Sequence
atgc intronic sequence ATGC exonic sequencegtgagcaatcaatcatctccaagctggactcatttattttcatggctaatatgatatccatccatgaaggaacttgtataactcttgacccttttcctatgtgtggtcatgaaaatctagTTTCTATCCCGACCCACAAAAGATGGGTCATACTTCAAGAATCTGCCCAAGTCAAGTGCCATCAAGCTCATTGATTTCGGAAGTACAACATTTGAACATC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53570.4 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53570.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 9
--------------------------gtgagcaatcaatcatctccaagctggactcatttattttcatggctaatatgatatc-catccatgaaggaacttgtataactcttgacccttttcctatgtgtggtcatgaaaatctagTTTCTATCCCGACCCACAAAAGATGGGTCATACTTCAAGAATCTGCCCAAGTCAAGTGCCATCAAGCTCATTGATTTCGGAAGTACAACATTTGAACATC
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gtggcttcaatactaaattttgtcattcgaactat-aatcttttgcaatttt-atccgttaacacttgtggttgccattacattatgtcaattagtacgagcatacatttattttttactgatttttatattgttttccataa--agGTTACAATACGGCCCCCAAAGGATGGTTCCTTTTTTAAGAATCTTCCAAAATCTAGTGCTATCAAGCTGATTGATTTTGGAAGTACAACATTCGAACACC
upper sequence: AT3G53570.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G33100.1 (Glycine max), 3'ss of exon 7
gtgagcaatcaatcatctccaagct--ggactcatttattttcatggctaatatgatatccatccatgaaggaacttgtataactcttgacccttttcctatgtgtggtc-atgaaaatctagTTTCTATCCCGACCCACAAAAGATGGGTCATACTTCAAGAATCTGCCCAAGTCAAGTGCCATCAAGCTCATTGATTTCGGAAGTACAACATTTGAACATC
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---------------cctgcaaccataggaagcacttatc------gct--tgtaattttcaatgatcaaaattttacatttgttcttttttgttggcttattcttcatctgtggcaattaagTTTCTATCACGGAATACAAAAGATGGCTCCTATTTCAAGAATCTACCCAAGTCAAGTGCCATTAAGCTCATTGATTTCGGGAGTACATCATTTGAACATC
upper sequence: AT3G53570.4 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 7
--gtgagcaatcaatcatctccaagctggactcatttattttcatggctaatatgatatccatccatgaaggaacttgtataactcttgacccttttcctatgtgtggtcatgaaaatctagTTTCTATCCCGACCCACAAAAGATGGGTCATACTTCAAGAATCTGCCCAAGTCAAGTGCCATCAAGCTCATTGATTTCGGAAGTACAACATTTGAACATC
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caataaccagtaaatt-tctcaaggttctgatt-tttattactatttttaattttat-tttatttacca-----tttattta---tttgaactctttcctctgc-----------aatttagTTTCTATCACGGACTATTAAAGATGGTTCCTATTTCAAGAATCTGCCTAAGTCAAGCGCCATTAAGCTCATTGATTTTGGGAGTACAACATTTGAACACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaggaacttgtataactcttgacccttttcctatgtgtggtcatgaaaatctagTTTCTATCCCGACCCACAAAAGATGGGTCATACTTCAAGAATCTGCCCAAGTCAAGTGCCATCAAGCTCATTGATTTCGGAAGTACAACATTTGAACATC
tcttgac putative branch site (score: 3)
ttgtataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcaatcaatcatctccaagctggactcatttattttcatggctaatatgatatccatccatgaaggaacttgtataactcttgacccttttcctatgtgtggtcatgaaaatctagTTTCTATCCCGACCCACAAAAGATGGGTCATACTTCAAGAATCTGCCCAAGTCAAGTGCCATCAAGCTCATTGATTTCGGAAGTACAACATTTGAACATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA