Sequence
atgc intronic sequence ATGC exonic sequence...atttgtcctgtatgtggtggttcattatatgtctttgtactagattgtatttattctgttgcctgaaattgatacctcactctgccaaattttctggcagGTATTCACAGCAGAATATTCCCTAATATGCAAAATTTCTGAGTACAAAAAACCATATATAAGCCTCATGGATGGCATTACAATGGGTTTTGGAATTGGAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g04290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g39344.2 (Oryza sativa), 3'ss of exon 3
atttgtcctgtatgtggtggttcattatatgtctttgtactagattgtatttattctgttgcctgaaattgatacctc----actctgccaaattttctggcagGTATTCACAGCAGAATATTCCCTAATATGCAAAATTTCTGAGTACAAAAAACCATATATAAGCCTCATGGATGGCATTACAATGGGTTTTGGAATTGGAC
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---ttctctctgctgcatgggaaaatggatgtagttgatatgtcctctgtccaaaatgtt-cttaaaatttacatcactgaaaaggtactttatttgttttcagGTCTTCACAGCAGAGTACTCTTTGATTTGTAAGATTCATGAGTATACAAAACCTTATATATGCCTGATGGATGGTGTGACAATGGGATTTGGAATTGGAT
upper sequence: Vv11s0016g04290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G04460.1 (Glycine max), 3'ss of exon 3
atttgtcctgtatgtggtggttcattatatgtctttgtactagattgtatt-tattctgttgcctgaaattgatacctcac-tctgccaaattttctggc--agGTATTCACAGCAGAATATTCCCTAATATGCAAAATTTCTGAGTACAAAAAACCATATATAAGCCTCATGGATGGCATTACAATGGGTTTTGGAATTGGAC
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----atgctgtcagcaattatgcattttgctgcatcttgcatttttgcatgacctgttaatgtactacataaaaattacgtacttgttatatttcatgttttagGTCTTCACTGCTGAGTATTCTTTGATATGCAAAATTTCTGATTACAAGAAGCCATATATAAGCTTCATGGATGGAATAACTATGGGTTTTGGAATTGGTT
upper sequence: Vv11s0016g04290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G35260.1 (Glycine max), 3'ss of exon 3
atttgtcctgtatgtg-gtggttcattatatgtctttgtactagattgtat-ttattctgttgcctgaaattgatac-ctcactctgccaaattttctggcagGTATTCACAGCAGAATATTCCCTAATATGCAAAATTTCTGAGTACAAAAAACCATATATAAGCCTCATGGATGGCATTACAATGGGTTTTGGAATTGGAC
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atgccatcagcaattatgcattttgctgcatcttgtatttttgcattatctgttaatgtactacataaaaatgatgtacttgttatgttgcatatttt---agGTCTTCACTGCTGAGTATTCTTTGATATGCAAAATTTCTGATTACAAGAAGCCATACATAAGCTTCATGGATGGAATAACTATGGGTTTTGGAATTGGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtatttattctgttgcctgaaattgatacctcactctgccaaattttctggcagGTATTCACAGCAGAATATTCCCTAATATGCAAAATTTCTGAGTACAAAAAACCATATATAAGCCTCATGGATGGCATTACAATGGGTTTTGGAATTGGAC
acctcac putative branch site (score: 3)
ttttct putative PPT
aaattgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgtcctgtatgtggtggttcattatatgtctttgtactagattgtatttattctgttgcctgaaattgatacctcactctgccaaattttctggcagGTATTCACAGCAGAATATTCCCTAATATGCAAAATTTCTGAGTACAAAAAACCATATATAAGCCTCATGGATGGCATTACAATGGGTTTTGGAATTGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - -tcctgta
- - - - - - -gtggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcctga