagGTGAGATATCCAGTTTTACTTACACCTGCTGAGAAACAAATGGCGAGAGAAGTTTGCATTGCATTTAGGCAAGCG
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----------------------------------------------------------------gtacgaagttttt-ttaatagaatgaacaaacatgtgccattgcaaagcaggccagaattgcttgcttgaaacagtaatttaacttctgaattgaagcatgt-ttatcatctcatttggcaggttagGTATCCAGTGTTACTGACCCCTGCTGAGAAGGAAATGGCAAGAGATGTTTGCATTGCATTCAGTCAAGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttatgatggtatagaatttgatcaaaaatcagtattgttattttattgaacagGTGAGATATCCAGTTTTACTTACACCTGCTGAGAAACAAATGGCGAGAGAAGTTTGCATTGCATTTAGGCAAGCG
atttgat putative branch site (score: 5)
ttatttt putative PPT
atcaaaaatcagtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctgctgatctttaccaaaccattccacatatgaaatcttatgtcgctttttccatgaacaatggagctatggttaacagggtactaaaggcgtcgagtatatagaggaattgtaacttatgtcttatgatggtatagaatttgatcaaaaatcagtattgttattttattgaacagGTGAGATATCCAGTTTTACTTACACCTGCTGAGAAACAAATGGCGAGAGAAGTTTGCATTGCATTTAGGCAAGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT