Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaatcttatccctaatctttacctacgtcatatattatcttttactattttggctgctctatcgtcttgttgtcactctgattctagtattttgaatatcaaaaaagGTACGAGCCTTATCTTTGGGAGAACGAAAAGCAGTCGTACCTACGCCATGCTGTACTCTTTGGTTTCTTTGTGCAACTAAACCGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G16300.4 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G16300.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G34570.1 (Glycine max), 3'ss of exon 4
-gtaagaaatcttatccctaatctttacctacgtcatatattatcttttactattttggctgctctatcgtcttgttgtcactctgattctagtattttgaatatcaaaaaagGTACGAGCCTTATCTTTGGGAGAACGAAAAGCAGTCGTACCTACGCCATGCTGTACTCTTTGGTTTCTTTGTGCAACTAAACCGAAT-------------
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agcatgca--tttcttgcaaagggttaaattggcagtgtgtaatgattttgtacttctagtaatttct-gcactgtcatc--tctgatctt-----tttttatgttaaa---gGTATGAGCCATATCTCTGGGAGAATGAGAGACAGTCTTACCTACGACATGCTGTTCTCTTTGGTTTCTTTGTGCAACTCAACCGTATGTACACAGATACT
upper sequence: AT5G16300.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G32980.1 (Glycine max), 3'ss of exon 4
---gtaagaaatcttatccctaatctttacctacgtcata--tattatcttttactattttggctgctctatcgtcttgttgtcactctgattctagtattttgaatatcaaaaaagGTACGAGCCTTATCTTTGGGAGAACGAAAAGCAGTCGTACCTACGCCATGCTGTACTCTTTGGTTTCTTTGTGCAACTAAACCGAAT-------------
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cttgcaaagggttaaattggcagtgtgtaatgattttgtacttctagacttctagtaattt--ctgcactgtcatct----------ctgatcttctttcttt--atgttaaa---gGTATGAGCCATATCTCTGGGAGAATGAGAGACAGTCTTACCTACGACATGCTGTTCTCTTTGGTTTCTTTGTACAACTCAACCGTATGTACACAGATACT
upper sequence: AT5G16300.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0340g00080.t01 (Vitis vinifera), 3'ss of exon 3
gtaagaaatcttatccctaatctttacctacgtcatatattatcttttactattttggctgctctatcgtcttgttgt-cactctgattctagtattttgaatatcaaaaaagGTACGAGCCTTATCTTTGGGAGAACGAAAAGCAGTCGTACCTACGCCATGCTGTACTCTTTGGTTTCTTTGTGCAACTAAACCGAAT-------------
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-------ttggtgtgtctgttttttttctttcttttctaaatcattcaaattaaatagtcattttttaatgtgatggtacatggtgatttatgt-taataaatttca-----gGTATGAGCCTTACCTCTGGGAGAACGAGAGGCAAGCATACCTCCGGCATGCTGTACTTTTTGGATTCTTTGTGCAACTTAATCGGATGTATACCGATACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgctctatcgtcttgttgtcactctgattctagtattttgaatatcaaaaaagGTACGAGCCTTATCTTTGGGAGAACGAAAAGCAGTCGTACCTACGCCATGCTGTACTCTTTGGTTTCTTTGTGCAACTAAACCGAAT
ctctgat putative branch site (score: 4)
tagtattttgaatatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaatcttatccctaatctttacctacgtcatatattatcttttactattttggctgctctatcgtcttgttgtcactctgattctagtattttgaatatcaaaaaagGTACGAGCCTTATCTTTGGGAGAACGAAAAGCAGTCGTACCTACGCCATGCTGTACTCTTTGGTTTCTTTGTGCAACTAAACCGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG