Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttttcgtttacatttaagttaataggttctttttggtagtcatctgaatgtatgaagttagttcttataaagatcacactttctgtaacttccagGTTAAAATAGTTTGTCATCTGCACCATGACCAGCTGAAGGCTGTTTTCCATGTTTCTCAAAGAATAAGAATGGCC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G35930.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G35930.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G05140.1 (Glycine max), 3'ss of exon 2
gtaagtttttcgtttacatttaagttaataggttcttt-ttggtagtcatctgaatgtatgaagttagttcttataaagatcacactttctgtaact---tccagGTTAAAATAGTTTGTCATCTGCACCATGACCAGCTGAAGGCTGTTTTCCATGTTTCTCAAAGAATAAGAATGGCC
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-gcattttactgtattcaatcaaatggcttagttatgtattaattcttatctgtttgaactatttctgttatgttga----cccattctctctgacttaattgagGTTAAAATACTATGCCACCTGCACCATGACCAACTGAGGGCTGTCTTCCATGTTTCTCAAAGAATTAGAAAAGCT
upper sequence: AT4G35930.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G23250.1 (Glycine max), 3'ss of exon 2
gtaagtttttcgtttacatttaagttaat-aggttcttt-ttggtagtcatctgaatgtatgaagttagttcttataaagatcacactttctgtaacttccagGTTAAAATAGTTTGTCATCTGCACCATGACCAGCTGAAGGCTGTTTTCCATGTTTCTCAAAGAATAAGAATGGCC
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--cattttactgtattcaattgattggcttaagttatgtattaattcttatctgtttgaaccatttctgttatgttgacacgttctctttcacttaattg-agGTTAAAATTCTGTGCCACCTGCACCATGACCAACTGAGGGCTGTCTTCCATGTTTCTCAAAAAATTAGAAAAGCT
upper sequence: AT4G35930.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s2668g00010.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtttttcgtttacatttaagttaataggttctttttggtagtcatctgaatgtatgaagttagttcttataaagatcacactt--tctgt-aacttccagGTTAAAATAGTTTGTCATCTGCACCATGACCAGCTGAAGGCTGTTTTCCATGTTTCTCAAAGAATAAGAATGGCC
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-ttattctttc--cagaatttaaactgagatcttcatggtattgat-atttcttaatattaactctgtggaagtactgatttcaattattttgtgaaatttgagGTTAAAATACTATGTCACCTGCACCATGACCAATTGAGGGCTGTTTTTCATGTCTCACAGAGGATTAGGAAGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catctgaatgtatgaagttagttcttataaagatcacactttctgtaacttccagGTTAAAATAGTTTGTCATCTGCACCATGACCAGCTGAAGGCTGTTTTCCATGTTTCTCAAAGAATAAGAATGGCC
ctgtaac putative branch site (score: 3)
ctttctgt CT-rich tract
ttagttcttataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttttcgtttacatttaagttaataggttctttttggtagtcatctgaatgtatgaagttagttcttataaagatcacactttctgtaacttccagGTTAAAATAGTTTGTCATCTGCACCATGACCAGCTGAAGGCTGTTTTCCATGTTTCTCAAAGAATAAGAATGGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA