Sequence
atgc intronic sequence ATGC exonic sequencegttgtattaattataatgagtggtgaattggttcttaatgttttcaaataaagttgcattaattatttgttattttcttctccattacagCAAGAAATCAAGCACACAATACAAAACAAGCTCCACCGAAATGCTGGCCCAGAAGATTTGGTTGCTACAGACGCAATGCTTGCAAGAATTACTAGGAACC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0062g00890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g20150.1 (Oryza sativa), 3'ss of exon 5
gttgtattaattataatgagtggtgaattggttcttaatgttttcaaataaagttgcattaatta-tttgttattttcttctccattacagCAAGAAATCAAGCACACAATACAAAACAAGCTCCACCGAAATGCTGGCCCAGAAGATTTGGTTGCTACAGACGCAATGCTTGCAAGAATTACTAGGAACC
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gtggtgatccctttctgcagttttgaac--------aatctcttca--ttggattactttacttagtttgatcttttcatgtcga---cagCAAGAAATCAAGCATACTATACAAAACAAACTTCATCGTAATGCTGGACCTGAGGATCTTATTGCTACAGAAGTCATGCTTGCTAGGATTACTAAGACCC
upper sequence: Vv05s0062g00890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G44540.1 (Glycine max), 3'ss of exon 4
gttgtattaattataatgagtggtgaattggttcttaatgttttcaaa---taaagttgcattaattatttgttattttcttctccattacagCAAGAAATCAAGCACACAATACAAAACAAGCTCCACCGAAATGCTGGCCCAGAAGATTTGGTTGCTACAGACGCAATGCTTGCAAGAATTACTAGGAACC------------
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gttgttcttttcaaagtacttgaactatgaaatctcattgtagttcaatgttaataataggtcaactgtattctgtattgcttattctc-cagtgacgaattaagCATACAATACAAAACAAGCTTCACCGAAATGCTGGACCTGAAGATTTGGTTGCTACAGAAGCTATGCTTGCTAGAATCACTAGAAACCCTGCAGAATATA
upper sequence: Vv05s0062g00890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G26570.1 (Arabidopsis thaliana), 3'ss of exon 5
gttgtattaattataatgagtggtgaattggttcttaatgttttcaaataaagttgcattaat--tatttgttattttcttctccattacagCAAGAAATCAAGCACACAATACAAAACAAGCTCCACCGAAATGCTGGCCCAGAAGATTTGGTTGCTACAGACGCAATGCTTGCAAGAATTACTAGGAACC
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------------gtaataactctt---ttctcctgttttgtcattagatca-gtttttttaatggtatccatataacatatctatgttccagCAAGAAATCAAGCATACGATACAAAATAAGCTTCACCGGAATGCTGGTCCAGAAGATCTAATTGCAACAGAAGCAATGCTTCAACGAATTACCGAGACCC
upper sequence: Vv05s0062g00890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ25586 (Selaginella moellendorffii), 3'ss of exon 4
gttgtattaattataatgagtggtgaattggttcttaatgttttcaaataaagttgcattaattatttgttattttcttctccattacagCAAGAAATCAAGCACACAATACAAAACAAGCTCCACCGAAATGCTGGCCCAGAAGATTTGGTTGCTACAGACGCAATGCTTGCAAGAATTACTAGGAACC
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---------------------------gtatttgtgaacatt--cgacttcgttttggctaatgacgtggtgtatttgta---aaagtagCAAGAGATAAAGCATACAATCCAGAACAAACTGCACAGAAATGCTGGTCCAGAAGATTTGGTTGCGACAGAAGCATTATTAGCTCGTGTGACCAAAACAC
upper sequence: Vv05s0062g00890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ22307 (Selaginella moellendorffii), 3'ss of exon 4
gttgtattaattataatgagtggtgaattggttcttaatgttttcaaataaagttgcattaattatttgttattttcttctccattacagCAAGAAATCAAGCACACAATACAAAACAAGCTCCACCGAAATGCTGGCCCAGAAGATTTGGTTGCTACAGACGCAATGCTTGCAAGAATTACTAGGAACC
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---------------------------gtatttgtgaacatt--caacttcgttttgactaatgacgtggtgtatttgta---aaagtagCAAGAGATAAAGCATACAATCCAGAACAAACTGCACAGAAATGCTGGTCCGGAAGATTTGGTTGCGACAGAAGCATTATTAGCTCGTGTGACCAAGACAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatgttttcaaataaagttgcattaattatttgttattttcttctccattacagCAAGAAATCAAGCACACAATACAAAACAAGCTCCACCGAAATGCTGGCCCAGAAGATTTGGTTGCTACAGACGCAATGCTTGCAAGAATTACTAGGAACC
cattaat putative branch site (score: 3)
ttatttgttattttct CT-rich tract
ttttcaaataaagttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtattaattataatgagtggtgaattggttcttaatgttttcaaataaagttgcattaattatttgttattttcttctccattacagCAAGAAATCAAGCACACAATACAAAACAAGCTCCACCGAAATGCTGGCCCAGAAGATTTGGTTGCTACAGACGCAATGCTTGCAAGAATTACTAGGAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA