Sequence
atgc intronic sequence ATGC exonic sequencegtaagttataatcacatcctattttgtcaatttccttccttgttgttcttattttcacatctgatttacatcttgtcgtctctgtgatccccatagGATGGTCATCTCAAAATGCTTGGAGGATATCTGGAGTTTTTCATGAAACCTACTTTAGCATATACATACCTTTCGTTAAAAAGAGAGCTCGACGAACTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G48650.2 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G48650.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 11
gtaagttataatcacatcctattttgtcaatttccttccttgttgttcttattttcacatctgatttacatcttgtcgtctctgtgatccccatagGATGGTCATCTCAAAATGCTTGGAGGATATCTGGAGTTTTTCATGAAACCTACTTTAGCATATACATACCTTTCGTTAAAAAGAGAGCTCGACGAACTTA
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----------------gtaagttcatttgaattacttatttgttgctgaaataagcaaaggtactat-tggctaatttttacttca--tgctgcagGATGGACATTTGAAAATGCTTGGAGGATATCTTGAGTTCTTCATGAGTCGTGATCTTGCATCAACTTACTTGAGTCTCAAGAGTGAACTTGATAATTTAA
upper sequence: AT1G48650.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA05G34180.1 (Glycine max), 3'ss of exon 17
gtaagttataatcacatcctattttgtcaatttccttc--cttgttgttcttattttcacatctgatttacatcttgtcgtctc-----------------tgtgatcccc---atagGATGGTCATCTCAAAATGCTTGGAGGATATCTGGAGTTTTTCATGAAACCTACTTTAGCATATACATACCTTTCGTTAAAAAGAGAGCTCGACGAACTTA
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gtaagttcttaccatatttcctcttcacttttcccctggatctgttgatcttgactgtatgtactaggtgtttccttttggctacttattgtgctttggcatgtgattcttttgacagGATGGTCACCTGAAAATGTTGGGAGGGTATTTGGAGTTTTTCATGAAACCAGAATTAGCCAAGACTTACTTGAGCTTAAAGATGGGACTGGAAGAACTGA
upper sequence: AT1G48650.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA08G05480.1 (Glycine max), 3'ss of exon 17
gtaagttataatcacatcctattttgtcaatttccttc--cttgttgttcttattttcacat-ctga----------tttacatcttgtcgtctct------gtgatcccc---atagGATGGTCATCTCAAAATGCTTGGAGGATATCTGGAGTTTTTCATGAAACCTACTTTAGCATATACATACCTTTCGTTAAAAAGAGAGCTCGACGAACTTA
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gtaagttcttaccatatttcctcttcactttccccctggatctgttgttcttgattgcacgtactaagtgtttccttttgactacttattgtgctttggcttgtgattcttttgacagGATGGTCACCTGAAAATGTTGGGAGGGTATTTGGAGTTTTTCATGAAACCAGAATTAGCCAAGACTTACTTGAGCTTAAAGATGGAACTGGAAGAACTGA
upper sequence: AT1G48650.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv17s0000g03030.t01 (Vitis vinifera), 3'ss of exon 16
---------------------------gtaagt-tataatcacatcctattttgtcaatttccttcct-----tgttgttcttattt-tcacatctgatttacatcttgtcgtctctgtgatccccatagGATGGTCATCTCAAAATGCTTGGAGGATATCTGGAGTTTTTCATGAAACCTACTTTAGCATATACATACCTTTCGTTAAAAAGAGAGCTCGACGAACTTA
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gtaagtttcttatcccacttatttgcagtattcctaggatgatacctcctttcaagaagatgattcctaaaaatatatttcaaattagttatatgccacattcgctagaatgatttcttgctttg-gtagGATGGACACCTGAAAATGTTGGGAGGATATTTGGAGTTCTTCATGAAACCTGACTTAGCAGATACATATCTGAGCCTCAAGAAAGAGCTTGAAGAACTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgttcttattttcacatctgatttacatcttgtcgtctctgtgatccccatagGATGGTCATCTCAAAATGCTTGGAGGATATCTGGAGTTTTTCATGAAACCTACTTTAGCATATACATACCTTTCGTTAAAAAGAGAGCTCGACGAACTTA
atctgat putative branch site (score: 4)
tccccat putative PPT
tcttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttataatcacatcctattttgtcaatttccttccttgttgttcttattttcacatctgatttacatcttgtcgtctctgtgatccccatagGATGGTCATCTCAAAATGCTTGGAGGATATCTGGAGTTTTTCATGAAACCTACTTTAGCATATACATACCTTTCGTTAAAAAGAGAGCTCGACGAACTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT