Sequence
atgc intronic sequence ATGC exonic sequence...caaaagaatattaattgtggactagtattttggtcgtgttaaattttccggttcgataaactcattgtggtttgacaaaaccggatttttgttgatgtagTTGTGGAGGTAGATGCCTTCCTATAGAATATATAGACAAAGTCGGAGAATTAGCCAAGAAACATGGTTTGAAGCTTCACATTGACGGAGCTAGGATTTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G04520.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G04520.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G36590.2 (Glycine max), 3'ss of exon 2
caaaagaatattaattgtggactagtattttg-gtcgtgttaaattttccggttcgataaactcattgtggtttgacaaaaccggatttttgttgatgtagTTGTGGAGGTAGATGCCTTCCTATAGAATATATAGACAAAGTCGGAGAATTAGCCAAGAAACATGGTTTGAAGCTTCACATTGACGGAGCTAGGATTTTC
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-ggcaatttgctaaattttcttttgttttaaaagtcccatcctgttgttaattgattcaaatttatagcaacattatgactcgtattttacctgaatgcagCTCTGGTGGCAGATGCCTCTCAGTTGAATATACAGACAGAGTTGGAGAGTTAGCTAAGAAGCATGGACTGAAGCTTCACATTGATGGGGCCCGTATTTTT
upper sequence: AT3G04520.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G30880.1 (Glycine max), 3'ss of exon 2
caaaagaatattaattgtggactagtattttggtcgtgttaaatt-ttccggttcgat--aaactcattgtggtttgacaaaaccggatttttgttgatgtagTTGTGGAGGTAGATGCCTTCCTATAGAATATATAGACAAAGTCGGAGAATTAGCCAAGAAACATGGTTTGAAGCTTCACATTGACGGAGCTAGGATTTTC
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--gcaatttgctaatttttctttag-gttttaaaagtcccatcttgttgttaattgattcaaatttatagcagcatcatgactcgtattttacctgaatgcagCTCTGGTGGCAGATGCCTCTCAGTTGAATATACAGACAGAGTTGGAGAGTTAGCTAAGAAGCATGGACTGAAGCTTCACATTGATGGGGCCCGTATTTTT
upper sequence: AT3G04520.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G41120.1 (Glycine max), 3'ss of exon 2
caaaagaatattaattgtggactagtattttggtcgtgttaaattttccggttcgataaactcattgtggtttgacaaaacc----ggatttttgtt-----gatgtagTTGTGGAGGTAGATGCCTTCCTATAGAATATATAGACAAAGTCGGAGAATTAGCCAAGAAACATGGTTTGAAGCTTCACATTGACGGAGCTAGGATTTTC
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---gtaagcaattatgctgttcaaaaattttctaaatagtacattaattggttaaatatcctttatataagcagtaagaatgattggtatttttttttcctgattgtagCTCTGGTGGTAGATGTCTTTCAGTTGAATATACAGACAGAGTAGGAGAGGTTGCTAAAAAACATGGATTGAAGCTTCACATTGATGGAGCCCGAATATTT
upper sequence: AT3G04520.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0036g00520.t01 (Vitis vinifera), 3'ss of exon 3
caaaagaatattaattgtggactagtattttggtcgtgttaaattttccggttcgataaactcatt-----gtggtttgacaaaaccggatttttgttga-tgtagTTGTGGAGGTAGATGCCTTCCTATAGAATATATAGACAAAGTCGGAGAATTAGCCAAGAAACATGGTTTGAAGCTTCACATTGACGGAGCTAGGATTTTC
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------attattccttgcccatttctctcttgcctttcttatttgtttatccttcactttctcgcttatgtacagtgttttactagtgcttctttattgaatgcagCTGTGGTGGTAGATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTTAGCCAAGAAACATGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccggttcgataaactcattgtggtttgacaaaaccggatttttgttgatgtagTTGTGGAGGTAGATGCCTTCCTATAGAATATATAGACAAAGTCGGAGAATTAGCCAAGAAACATGGTTTGAAGCTTCACATTGACGGAGCTAGGATTTTC
tgttgat putative branch site (score: 4)
tttttgtt CT-rich tract
atttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaaagaatattaattgtggactagtattttggtcgtgttaaattttccggttcgataaactcattgtggtttgacaaaaccggatttttgttgatgtagTTGTGGAGGTAGATGCCTTCCTATAGAATATATAGACAAAGTCGGAGAATTAGCCAAGAAACATGGTTTGAAGCTTCACATTGACGGAGCTAGGATTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT