Sequence
atgc intronic sequence ATGC exonic sequencegtataactacaatatttgggtttctctatttccccagcacatcgaaaattggctgcaaaagtgttataatgatgtctcatgctctaaattgcatcatgattggtctaatttttgtgatgtgcgtgatattctaacctacttatcttttttcagGAGCACAATTACCCGTGAGAAGTTTGAGGAACTGTGTAAAGATCTGTGGGAGAGATCTCTTACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16660.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16660.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0043g00710.t01 (Vitis vinifera), 3'ss of exon 3
gtataactacaatatttgggtttctctatttccccagcacatcgaaaattggctgcaaaagtgttataatgatgtctcatgctctaaattgcatcatgattggtctaatttttgtgatgtgcgtgatattctaacctacttatcttttttcagGAGCACAATTACCCGTGAGAAGTTTGAGGAACTGTGTAAAGATCTGTGGGAGAGATCTCTTACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAG
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---------------------------------------------acttcctttaccttggagttatg----cgtttgatggt-tggcttaggtaa--ataagctaaacattattaatttttcttat-cagagatttgctttttctctgccagGAGTGCCATAACTTGTGAGAAGTTTGAGGAGCTCTGCGAAGATTTGTGGGAGAGATCTCTTATTCTTGTGAAGGAAGTGCTTAAGAATTCAGGTTTGAAG
upper sequence: AT4G16660.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0008g04410.t01 (Vitis vinifera), 3'ss of exon 2
gtataactacaatatttgggtttctctatttccccagcacatcgaaaattggctgcaaaagtgttataatgatgtctcatgctctaaattgcatcatgattggtctaatttttgtgatgtgcgtgatattctaacctacttatcttttttcagGAGCACAATTACCCGTGAGAAGTTTGAGGAACTGTGTAAAGATCTGTGGGAGAGATCTCTTACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAG
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---------------------------------------------actttctttaccttggagttatg----cgtttgatggt-tggcttaggt--agataaactaaacattattaatcttgcttat-cagagattggccttttctctgccagGAGTACCATAACTCGTGAGAAGTTTGAGGAGCTCTGTGAAGATTTGTGGGAGAGATCTCTTATTCCTGCGAAGGAAGTGCTTAAGAATTCAGGTTTGAAG
upper sequence: AT4G16660.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0096g00090.t01 (Vitis vinifera), 3'ss of exon 4
gtataactacaatatttgggtttctctatttccccagcacatcgaaaattggctgcaaaagtgttataatgatgtctcatgctctaaattgcatcatgattggtctaatttttgtgatgtgcgtgatattctaacctacttatcttttttcagGAGCACAATTACCCGTGAGAAGTTTGAGGAACTGTGTAAAGATCTGTGGGAGAGATCTCTTACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAG
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---------------------------------------------acttcctttaccttggagttatg----cgtttgatggt-tggcttaggtaa--ataagctaaatattattaatttttcttat-cagagatttgctttttctctgccagGAGTGCCATAACTCGTGAGAAGTTTGAGGAGCTCTGCGAAGATTTGTGGGAGAGATCTCTTATTCCTGTGAAGGAAGTGCTTAAGAATTCAGGTTTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attggtctaatttttgtgatgtgcgtgatattctaacctacttatcttttttcagGAGCACAATTACCCGTGAGAAGTTTGAGGAACTGTGTAAAGATCTGTGGGAGAGATCTCTTACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAG
ttctaac putative branch site (score: 1)
cctacttatctttttt CT-rich tract
tacttatctttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataactacaatatttgggtttctctatttccccagcacatcgaaaattggctgcaaaagtgttataatgatgtctcatgctctaaattgcatcatgattggtctaatttttgtgatgtgcgtgatattctaacctacttatcttttttcagGAGCACAATTACCCGTGAGAAGTTTGAGGAACTGTGTAAAGATCTGTGGGAGAGATCTCTTACACCTTTAAAAGATGTGCTCAAGCATTCAGGTTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG