Sequence
atgc intronic sequence ATGC exonic sequencegttgcattataaggtttcatcttatttatttatttaataataagtttctttttttttctttggggacagaggtcctctctgggatggttgagaggaagaagcgtatgacatgtccactgctttttatcctttttgtatacttatgttgaatgcagAGTTTTAGGTGGACTTCTTAGTGCATATGATCTTTCCGGTGACAAAGTCTTCCTTGAAAAGGCTCAAGATATTGCAGATAGATTGCTGCCTGCTTGGAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 5
gttgcattataaggtttcatcttatt----tatttatttaataataagtttctttttttttctttggggacagaggtcctctctgggatggttgagaggaagaagcgtatgacatgtccactgctttttatcctttttgtatacttatgttgaatgcagAGTTTTAGGTGGACTTCTTAGTGCATATGATCTTTCCGGTGACAAAGTCTTCCTTGAAAAGGCTCAAGATATTGCAGATAGATTGCTGCCTGCTTGGAAT
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gttgccttataaggtttactattgttgtagtattttttttcttaaaatatttgacttctttgatcgatgctatgtaggcagaccacattttttagaacataaaagtatat-------ctagttttttctaagtttctgttttatttttat---attcagAGTTGTTGGAGGCCTCCTCAGTGCATATGATCTATCTGGTGACAAAGTATTTCTTGAGAAGGCCAAAGATATTACTGACCGTCTACTACCTGCTTGGGAT
upper sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G128914_T02 (Zea mays), 3'ss of exon 5
gttgcattataaggtttcatcttat--------ttatttatttaataata--agtttctttttttttctttggggacagaggtcctctctgggatggttgagaggaagaagcgtatg---acatgtccactgctttttatcct--ttttgtatacttatgttgaatgcagAGTTTTAGGTGGACTTCTTAGTGCATATGATCTTTCCGGTGACAAAGTCTTCCTTGAAAAGGCTCAAGATATTGCAGATAGATTGCTGCCTGCTTGGAAT
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gttgcattataaggtttacctttattacagtatttgtttatcttctcatattagtttgttccttgcagatgtttggctgaaaaagccaatggatgcaccttcattatgatccctatagaaaaataactacagctaggttgtctaattttattttctttgtttgtattcagGGTTGTTGGAGGTTTGCTTAGTGCATATGATCTATCTGGTGATAAAGTATTTCTTGATAAGGCTAAAGATATTACAGATCGTCTATTACCTGCTTGGGAT
upper sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G06600.1 (Glycine max), 3'ss of exon 5
gttgcattataaggtttcatcttatttatttatttaataataagtttctttttttttctttggggacagaggtcctctctgggatggttgagaggaagaagcgtatgacatgtccactgctttttatcctttttgtatacttatgttgaatgcagAGTTTTAGGTGGACTTCTTAGTGCATATGATCTTTCCGGTGACAAAGTCTTCCTTGAAAAGGCTCAAGATATTGCAGATAGATTGCTGCCTGCTTGGAAT
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gttgaattagaaggttcaatcttagtt------ttgttgacataatttctccgccacctt-----aaagttgttgtaactttgctagttgcaacaaa------ttttgctt-tctagtccattttgtctcatttgtcta-ttattttggtt-tagAGTTCTAGGTGGCCTTCTCAGTGCTTATGATCTCTCTGGTGACAAAGTTTTCCTTGAGAAGGCTAAAGATCTTGCAGATAAGTTATTACCTGCTTGGAAT
upper sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 5
gttgcattataaggtttcatcttatttatttatttaataat--aagtttctttttttttctttggggacagaggtcctctctgggatggttgagaggaagaagcgtatgacatgtccactgctttttatcctttttgtatacttatgttgaatgcagAGTTTTAGGTGGACTTCTTAGTGCATATGATCTTTCCGGTGACAAAGTCTTCCTTGAAAAGGCTCAAGATATTGCAGATAGATTGCTGCCTGCTTGGAAT
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gtggctttaacaggtttactgtggttgttttctgtaattatcgtaggaagagtcagtttatttgcgattatcagtt--------ggtgacataagatggggaacggatattgcatctgct----tatattctttttctttatctgcctt-----cagAGTTGTAGGCGGACTTCTTAGTGCGTATGATCTTTCTGGGGACAAAATGTTCCTTGAAAAGGCTAAGGATATTGCAGACAGATTATTGCCTGCATGGAAT
upper sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 5
gttgcattataaggtttcatcttatttatttatttaat--aataagtttctttttttttctttgggga-cagaggtcctctctgggatggttgagaggaagaagcgtatgacatgtccactgctttttatcctttttgtatacttatgttgaatgcagAGTTTTAGGTGGACTTCTTAGTGCATATGATCTTTCCGGTGACAAAGTCTTCCTTGAAAAGGCTCAAGATATTGCAGATAGATTGCTGCCTGCTTGGAAT
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gttgcatttaacaggtttaccatgttttttttctacatgtactaagaagagtcatcttgtttaggttatctgttgtgtgtagttaacaaaatatgtggtatggaagtgtggcatctgtgcttatatattttctctttgttggcttt---------cagAGTGGTAGGAGGGCTTCTCAGTGCGTATGATCTTTCTGGGGATAAAATTTTCCTTGAAAAGGCTATGGATATTGCAGACAGATTATTGCCTGCATGGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgtatgacatgtccactgctttttatcctttttgtatacttatgttgaatgcagAGTTTTAGGTGGACTTCTTAGTGCATATGATCTTTCCGGTGACAAAGTCTTCCTTGAAAAGGCTCAAGATATTGCAGATAGATTGCTGCCTGCTTGGAAT
tttttgtatacttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgcattataaggtttcatcttatttatttatttaataataagtttctttttttttctttggggacagaggtcctctctgggatggttgagaggaagaagcgtatgacatgtccactgctttttatcctttttgtatacttatgttgaatgcagAGTTTTAGGTGGACTTCTTAGTGCATATGATCTTTCCGGTGACAAAGTCTTCCTTGAAAAGGCTCAAGATATTGCAGATAGATTGCTGCCTGCTTGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC