Sequence
atgc intronic sequence ATGC exonic sequencegtaaggcttcaaagtctttacctgccgacaaaacatcatttttatgtctctctcttacatatatatttggttttgttatgtttagATGCTAGAAGTTGTTAGACTGGAAGGTCATTCTCTTGCTCAAGAAGATGCATTTATGTCACGGGATGTCCATCTCCTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60690.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA12G08080.1 (Glycine max), 3'ss of exon 12
---------------------------------------------------------------------------------------------gtaaggcttcaaagtc-tttacctgccgacaaaacatcatttttatgtctctctcttacat-atatatttggttttgttat--gtttagATGCTAGAAGTTGTTAGACTGGAAGGTCATTCTCTTGCTCAAGAAGATGCATTTATGTCACGGGATGTCCATCTCCTTCAG
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gtaggtttgcattcccttaaaaattggatgaaggatgcatatttgctttgggccaagatttgtttgacatatgatatatttacatattattcagtagagtatgtcagcaatttatggtctgatctttttggacatttgtaattgtaagcaacattactgataaaattgtattttcactacagATGCTGGAAGTTATTAGGCTGGAAGGTCACTCTCTTGCTCAAGAAGATGCTTTTGTTTCTAGGGACATTCATCTCTTACAG
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA11G20520.1 (Glycine max), 3'ss of exon 12
-----------------------------------------------------------------------------------gtaaggcttcaaagtct-ttacctgccgacaaaacatcatttttatgtctctct-cttacat---atatatttggttttgttatgttt-------agATGCTAGAAGTTGTTAGACTGGAAGGTCATTCTCTTGCTCAAGAAGATGCATTTATGTCACGGGATGTCCATCTCCTTCAG
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gtaggtttgcattcccttaaaaattggatggaggatgcatatttggtttgggccaagatttttttgacatatgatatatttacatattattcagtagtctgtcagcaatttatggtctgatctttttggacatttgtacttgtaagcaacattactgaaaaagttgtgttttcactacagATGCTTGAAGTTATTAGGTTGGAAGGTCACTCTCTTGCTCAAGAAGACGCTTTTGTTTCTAGGGACATTCATCTCTTACAG
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 3'ss of exon 12
--------gtaaggcttcaaagtctttacctgccgacaaaacatcatttttatgtctctctcttacatatatatttggt----tttg--ttatgt-ttagATGCTAGAAGTTGTTAGACTGGAAGGTCATTCTCTTGCTCAAGAAGATGCATTTATGTCACGGGATGTCCATCTCCTTCAG
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atgtagatatctggggtgagaaatgccaacttttgtcattagatcacattcaaaataattcaatatggcgatcctttgtaacttttactttatgtgccagTTGCTTGAAGTAATTCGACTTGAAGGCCATTCTCTTGCTCATGAAGATGCTTTTATGTCGAGGGACATTCATCTCCTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacatcatttttatgtctctctcttacatatatatttggttttgttatgtttagATGCTAGAAGTTGTTAGACTGGAAGGTCATTCTCTTGCTCAAGAAGATGCATTTATGTCACGGGATGTCCATCTCCTTCAG
ctcttac putative branch site (score: 3)
ttttgtt putative PPT
atatatatttggtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggcttcaaagtctttacctgccgacaaaacatcatttttatgtctctctcttacatatatatttggttttgttatgtttagATGCTAGAAGTTGTTAGACTGGAAGGTCATTCTCTTGCTCAAGAAGATGCATTTATGTCACGGGATGTCCATCTCCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG