Sequence
atgc intronic sequence ATGC exonic sequencegtatttgtatttcactttattgctccttcccacttaaagaatgttttttacgagtatgttgaccataatgtggtttctgccattttcgtggacaatagaatgtgatatcaagatgaaggacgtgaaacaattactaaataaaggaagagatctaatttattcaaatgacaccttaatgttcttcttgtacttcatgcagATCCACACCCACATGTGCTACTCAAATTTCAACGACATCATCCACTCAATTATTGATATGGATGCTGATGTGATCACTATTGAGAACTCACGGTCAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20980.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA04G30350.1 (Glycine max), 3'ss of exon 11
gtatttgtatttcactttattgctccttcccacttaaagaatgttttttacgagtatgttgaccataatgtggtttctgccattttcgtggacaatagaatgtgatatcaagatgaaggacgtgaaacaattactaaataaaggaagagatctaatttattcaaatgacaccttaatgttcttcttgtacttcatgcagATCCACACCCACATGTGCTACTCAAATTTCAACGACATCATCCACTCAATTATTGATATGGATGCTGATGTGATCACTATTGAGAACTCACGGTCAGATG
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----------------------------------------------------------------------------------------------gttcagcttcacttctcatgtttcaatctttaataatgattacacaa---------tcttatatattaatat-------taatata-tcgtgatatttca--cagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATCATAGACATGGATGCTGATGTGATCACCATTGAGAACTCCAGATCAGATG
upper sequence: AT5G20980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G15140.2 (Glycine max), 3'ss of exon 10
gtatttgtatttcactttattgctccttcccacttaaagaatgttttttacgagtatgttgaccataatgtggtttctgccattttcgtggacaatagaatgtgatatcaagatgaaggacgtgaaacaattactaaataaaggaagagatctaatttat-tcaaatgacaccttaatgttcttcttgtacttcatgcagATCCACACCCACATGTGCTACTCAAATTTCAACGACATCATCCACTCAATTATTGATATGGATGCTGATGTGATCACTATTGAGAACTCACGGTCAGATG
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---------------------------------------------------------------------------------------------------------------gttcagcttcacttctcatgttctaatctttactaatgat-tagtcaatcttatatattaatattaagatactgtaatatttga--cagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATCATAGACATGGATGCTGATGTGATCACCATTGAGAACTCTAGATCAGACG
upper sequence: AT5G20980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv06s0009g01080.t01 (Vitis vinifera), 3'ss of exon 11
gtatttgtatttcactttattgctccttcccacttaaagaatgttttttacgagtatgttgaccataatgtggtttctgccattttcgtggacaatagaatgtgatatcaagatg-aaggacgtgaaacaattactaaataaaggaagagatctaatttattcaaatgacaccttaatgttcttcttgtacttcatgcagATCCACACCCACATGTGCTACTCAAATTTCAACGACATCATCCACTCAATTATTGATATGGATGCTGATGTGATCACTATTGAGAACTCACGGTCAGATG
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-----------------------------------------------------------------------------------------tgttaggagtatgtgatcgtatcatataaggaaacgtatgcaaaaggaaatgaaacagtgactagaattc---tgaacgtctttttaatattgtttcta--------acagATCCATACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATCATAGACATGGATGCTGACGTGATCACCATTGAGAACTCCAGATCAGATG
upper sequence: AT5G20980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ05611 (Selaginella moellendorffii), 3'ss of exon 11
gtatttgtatttcactttattgctccttcccacttaaagaatgttttttacgagtatgttgaccataatgtggtttctgccattttcgtggacaatagaatgtgatatcaagatgaaggacgtgaaacaattactaaataaaggaagagatctaatttattcaaatgacaccttaatgttcttcttgtacttcatgcagATCCACACCCACATGTGCTACTCAAATTTCAACGACATCATCCACTCAATTATTGATATGGATGCTGATGTGATCACTATTGAGAACTCACGGTCAGATG
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------------------------------------------------------------------------------------------------------------------------------------gtaaaagacgcgacgagtttctatagcttcgtgaatgacactggcgttgtt--tgaaatcca--cagATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG
upper sequence: AT5G20980.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
gtatttgtatttcactttattgctccttcccacttaaagaatgttttttacgagtatgttgaccataatgtggtttctgccattttcgtggacaatagaatgtgatatcaagatgaaggacgtgaaacaattactaaataaaggaagagatctaatttattcaaatgacaccttaatgttcttcttgtacttcatgcagATCCACACCCACATGTGCTACTCAAATTTCAACGACATCATCCACTCAATTATTGATATGGATGCTGATGTGATCACTATTGAGAACTCACGGTCAGATG
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------------------------------------------------------------------------------------------------------------------------------------gtaaaagacgcgacgagtttctatagcttcgtgactgacactggcgttgtt--tgaaatcca--cagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagagatctaatttattcaaatgacaccttaatgttcttcttgtacttcatgcagATCCACACCCACATGTGCTACTCAAATTTCAACGACATCATCCACTCAATTATTGATATGGATGCTGATGTGATCACTATTGAGAACTCACGGTCAGATG
ttcttcttgtacttc CT-rich tract
atctaatttattcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttgtatttcactttattgctccttcccacttaaagaatgttttttacgagtatgttgaccataatgtggtttctgccattttcgtggacaatagaatgtgatatcaagatgaaggacgtgaaacaattactaaataaaggaagagatctaatttattcaaatgacaccttaatgttcttcttgtacttcatgcagATCCACACCCACATGTGCTACTCAAATTTCAACGACATCATCCACTCAATTATTGATATGGATGCTGATGTGATCACTATTGAGAACTCACGGTCAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG