Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttaagcacagcatacatattgacaaacacatacacatagaggcaatcataaatcggggtgtttgtgtgtgttttcctgcaatccaatcagaatgtgctgatcatttgaacttttcatggtaacatcagGCACTCCCACTTGTGAGCACTTTCTGGGGAATAGTTCTGTTTGGAGAATACCGAAAATCGTCAAGAAGAACATATATATTGCTTGGGAGCATGCTGTTCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0011g00530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os12g31850.3 (Oryza sativa), 3'ss of exon 7
gtgagtttaagcacagcatacatattgacaaacacatacacatagaggcaatcataa-atcggggtgtttgtgtgtgttttcctgcaatccaatcagaatgtgctgatcatttgaacttttcatggtaacatcagGCACTCCCACTTGTGAGCACTTTCTGGGGAATAGTTCTGTTTGGAGAATACCGAAAATCGTCAAGAAGAACATATATATTGCTTGGGAGCATGCTGTTCA
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-----------------------ccaggcaaattctt-caggtttagcagttcacactatcttcagagaagtaca-acttttctggactatgatt--------ctaactgcttcagcattgct--gtttcatcagGCATTGCCACTTGTGAGCACATTCTGGGGAATACTCCTGTTTGGGGAGTACCGGAAATCGTCGCGAAAGACGTATATCCTGCTCGGGTTCATGCTGTTCA
upper sequence: Vv01s0011g00530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G12980.1 (Glycine max), 3'ss of exon 6
gtgagtttaagcacagcatacatattgacaaacacatacacatagaggcaatcataa-atcggggtgtttgtgtgtgttttcctgcaatccaatcagaatgtgctgatcatttgaacttttcatggtaacatcagGCACTCCCACTTGTGAGCACTTTCTGGGGAATAGTTCTGTTTGGAGAATACCGAAAATCGTCAAGAAGAACATATATATTGCTTGGGAGCATGCTGTTCA
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-----------------------------------gcttaccgaaaaacactcattttaacatttgacttgtgattgttcctcaaactaccaatttcaatttcatggtaacagaagatgtgttttgtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTACCGCAAATCATCAAGAAGAACATATGTGCTACTTGGGAGCATGTTGCTTA
upper sequence: Vv01s0011g00530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G03590.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagtttaagcacagcatacatattgacaaacacatacacatagaggcaatcataaatcggggtgtttgtgtgtgttttcctgcaatccaatcagaatgtgctgatcatt-tgaacttttcatggtaacatcagGCACTCCCACTTGTGAGCACTTTCTGGGGAATAGTTCTGTTTGGAGAATACCGAAAATCGTCAAGAAGAACATATATATTGCTTGGGAGCATGCTGTTCA
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-----------------------------------------gtttagacaat----aaacaaatcctctgt-tccatgatttaagagtgaaat----atgttttacttattatgatttgaatatgtt----tcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATATAGAAGATCATCAAGAAAAACATATACACTTCTCATCAGTATGCTTCTTA
upper sequence: Vv01s0011g00530.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G03530.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgagtttaagcacagcatacatattgacaaacacatacacatagaggcaatcataaatcggggtgtttgt--gtgtgttttcctgcaatccaatcagaatgtgctgatcatttgaacttttcatggtaacatcagGCACTCCCACTTGTGAGCACTTTCTGGGGAATAGTTCTGTTTGGAGAATACCGAAAATCGTCAAGAAGAACATATATATTGCTTGGGAGCATGCTGTTCA
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-------------------------------------------------gttcatatattcacatttctttcaaaatattttggcaaaattcaagaatcaatctttatggttttgagtattttgtg-tcttat-agGCTCTTCCACTTGTGAGTACATTTTGGGGAGTGGTTTTGTTTGGAGAATACAGAAGATCGTCACGGAAAACTTATCTACTTCTCTTCTGTATGTTGTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctgcaatccaatcagaatgtgctgatcatttgaacttttcatggtaacatcagGCACTCCCACTTGTGAGCACTTTCTGGGGAATAGTTCTGTTTGGAGAATACCGAAAATCGTCAAGAAGAACATATATATTGCTTGGGAGCATGCTGTTCA
tggtaac putative branch site (score: 2)
atcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttaagcacagcatacatattgacaaacacatacacatagaggcaatcataaatcggggtgtttgtgtgtgttttcctgcaatccaatcagaatgtgctgatcatttgaacttttcatggtaacatcagGCACTCCCACTTGTGAGCACTTTCTGGGGAATAGTTCTGTTTGGAGAATACCGAAAATCGTCAAGAAGAACATATATATTGCTTGGGAGCATGCTGTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT