Sequence
atgc intronic sequence ATGC exonic sequencegttgctttctatgtctagttttgctggtttcttcttgttaatttgaagatatggagaaaggagggttaagcttcaggcaaatgtttaattcagaaagatatgttttggtcttctagtgctgtatttgtatatgttgcactgtatggctatatgtttaaagtctgtttatcttaactttcacctgtgctactttttccagAAAGCCCATGTTCAACAATTTTTGGCTACTGAAGATGCACTAAACAAAGCAGCTGAAGCTCGTGATTTATGCCACAAGTTTATTAACCGTTTGCATGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G38880.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G38880.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G50960.1 (Glycine max), 3'ss of exon 3
gttgctttctatgtctagttttgctggtttcttcttgttaatttgaagatatggagaaaggagggttaagcttcaggcaaatgtttaattcagaaagatatgttttggtcttctagtgctgtatttgtatatg-ttgcactgtatggctatatgtttaaagtctgtttatcttaactttcacctgtgctactttttccagAAAGCCCATGTTCAACAATTTTTGGCTACTGAAGATGCACTAAACAAAGCAGCTGAAGCTCGTGATTTATGCCACAAGTTTATTAACCGTTTGCATGGAA
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-----------------------------------------------------------------------------------------------------------------------ggtctttattcatccttaaactgcatattttgttgtcataagaggagttat-tgaactggtgcc-gtatctctgttcacaGAAAGCTCATGTTCAACAATTTTTGGCTACTGAAGATGCACTAAACAAAGCTGCAGAAGCAAGGGACATGTGTGAAAAACTTATGAAACGTTTGCATGGA-
upper sequence: AT5G38880.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 3
gttgctttctatgtctagttttgctggtttcttcttgttaatttgaagatatggagaaaggagggttaagcttcaggcaaatgtttaattcagaaagatatgttttggtcttctagtgctgtatttgtatat-gttgcactgtatggctatatgtttaaagtctgtttatcttaactttcacctgtgctactttttccagAAAGCCCATGTTCAACAATTTTTGGCTACTGAAGATGCACTAAACAAAGCAGCTGAAGCTCGTGATTTATGCCACAAGTTTATTAACCGTTTGCATGGAA
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------------------------------------------------------------------------------------------------------------------------gtcttgattcatcattaaactgcatattttgttgtcataagaggagttat-tgaactggtgc-tgtatctctgttcacagAAAGCTCATGTTCAACAATTTTTGGCTACTGAAGATGCACTAAACAAGGCTGCAGAAGCAAGGGATATGTGTGAAAAACTTATGAAACGTTTGCATGGAG
upper sequence: AT5G38880.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0083g00990.t01 (Vitis vinifera), 3'ss of exon 3
gttgctttctatgtctagttttgctggtttcttcttgttaatttgaagatatggagaaaggagggttaagcttcaggcaaatgtttaattcagaaagatatgttttggtcttctagtgctgtatttgtatatgttgcactgtatggctatatgtttaaagt-ctgtttatcttaactttcacctgtgctactttttccagAAAGCCCATGTTCAACAATTTTTGGCTACTGAAGATGCACTAAACAAAGCAGCTGAAGCTCGTGATTTATGCCACAAGTTTATTAACCGTTTGCATGGAA
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---------------------------------------------------------------------------------------------------attttgtgg-cacattttgctacttatgtttattgcattctactcagatttatctctgtggagttgtttaattgatatcaagccaatgttcactcctgcagAAAGCACATGTTCAGCAATTTGTAGCTACTGAAGATGCACTCAATAAAGCAGCAGAAGCTAGAAATTTGTGTCAAAAGCTTATAAAACGTCTACAAGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggctatatgtttaaagtctgtttatcttaactttcacctgtgctactttttccagAAAGCCCATGTTCAACAATTTTTGGCTACTGAAGATGCACTAAACAAAGCAGCTGAAGCTCGTGATTTATGCCACAAGTTTATTAACCGTTTGCATGGAA
tcttaac putative branch site (score: 2)
ctactttttcc putative PPT
tttatcttaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgctttctatgtctagttttgctggtttcttcttgttaatttgaagatatggagaaaggagggttaagcttcaggcaaatgtttaattcagaaagatatgttttggtcttctagtgctgtatttgtatatgttgcactgtatggctatatgtttaaagtctgtttatcttaactttcacctgtgctactttttccagAAAGCCCATGTTCAACAATTTTTGGCTACTGAAGATGCACTAAACAAAGCAGCTGAAGCTCGTGATTTATGCCACAAGTTTATTAACCGTTTGCATGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA