Sequence
atgc intronic sequence ATGC exonic sequencegtataatcacttttttcaagcagacattatacatcacaatatgaaactttgtcaatcatttcgatcttctttattatctctgttgaattacatttcaagtcctcattcagagttatgtgttgcagATATTACTTGGTGGAAAAAGCTAAGGATGCGAATATTATAGGTATTTTGGTGGGGACTCTTGGTGTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G59630.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G59630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g16430.1 (Oryza sativa), 3'ss of exon 5
gtataatcacttttttcaagcagacattatacatcacaatatgaaactttgtcaatcatttcgatcttctttattatctctgttgaattacatttcaagtcctcattcagagttatgtgttgcagATATTACTTGGTGGAAAAAGCTAAGGATGCGAATATTATAGGTATTTTGGTGGGGACTCTTGGTGTTG
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-----gtcatcttatgca-gcatatataatactttat---------ttttgcgtgaaatgaaagattttttttttgtcattgtagcattatttacaaaatagt---------ttgtatat-gcagATATTACCTTGTGGAGAAGGCGAAGGATGCAAATATTGTTGGCATTTTGGTGGGGACCCTGGGTGTTG
upper sequence: AT3G59630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: AC217358.3_FGT003 (Zea mays), 3'ss of exon 5
gtataatcacttttttcaagcagacattatacatcacaatatgaaactttgtcaatcatttcgatcttctttattatctctgttgaattacatttcaagtcctcattcagagttatgtgttgcagATATTACTTGGTGGAAAAAGCTAAGGATGCGAATATTATAGGTATTTTGGTGGGGACTCTTGGTGTTG
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--------------------------------------gtattttgtttttgcagca---tcgatatactattttcttactat---atttggtgttgattacaaaatatgaattgta-attgtagATATTACCTCGTGGAGAAGGCGAAGGATGCAAATATTATTGGCATTTTGGTGGGAACTCTGGGTGTAG
upper sequence: AT3G59630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G01090.1 (Glycine max), 3'ss of exon 5
gtataatcacttttttcaagcagacattatacat-cacaatatgaaactttgtcaatcatttcgatcttctttattatctctgttgaattacatttcaagtcctcattcagagttatgtgt-tgcagATATTACTTGGTGGAAAAAGCTAAGGATGCGAATATTATAGGTATTTTGGTGGGGACTCTTGGTGTTG
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--------------------------gtatgtaaacacaatataaa--cacactactctgttgtgtaagccatcttatgtcttcaaaatt----------tactaagctagggtgatgactatgcagATATTACCTGGTGGAGAGAGCTAAAGATGCTAATATTGTTGGGATTTTAGTTGGAACTCTTGGTGTTG
upper sequence: AT3G59630.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0094g00370.t01 (Vitis vinifera), 3'ss of exon 5
---gtataatcacttttttcaagcagacattatacatcacaatatgaaactttgtcaatcatttcgatcttctttattatctctgttgaatta--cattt-caagtcct---------cattcagagttatgtgttg-cagATATTACTTGGTGGAAAAAGCTAAGGATGCGAATATTATAGGTATTTTGGTGGGGACTCTTGGTGTTG
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gtagtacttgtgcttctgctaaacttacaatgcat-ttaatgtctatgtccttatgtgatgatgtaattctctctcttgttcctttataatcagttgtttactagttttgttgcatgattttctgaggaatatgttgacagATATTACTTAGTGGAGAAGGCAAAGGATTCTAATATTATTGGGCTTTTGGTGGGAACTCTTGGTGTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattatctctgttgaattacatttcaagtcctcattcagagttatgtgttgcagATATTACTTGGTGGAAAAAGCTAAGGATGCGAATATTATAGGTATTTTGGTGGGGACTCTTGGTGTTG
aattacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataatcacttttttcaagcagacattatacatcacaatatgaaactttgtcaatcatttcgatcttctttattatctctgttgaattacatttcaagtcctcattcagagttatgtgttgcagATATTACTTGGTGGAAAAAGCTAAGGATGCGAATATTATAGGTATTTTGGTGGGGACTCTTGGTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG