Sequence
atgc intronic sequence ATGC exonic sequencegtattccattcaaagcttttttgattttgttcacccttcttactactcttagagtacggaacaattaaatcttttttgcaactattcctgcagAATGTGCAGGACGCTCATGCCTGGAGATGAAGAAACTATGAGTGATGAAGCCATATGGGAAACACTTCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G68820.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G68820.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g49900.1 (Oryza sativa), 3'ss of exon 4
gtattccattcaaagcttttttgattttgttcacccttcttactactcttagagtacgg---aacaattaaatctttt--ttgcaactattcc----tgcagAATGTGCAGGACGCTCATGCCTGGAGATGAAGAAACTATGAGTGATGAAGCCATATGGGAAACACTTCCT
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--aaaatatctagagatattagttgttaatacaatagtagcgctaaagttaatttggatgttaacctttattttttttccttgcattggtttgactattcagAATGTGTAGAGCTTTAATGCCAGGAGATGAAGAAAGTATGAGCGATGAAGCTATTTGGGAGACACTTCCT
upper sequence: AT1G68820.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G024690_T02 (Zea mays), 3'ss of exon 4
gtattccattcaaagct-tttttgattttgttcacccttct-tactactcttagagtacgg-aacaattaaatcttttttgcaactattcctg-------cagAATGTGCAGGACGCTCATGCCTGGAGATGAAGAAACTATGAGTGATGAAGCCATATGGGAAACACTTCCT
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---tactattatttgttatttttggtgggctgctgcctactgtattagtcactatggacattgacgtctatgcatttcttggcatggttcttttatttgtcagAATGTGTAGAGCTTTAATGCCTGGGGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACACTTCCT
upper sequence: AT1G68820.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G704032_T01 (Zea mays), 3'ss of exon 4
gtattccattcaaagcttttttgattttgttcacccttcttactact--cttagagtacggaacaattaaatcttttttgcaactattcc-----tgcagAATGTGCAGGACGCTCATGCCTGGAGATGAAGAAACTATGAGTGATGAAGCCATATGGGAAACACTTCCT
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gaaaaataaactattatttgttatttttggagacttactgtattagtcactctggacattgacgtgtatgcatttcttggcatgttttttcattattcagAATGTGTAGAGCTTTAATGCCTGGAGATGAAGAAAGCATGAGTGATGAAGCTATTTGGGAGACGCTTCCT
upper sequence: AT1G68820.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0011g02950.t01 (Vitis vinifera), 3'ss of exon 4
-gtattccattcaaagcttttttgattt-tgttcacccttcttacta-----ctcttagagtacggaacaattaaatcttttt-tgcaactattcctgcagAATGTGCAGGACGCTCATGCCTGGAGATGAAGAAACTATGAGTGATGAAGCCATATGGGAAACACTTCCT
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tatattac-tttgcagttgtattacttagtgtcaagtaatagtaaaataattctgtcaaattgtgcatcagcctgattaacaaatgcatgttttattttagGATGTGTAAGGCTTTAATGCCTGGAGATGATGAAAGCATTAGTGATGAAGCAATATGGGAGACCCTTCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttactactcttagagtacggaacaattaaatcttttttgcaactattcctgcagAATGTGCAGGACGCTCATGCCTGGAGATGAAGAAACTATGAGTGATGAAGCCATATGGGAAACACTTCCT
ttcttac putative branch site (score: 2)
ctattcct putative PPT
aacaattaaatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattccattcaaagcttttttgattttgttcacccttcttactactcttagagtacggaacaattaaatcttttttgcaactattcctgcagAATGTGCAGGACGCTCATGCCTGGAGATGAAGAAACTATGAGTGATGAAGCCATATGGGAAACACTTCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC