Sequence
atgc intronic sequence ATGC exonic sequencegtgatagaatgttttcaattgaaaagttcttcacatttcgaatcaatttcataaaatgttatctgatttgaaatcatgagtaattttttgaagttgaatgatatggtttttgttaaaacagAGTCAGGGAAGCTAATTACATGGGGTTCTACAGATGATCTAGGTCAAAGCTACGTCACATCTGGGAAACACGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G55580.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G41810.2 (Glycine max), 3'ss of exon 1
gtgatagaatgttttcaattgaaaagttcttcacatttcgaatcaat-ttcataaaatgttatctgatttgaaatcatgagtaattttttgaagttgaatgatatggtttttgttaaaacagAGTCAGGGAAGCTAATTACATGGGGTTCTACAGATGATCTAGGTCAAAGCTACGTCACATCTGGGAAACACGGG
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-------------tacatctttgcatccctctatctctctattagctgcttttcttttaccattttatttg----tataaagggttcatcattgctca----cgtgttcgtccttaat-cagAATCAGGGAAGCTCATCACATGGGGCTCAACAGATGATCTAGGCCAAAGCTATGTGACTTCTGGCAAGCATGGG
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 1
gtgatagaatgttttcaattgaaaagttcttcacatttcgaatcaatttcataaaatgttatctgatttgaaatcatgagtaattttttgaagttgaatgatatggtttttgttaaaacagAGTCAGGGAAGCTAATTACATGGGGTTCTACAGATGATCTAGGTCAAAGCTACGTCACATCTGGGAAACACGGG
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------------tttcttttgaagggagtt----atcccagtgcacatctctctgttcttcccttttcttctaacgtaaaggaatcgtca----ttacttatattttcttccttgat-cagAGCCTGGAAAGCTCATAACATGGGGTTCAACAGATGATTTAGGCCAAAGCTATGTTACATCTGGCAAACATGGG
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 1
gtgatagaatgttttcaattgaaaagttcttcacatttcgaatcaatttcataaaatgttatctgatttgaaatcatgagtaattttttgaagttgaatgatatggtttttgttaaaacagAGTCAGGGAAGCTAATTACATGGGGTTCTACAGATGATCTAGGTCAAAGCTACGTCACATCTGGGAAACACGGG
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------------tttcttttgaagggagtt----atcccaatgcatatctctctgttcttcccttttcttataacgtaaaggaatcatca----ttacttatactttcttccttgat-cagAGCCTGGAAAGCTCATAACATGGGGTTCAACAGATGATTTAGGCCAAAGCTATGTTACATCTGGCAAACATGGG
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G07160.1 (Glycine max), 3'ss of exon 1
gtgatagaatgttttcaattgaaaagttcttcacatttcgaatcaatt-tcataaaatgttatctgatttgaaatcatgagtaattttttgaagttgaatgatatggtttttgttaaaacagAGTCAGGGAAGCTAATTACATGGGGTTCTACAGATGATCTAGGTCAAAGCTACGTCACATCTGGGAAACACGGG
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------gtacgtatttggtt-------cctttatctctctattcgcttgttttcttttaccattttatttg----tataaagcattcaccattgctcacgtgcacgtcctt-----aatcagAATCGGGGAAGCTCATCACATGGGGCTCAACAGATGATCTAGGCCAAAGCTATGTGACTTCTGGCAAGCATGGG
upper sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 1
gtgatagaatgttttcaattgaaaagttcttcacatttcgaatcaatttcataaaatgttatctgatttgaaatcatgagtaattttttgaagttgaatgatatg----gtttttgttaaaacagAGTCAGGGAAGCTAATTACATGGGGTTCTACAGATGATCTAGGTCAAAGCTACGTCACATCTGGGAAACACGGG
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-------------------------ttcctttcaacagcagctctactcaatgatttccctgcaattctttcattttaattattttccaaaagttgtgttttttctcatgcttctgtttaatcagAGTCTGGAAAGCTCATCACCTGGGGTTCAACGGATGATCTAGGTCAAAGCTATGTGACATCTGGAAAGCATGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgaaatcatgagtaattttttgaagttgaatgatatggtttttgttaaaacagAGTCAGGGAAGCTAATTACATGGGGTTCTACAGATGATCTAGGTCAAAGCTACGTCACATCTGGGAAACACGGG
tttttgtt CT-rich tract
taattttttgaagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatagaatgttttcaattgaaaagttcttcacatttcgaatcaatttcataaaatgttatctgatttgaaatcatgagtaattttttgaagttgaatgatatggtttttgttaaaacagAGTCAGGGAAGCTAATTACATGGGGTTCTACAGATGATCTAGGTCAAAGCTACGTCACATCTGGGAAACACGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG