Sequence
atgc intronic sequence ATGC exonic sequencegtgatttcctacaacatgctaggtctatctgttatttataaacatagagaggtaagttcgcttgcttacatttaccttacactctcgtagGCATGGGCTAGGCTTTGCAAGTGTCTAGGTCAAGATTTCCTCCCATACATGAAGGTTGTGATGCCTCCTTTGCTTCAGTCAGCTCAACTTAAGCCAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G19820.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g49420.2 (Oryza sativa), 3'ss of exon 5
gtgatttcctacaacatgctaggtctatctgttatttataaacatagagaggtaagttcgcttgcttacatttaccttacactctcgtagGCATGGGCTAGGCTTTGCAAGTGTCTAGGTCAAGATTTCCTCCCATACATGAAGGTTGTGATGCCTCCTTTGCTTCAGTCAGCTCAACTTAAGCCAGATG
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---gtatgttgtagc---ttaaatactattgccattttatgccatcactagtttgcttcagttttgcttattctaattgcattttc-tagGCATGGGCGAGATTGTGTAAATGCCTTGGTCAGGACTTCTTACCATACATGAATGTTGTTATGCCTCCTCTGCTCCAGTCTGCTCAGCTTAAACCAGATG
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G887631_T01 (Zea mays), 3'ss of exon 6
gtgatttcctacaacatgctaggtctatctgttatttataaacatagagaggtaagttcgcttgcttacatttaccttacactctcgtagGCATGGGCTAGGCTTTGCAAGTGTCTAGGTCAAGATTTCCTCCCATACATGAAGGTTGTGATGCCTCCTTTGCTTCAGTCAGCTCAACTTAAGCCAGATG
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-------------gtatgcttcaaagcaatgaaatctagtcttaaaaacaccttaat---cattctaacacttatctccacatgttatagGCTTGGGCTAGGCTATGCAAATGTCTTGGACAGGATTTCCTTCCTTACATGAGTGTTGTTATGCCTCCACTGCTTCAGTCTGCTCAACTCAAGCCTGATG
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G28950.1 (Glycine max), 3'ss of exon 8
gtgatttcctacaacatgctaggtctatctgttatttataaa-catagagaggtaagttcgcttgcttacatttaccttacactctcgtagGCATGGGCTAGGCTTTGCAAGTGTCTAGGTCAAGATTTCCTCCCATACATGAAGGTTGTGATGCCTCCTTTGCTTCAGTCAGCTCAACTTAAGCCAGATG
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--gtatgctttttatatatta--tttacatcatatgcataaagtgccaattggtatatgttttagtctaa--caactttaatttgttacagGCATGGGCTAGACTTTGCAAATGTCTGGGACAAGATTTTCTTCCTTACATGGAGTTTGTCATGCCTCCACTGCTTCAATCTGCTTCACTTAAGCCTGATG
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 6
gtgatttcctacaacatgctaggtctatctgttatttataaacatagagaggtaagttcgcttgcttacatttaccttacactctcgtagGCATGGGCTAGGCTTTGCAAGTGTCTAGGTCAAGATTTCCTCCCATACATGAAGGTTGTGATGCCTCCTTTGCTTCAGTCAGCTCAACTTAAGCCAGATG
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--gtatgtttttagtatatta--tttaaagcatatgcataaagctccagttg-gactatgttttagtctaacgactttaatttgttacagGCATGGGCTAGACTCTGCAAATGTCTGGGACAAGATTTTCTTCCTTACATGGAGTTTGTCATGCCTCCACTACTTCAATCTGCTGCACTTAAGCCCGATG
upper sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 6
gtgatttcctacaacatgctaggtctatctgttatttataaacatagagaggtaagttcgcttgcttacatttaccttac-actctcgtagGCATGGGCTAGGCTTTGCAAGTGTCTAGGTCAAGATTTCCTCCCATACATGAAGGTTGTGATGCCTCCTTTGCTTCAGTCAGCTCAACTTAAGCCAGATG
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gtatgcttgtgaattataatgtgtggatcacttttatatcttc-cacttgtttcacttctttgtgtgatgaatatttaattattgctgcagGCTTGGGCCAGACTCTGCAAGTGCCTGGGACAAGACTTCCTCCCTTACATGAGTGTTGTCATGCCCCCTTTGCTTCAATCTGCTCAACTTAAACCTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttataaacatagagaggtaagttcgcttgcttacatttaccttacactctcgtagGCATGGGCTAGGCTTTGCAAGTGTCTAGGTCAAGATTTCCTCCCATACATGAAGGTTGTGATGCCTCCTTTGCTTCAGTCAGCTCAACTTAAGCCAGATG
cactctc CT-rich tract
ttacattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatttcctacaacatgctaggtctatctgttatttataaacatagagaggtaagttcgcttgcttacatttaccttacactctcgtagGCATGGGCTAGGCTTTGCAAGTGTCTAGGTCAAGATTTCCTCCCATACATGAAGGTTGTGATGCCTCCTTTGCTTCAGTCAGCTCAACTTAAGCCAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG