Sequence
atgc intronic sequence ATGC exonic sequencegtattggacgttatccctagtttgcattttgatgaattgtgtgtctgagctctttacctccgctaatagctgttttccagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTCCTCAATTTTTTCTGGACCCAAATACGGAGTTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01770.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 7
gtattggacg---ttatccctagtttgcat--tttgatgaattgtgtgtctgagctctttacctccgctaatagctgttttccagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTCCTCAATTTTTTCTGGACCCAAATACGGAGTTTCAG
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gtaattgatggcactagccattctttttatagtttagctacctct-tctccattttctttaatttcctaaatttcaatttt--agGGATGCATGGGACATGGCTGCAGAGATCTGCCTTTCTAAGCTTCCTCAATTAATTGCTGATCCTAATGCAGAGTTTCAG
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 8
gtattggacgttatcc-ctagtttgcattttgatgaattgtgtgt-ctgagctctttacctccgctaatagctgttttccagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTCCTCAATTTTTTCTGGACCCAAATACGGAGTTTCAG
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gtaattgatggcactagccattctttttatagtttagctacctcttctgcattttctttaatttcctaaattttaattttagGGATGCATGGGACATGGCTGCAGAGATCTGCCTTTCTAAGCTTCCTCAATTAATTGCTGATCCTAATGCAGAGTTTCAG
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 8
gtattggacgttatccctagtt-tgcattttgatgaattgtgtgtctgagctctttacctccgctaata-gctgttttccagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTCCTCAATTTTTTCTGGACCCAAATACGGAGTTTCAG
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------gtaactaacctgacttgttcttttttttgcattaactacct----tttgtgtgatttgtaacatgctaaatctcagGGATGCATGGGACATGGCTGCTGAGATTTGCCTTTCCAAGCTTCCTCAGTTAATTGCTGATCCAAATGCAGAGTTTCAG
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 8
---gtattggacgttatccctagtttgcattttgatgaattgtgtgtctgagctctttacc----tccgctaatagctgttttccagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTCCTCAATTTTTTCTGGACCCAAATACGGAGTTTCAG
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gtattgttggtgattatttttatgatatttttttctaaacgtgttgtcaaattttgtcaacagtttatgtttttatctgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCGTCTTTAGTTGAGGATCCTAATGCTGAATTTCAG
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 8
---gtattggacgttatccctagtttgcattttgatgaattgtgtgtctgagctcttt-----acctccgctaatagctgttttccagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTCCTCAATTTTTTCTGGACCCAAATACGGAGTTTCAG
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gtattgttggtgattattgttatgataatttttttctaaacgtgttgccaacttttgtcaacagtttatgtttttatccgcactgcagGGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCATCTTTAGTTGAGGATCCTAATTCTGAATTTCAG
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 8
gtattggacgttatccctagttt-gcattttgatgaattgtgtgtctgagctctttacctc------cgcta-atagctgttttccagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTCCTCAATTTTTTCTGGACCCAAATACGGAGTTTCAG
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gtacctactggaaatactagataagtaattttgttaagtgttcaa-taatccatttgtctcataatgtgccatgcatgtgtgctatagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTAAGTCATTGGTTGATGATCCCAATGCAGAGTTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttgatgaattgtgtgtctgagctctttacctccgctaatagctgttttccagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTCCTCAATTTTTTCTGGACCCAAATACGGAGTTTCAG
cgctaat putative branch site (score: 3)
ctgttttcc putative PPT
atgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattggacgttatccctagtttgcattttgatgaattgtgtgtctgagctctttacctccgctaatagctgttttccagGGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTCCTCAATTTTTTCTGGACCCAAATACGGAGTTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT