Sequence
atgc intronic sequence ATGC exonic sequence...tatagaaaacttagggaactctgctgcagtttctgttccgaagtatttgtgtgtggatggtttatatgagtttgttttgtgctcctcgaatctcttgcagAAGCTTTATGTGACAATGTTCCCTTGCAATGAATGTGCCAAGATTATTTTACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G48540.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G48540.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G124091_T04 (Zea mays), 3'ss of exon 6
tatagaaaacttagggaactctgctgcagtttctgttccgaagtatttgtgtgtggatggtttatatgagtttgttttgtgctcctcgaatctcttgcagAAGCTTTATGTGACAATGTTCCCTTGCAATGAATGTGCCAAGATTATTTTACAG
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---gtttggttgtttgagtcctacacaattatacacttcattaaacttttat-caaaagatttac------tggttttatgtgttt--attcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATTCAG
upper sequence: AT3G48540.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv17s0000g01370.t01 (Vitis vinifera), 3'ss of exon 6
tatagaaaac-ttagggaactctgctgcagtttctgttccgaagtatttgtgtgtggatggt--ttatatgagtttgttttgtgctcctcgaatctcttgcagAAGCTTTATGTGACAATGTTCCCTTGCAATGAATGTGCCAAGATTATTTTACAG
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-atcaacaatgtttgctgatttttctg-agtttttatttgaagagaaccttgggtgattactggtactaaaagaatgtttctcttatgtttgatct-ttgcagAGGCTTTATGTGACCATGTTTCCTTGCAACGAATGTGCCAAGATAATCATTCAG
upper sequence: AT3G48540.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S426_43V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------------------tatagaaaacttagggaactctgctgcagttt----ctgttccgaagtatttgtgt--gtggatggtttatatgagtttgttttgtgctcctcgaatctcttgcagAAGCTTTATGTGACAATGTTCCCTTGCAATGAATGTGCCAAGATTATTTTACAG
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gtaagcttccaggttgtgtcatgcttggcctgattagaaccagtttttcgaacttaaggtgaaaaagctttagtagttgatccagaagctttttacttttctaaaaatagtatactagtcgttgtttctgtcaagtaagatgcataccttgtgaaa-tgtggcagAGACTGTACGTGACCCTCTTCCCTTGCAATGAATGTGCCAAGATAATTATTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtgtgtggatggtttatatgagtttgttttgtgctcctcgaatctcttgcagAAGCTTTATGTGACAATGTTCCCTTGCAATGAATGTGCCAAGATTATTTTACAG
tctcttgc CT-rich tract
tttatatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatagaaaacttagggaactctgctgcagtttctgttccgaagtatttgtgtgtggatggtttatatgagtttgttttgtgctcctcgaatctcttgcagAAGCTTTATGTGACAATGTTCCCTTGCAATGAATGTGCCAAGATTATTTTACAG
- - gaaaact
- - - - - - - - - - ctgctgc
- - - - - - - - - - - - - - - - ctgttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtttat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgctcc