Sequence
atgc intronic sequence ATGC exonic sequencegtgaatttcatcacattctatgcttactttatatattctcagtatgtcatttggggctgcatttttattggtttagaacagctagataataaacttgataaattttatcttatacatattgtgagcattttgtttgattgattttgttgttggaaccgtcttgggcttgcagAGATATTTGAATTTGATGCAATGGATGAGCCTCCATCTATGCTGGATGTGGAAGTTTTGGATTTTGATGGACCTTTTGATGAAGCTACATCACTGGGCCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os06g40570.1 (Oryza sativa), 3'ss of exon 3
gtgaatttcatcacattctatgcttactttatatattctcagtatgtcatttggggctgcatttttattggtttagaacagctagataataa--acttgataaattttatcttatacatattgtgagcattttgtttgattgattttgttgttggaaccgtcttgggcttgcagAGATATTTGAATTTGATGCAATGGATGAGCCTCCATCTATGCTGGATGTGGAAGTTTTGGATTTTGATGGACCTTTTGATGAAGCTACATCACTGGGCCA--
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--------------------------gttagcttctttccctgctgtcat-----gtttctttttcctcatctgtgaagagctagagattcactatcccagtagtacagtcctaaatggactg---gcccctgactcatttgatgtc----------------tgaatttctagAGATATATGAATTTGATGCAATGGATGATCCTCCATCAAGAATGGATGTGGCTATTCATGACGCTAATGGGCCATTTGATCAATCCCC--CATTGGTCACGC
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g10630.1 (Oryza sativa), 3'ss of exon 3
gtgaatttcatcacattctatgcttactttatatattctcagtatgtcatttggggctgcatttttattggtttagaacagctagataataaacttgataaattttatcttatacatattgtgagcattttgtttgattgattttgttgttggaaccgtcttgggcttgcagAGATATTTGAATTTGATGCAATGGATGAGCCTCCATCTATGCTGGATGTGGAAGTTTTGGATTTTGATGGACCTTTTGATGAAGCTACATCACTGGGCCA--
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------------------------------------------------------------------gtcagttctgccc--ccacattattcatgttggaaagttacttatccttatgatctttgcagatcattttcctggttatcttaccttcttttttctg---ttctagAGATATTTGAATTCAATGCAATGGATGATCCTCCATCAAGGTTGGAAGTAGTTGTGCATGATTCAGAGGGACCACATAATAAAATTCC--TATTGGTCAAAC
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA15G12790.1 (Glycine max), 3'ss of exon 7
gtgaatttcatcacattctatgcttactttatatattctcagtatgtcatttggggctgcatttttattggtttagaacagctagataataaacttgataaattttatcttatacatattgtgagcattttgtttgattgattttgttgttggaaccgt-cttgggcttgcagAGATATTTGAATTTGATGCAATGGATGAGCCTCCATCTATGCTGGATGTGGAAGTTTTGGATTTTGATGGACCTTTTGATGAAGCTACATCACTGGGCCA
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gtgagtgtcatgtcatcattta-ttattttctgt-tttacaacttg--gatcaaacctctgaaaccggtgatctaatcaacacatgatctgtattttatatatatatatatatatatat-atatatatatttttttttt--ttttgtt-taagaacaatatctatctttgcagAAATATTTGAGTTTGATGCAATGGATGATCCTCCTTCTGTGCTGGATGTGGTAGTTTATGATTTTGATGGACCTTTTGATGAAGCTGCATCTCTAGGACA
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 3
gtgaatttcatcacattctatgcttactttatatattctcagtatgtcatttggggctgcatttttattggtttagaacagctagataataaacttgataaattttatcttatacatattgtgagcattttgtttgattgattttgttgttggaaccgtcttgggctt-gcagAGATATTTGAATTTGATGCAATGGATGAGCCTCCATCTATGCTGGATGTGGAAGTTTTGGATTTTGATGGACCTTTTGATGAAGCTACATCACTGGGCCA
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-----------------------gtgagtatcatgtcatcatt-tattattttttgttttacaact--tggatcaaacctctgaattcggtgatctaatgtagttttcccaacacactatgt----attttatattattgttttttggttaagaacaatgtctatctttgcagAAATATTTGAGTTTGATGCAATGGATGATCCTCCTTCTGTGCTGGATGTGGTAGTTTATGATTTTGACGGACCTTTTGATGAAGCTGCATCTCTAGGACA
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G39920.1 (Glycine max), 3'ss of exon 4
gtgaatttcatcacattctatgcttactttatatattctcagtatgtcatttggggctgcatttttattggtttagaacagctagataataaacttgataaattttatcttatacatattgtgagcattttgtttgattgattttgttgttggaaccgtcttgggcttgcagAGATATTTGAATTTGATGCAATGGATGAGCCTCCATCTATGCTGGATGTGGAAGTTTTGGATTTTGATGGACCTTTTGATGAAGCTACATCACTGGGCCA
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------------------------------------------------------------------attttattaaaaaaggtgttttttttatataaaaaaatg-agcttaaacaaatgg-gccaactatgataaagta---ttcttgagaaaattgtctctc-tttgcagAAATTTTTGAATTTGATGCAATGGATGACCCTCCTTCTGTGCTGGATGTGGAAGTTTATGATTTTGATGGACCCTGTGATAAAGCTGCATCTCTGGGACG
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G00850.1 (Glycine max), 3'ss of exon 5
gtgaatttcatcacattctatgcttactttatatattctcagtatgtcatttggggctgcatttttattggtttagaacagctagataataaacttgataaattttatcttatacatattgtgagcattttgtttgattgattt-tgttgttggaaccgtcttgggcttgcagAGATATTTGAATTTGATGCAATGGATGAGCCTCCATCTATGCTGGATGTGGAAGTTTTGGATTTTGATGGACCTTTTGATGAAGCTACATCACTGGGCCA
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-------------------------------------------------------------tttttatta----aaaaaagttgctttgt----ttaaaaaatg--agcttaaacaaacag-gccaactatgataaagtattttctgttgagaaaattgtctctc-tttacagAAATATTTGAATTTGATGCGATGGATGACCCTCCTTCTGTGCTGGATGTGGAAGTTTATGATTTTGATGGACCCTGTGATGGAGCTGCATCTCTCGGACA
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgaatttcatcacattctatgcttactttatatattctcagtat-gtcattt--ggggctgcatttttattggtttagaacagctagataataaacttgataaattttatcttatacatattgtgagcattttgtttgattgattttgttgttggaaccgtcttgggcttgcagAGATATTTGAATTTGATGCAATGGATGAGCCTCCATCTATGCTGGATGTGGAAGTTTTGGATTTTGATGGACCTTTTGATGAAGCTACATCACTGGGCCA
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---------------gtaaatggttactctatggtttttatgtctagttatcttagtggtagcatggtc-ttatcctcaagctgacttttcatccacttgttttcgtcaattct-tgaatgtt-tcaactctttgttt------ttttgagggtggaattttgtttg---tgcagAAATATTTGAATTCGATGCAATGGCTGATCCTCCTTCTGTACTGAATGTTGAAGTTTTTGATTTCGATGGACCTTTTGACGAGGCTGTTTCATTGGGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtgagcattttgtttgattgattttgttgttggaaccgtcttgggcttgcagAGATATTTGAATTTGATGCAATGGATGAGCCTCCATCTATGCTGGATGTGGAAGTTTTGGATTTTGATGGACCTTTTGATGAAGCTACATCACTGGGCCA
gattgat putative branch site (score: 4)
attttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatttcatcacattctatgcttactttatatattctcagtatgtcatttggggctgcatttttattggtttagaacagctagataataaacttgataaattttatcttatacatattgtgagcattttgtttgattgattttgttgttggaaccgtcttgggcttgcagAGATATTTGAATTTGATGCAATGGATGAGCCTCCATCTATGCTGGATGTGGAAGTTTTGGATTTTGATGGACCTTTTGATGAAGCTACATCACTGGGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC