Sequence
atgc intronic sequence ATGC exonic sequencegttagttgttatatgaccttttgggtttactgattactgtgaggagagcaatgatttttgttcactagttttacttaacataatctctcctttttttgctgtggaattgtagGCTTTGTTTGGTTTATTCTCACGCTGAAAAAGAAGATGTACAAATATCAGTTTAGCCAATATGCATGGACACATATGATATTAATTGTGGTGTTTACTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G22340.3 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G22340.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g17990.1 (Oryza sativa), 3'ss of exon 4
gttagttgttatatgaccttttgggtttactgattactgtgaggagagcaatgatttt-tgttcactagttttacttaacataatctctcctttttttgctgtggaattgtagGCTTTGTTTGGTTTATTCTCACGCTGAAAAAGAAGATGTACAAATATCAGTTTAGCCAATATGCATGGACACATATGATATTAATTGTGGTGTTTACTCA
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-----------cataaacttattgatatatagatgagtccattgc-accattgataaaattttaactacgtgctgccaatata-tcaatttggttattacttctgtcatacagGGTTTGTATGGTTTATTCTCACTCTAAAGAAAAAGGCGTACAAGTATCAATTCAGTCAATATGCATGGACTCACATGATCCTATTGATGGTATTTGCACA
upper sequence: AT4G22340.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G062416_T03 (Zea mays), 3'ss of exon 3
gttagttgttatatgaccttttgggtttactgattactgtgaggagagcaatgatttttgttcactagttttacttaacataatctctcctttttttgctgtggaattg-tagGCTTTGTTTGGTTTATTCTCACGCTGAAAAAGAAGATGTACAAATATCAGTTTAGCCAATATGCATGGACACATATGATATTAATTGTGGTGTTTACTCA
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-----------cgtaagctgttttttttacaaaaaaatgaggcaaatgcattctcataaagtt-tgaaaattgcttg-cttattgccaccatagtaatttatttattttctagGTTTTGTTTGGTTTATTATCACACTAAAGAAAAAGACATACAAGTACCAGTTCAGTCAATATGCATGGACTCACATGATCCTTCTCATGGTATTTGCCCA
upper sequence: AT4G22340.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------gttagttgttatatgaccttttgggt--ttactgattactgtgaggagagcaatgatttt-tgttcact-----agttttacttaacataatctctcctttttttgctgtggaattgtagGCTTTGTTTGGTTTATTCTCACGCTGAAAAAGAAGATGTACAAATATCAGTTTAGCCAATATGCATGGACACATATGATATTAATTGTGGTGTTTACTCA
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gtaacttatgcttatctacttatcttataacgttcattagccagtgcttgtgcaatgtttctgtcagatgcctggcaaatttcgagctagttttctacctttgtgattttactggctattttctaaatattgtgagagtgttactgctttggttatctacccttttattggttgagt-gcagGATTTATGTGGTTCATTCTCACGTTGAAGAAGAAGATGTACAAGTACCAATTTGGCCAGTATGCTTGGACACACATGATTCTAATTGTTGTATTTGGCCA
upper sequence: AT4G22340.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------gttagttgttatatgaccttttgggttta--ctgattactgtgaggagagcaatgatttttgttcactagtt-ttac-------ttaaca---taatctctcctttttttgctgtggaattgtagGCTTTGTTTGGTTTATTCTCACGCTGAAAAAGAAGATGTACAAATATCAGTTTAGCCAATATGCATGGACACATATGATATTAATTGTGGTGTTTACTCA
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gtaacttatgcttatctattttgtccttataatgttcattagccagtgcttgttcaaagtctctatcagatgcctggcattttcaagctagtttttttaccttggccgtgattttactggctattttctaaatattgcgagggtgctaatactttggttatctacccttttattggttgagtgcagGATTTATGTGGTTCATTCTCACATTGAAGAAGAAGATGTACAAGTACCAATTTGGCCAGTATGCTTGGACACACATGATTCTAATTGTTGTATTTGGCCA
upper sequence: AT4G22340.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 4
gttagttgttatatgaccttttgggtttactgattactgtgaggagagcaatgatttttgttcactagttttacttaacataatctctcctttttttgctgtggaattgtagGCTTTGTTTGGTTTATTCTCACGCTGAAAAAGAAGATGTACAAATATCAGTTTAGCCAATATGCATGGACACATATGATATTAATTGTGGTGTTTACTCA
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---tgttgctttattttgatttccgtttatattttcctttgt------cttttattttt-ttaataatttattgctgctgaaattattactctttgtgtgatgggct--cagGTTTTATGTGGTTTATTCTTACGTTAAAGAAGAAGATGTACAAGTATCAATTTGGCCAGTATGCATGGACACACATGATTCTAATTGTGGTGTTTACCCA
upper sequence: AT4G22340.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0598g00010.t01 (Vitis vinifera), 3'ss of exon 4
gttagttgttatatgaccttttgggtttactgattactgtgaggagagcaatgatttttgttcactagttttacttaacataatctctcctttttttgctgtggaattgtagGCTTTGTTTGGTTTATTCTCACGCTGAAAAAGAAGATGTACAAATATCAGTTTAGCCAATATGCATGGACACATATGATATTAATTGTGGTGTTTACTCA
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---tgttgctttattttgatttccgtttatattttcctttgc------cttttattttt-ttaataatttattgctgctgaaattattactctttgtgtgatgggct--cagGTTTTATGTGGTTTATTCTTACGTTAAAGAAGAAGATGTACAAGTATCAATTTGGCCAGTATGCATGGACACACATGATTCTAATTGTGGTGTTTACCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttcactagttttacttaacataatctctcctttttttgctgtggaattgtagGCTTTGTTTGGTTTATTCTCACGCTGAAAAAGAAGATGTACAAATATCAGTTTAGCCAATATGCATGGACACATATGATATTAATTGTGGTGTTTACTCA
acttaac putative branch site (score: 3)
ttttacttaacataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttgttatatgaccttttgggtttactgattactgtgaggagagcaatgatttttgttcactagttttacttaacataatctctcctttttttgctgtggaattgtagGCTTTGTTTGGTTTATTCTCACGCTGAAAAAGAAGATGTACAAATATCAGTTTAGCCAATATGCATGGACACATATGATATTAATTGTGGTGTTTACTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA