Sequence
atgc intronic sequence ATGC exonic sequence...ttcattataatgtgaatagaatttctctgttgtcaagagtaatttctcgaatttattttttctaaatcttatataatgtgttctcactattctcctgcagAATGTTCACCATGCAGGACAGCCAATGCCAGGTGATGAGCAGGAGGACATTGTAATGACCAGTACACAATGCAACCTCTTGAATATTACTTGCCCATTAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0014g02100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g48880.1 (Oryza sativa), 3'ss of exon 4
ttcattataatgt---gaatagaatttctctgttgtcaagagtaatttctcgaatttattttttctaaatcttatataatgtgttctcactattctcctgcagAATGTTCACCATGCAGGACAGCCAATGCCAGGTGATGAGCAGGAGGACATTGTAATGACCAGTACACAATGCAACCTCTTGAATATTACTTGCCCATTAA
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-ttagtatggtatctccaataggtcatgtttggagaaagtaaaaggtttgtgcattacttctaattattttctctctc-tgtaattgtgttgt-cttctacagAATGTTCACCATGCTGGCCAACCAATGCCTGGTGATGAACAGGAGGATGTTCTTATGACCAGTACCCAAACTAGCATCTTAAATGTCACGTGCCCATTAA
upper sequence: Vv19s0014g02100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G022065_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------------------------------------------------ttcattataatgtgaatagaatttctctgttgtcaagagtaatttctcgaatttattttttctaaa--tcttatataatg-tgttctcactattctcctgcagAATGTTCACCATGCAGGACAGCCAATGCCAGGTGATGAGCAGGAGGACATTGTAATGACCAGTACACAATGCAACCTCTTGAATATTACTTGCCCATTAA
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gtatgtgtttacagagtagcatgctcatggtcatgtgatgaccattgaggattatgcattgtacctgtgctccgggcattacctagttactcacatacgattacaatagctagattatgaatttggaaacataaatgatttgttttgtgtaatttcgcaaaaggtcttatgttttggtgtcttatttttttttctgcagAATGTTCACCATGCTGGTCAGCCTATGCCTGGTGAGGAACAGGAGGACATTGTCATGACTAGCACTCAGATGAGCATCTTAAATGTCACATGCCCATTAA
upper sequence: Vv19s0014g02100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G34860.1 (Glycine max), 3'ss of exon 4
--ttcatt-ataatgtgaatagaatttctctgttgtcaagagtaatttctcgaatttattttttctaaatcttatataatgtgttctcactattctcctgcagAATGTTCACCATGCAGGACAGCCAATGCCAGGTGATGAGCAGGAGGACATTGTAATGACCAGTACACAATGCAACCTCTTGAATATTACTTGCCCATTAA
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tgtgtactgatattatttttataagttccttctgcaagagtgttgttaactggattcctgtaacc--aatctaatgtgtt-tgctgtttatctgggaccttagAATGTTCATCATGCGGGGCAGCCAATGCCAGGCGAAGAGCAGGAGGATATTGTAATGACCAGTATCCAGTCCAACATTTTGAATATTACCTGTCCATTGA
upper sequence: Vv19s0014g02100.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G15150.1 (Arabidopsis thaliana), 3'ss of exon 4
ttcattataatgtgaatagaatttctctgttgtcaagagtaatttctcgaatttattttttctaaatcttatataatgtgttctcactattctcctgcagAATGTTCACCATGCAGGACAGCCAATGCCAGGTGATGAGCAGGAGGACATTGTAATGACCAGTACACAATGCAACCTCTTGAATATTACTTGCCCATTAA
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---------gtatgtttttaacttaaa-gttcttggcttgtatctaataggtctatagtc-cgatttcctttttaagttattgtcaatgttttgctgcagAATGTTCATCATGCAGGTGAACCAATGCCTGGTGACGATGATGAGGACATTGTTATGACCAGTACTCAGTGCCCTCTTCTAAACATGACATGTCCCTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcgaatttattttttctaaatcttatataatgtgttctcactattctcctgcagAATGTTCACCATGCAGGACAGCCAATGCCAGGTGATGAGCAGGAGGACATTGTAATGACCAGTACACAATGCAACCTCTTGAATATTACTTGCCCATTAA
ttctcac putative branch site (score: 2)
ttctcactattctcct CT-rich tract
atttattttttctaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcattataatgtgaatagaatttctctgttgtcaagagtaatttctcgaatttattttttctaaatcttatataatgtgttctcactattctcctgcagAATGTTCACCATGCAGGACAGCCAATGCCAGGTGATGAGCAGGAGGACATTGTAATGACCAGTACACAATGCAACCTCTTGAATATTACTTGCCCATTAA
- - - - - - - aatagaa
- - - - - - - - - - - - - -tgttgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcacta