Sequence
atgc intronic sequence ATGC exonic sequencegtatttgtcatttacttgttatacaaattttgttcctatttctattagtgtttttcttttattttttggttttgtgatgaataattgctgaattgtcctcatgtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------------------------------------gtatttgtcatttacttgttatacaaattttgttcctatttctattagtgtttttcttttattttt--tggttttgtgatgaataattgc---tgaattgtcct-----catgtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
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gtacggacatttcgttttctcttaacacgctaaagctttaattttgctattctatatattaattagaagaacaattttgattcacactgga-atctactgagca-acagagttgctctgaatgaaacgaaatatatagcctcagttcatgacaattctaggagaaataccttcaccttatttgttttttgggcacatacagGTGAAACTTGGATCCCAGTACTATTTCTACATGGAGACACAAACGGCTTTAGCTTTCCCTGATGAAGATAACTGTATAACCGTCTACTGCTCAGCGCAAA
upper sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g18120.1 (Oryza sativa), 3'ss of exon 4
gtatttgtcatttacttgttatacaaattttgttcctatttctattagtgtttttcttttattttttggttttgtgatgaataattgctgaattgtcctcatgtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
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ggagtgaccaatt-tttctcaagctatcagtaaggctcatctaaggggcaacatagtataacattttc-tcatgtaataa-----tgcgtgatattgattat-tacagGTCAAACTTGCTTCTCAGTACTACTTCTACATGGAAACACAGACAGCACTAGCAATTCCAGATGAAGATAACACCATGACAGTATACAGTTCATCACAAT
upper sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g18154.2 (Oryza sativa), 3'ss of exon 5
gtatttgtcatttacttgttat-acaaattttgttcctatttctattagtgtttttct-------tttattttttggttttgtgatgaataattgctgaattgtcctcatgtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
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---------------ttggagtgaccaattttcctcaagctataagtaaggctcatctaaggcaacatagtataacatcttctcatgtaataatgcgtgatattgattat-tacagGTCAAACTTTCTTCTCAGTACTACTTCTACATGGAAACACAGACAGCACTAGCAATTCCAGATGAAGATAACACCATGACAGTATACAGTTCATCACAAT
upper sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G04950.1 (Glycine max), 3'ss of exon 4
-------------------------gtatttgtcatttacttgttatacaaattttg-ttcctatttcta---ttagtgtttttctt------ttattttttggtt--ttgtgatgaataattgctga--attgtcc-tcatgtcca------------gATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
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gtacattgtttactttgcttcccctcttcctctcattccatacctttgtgaaccttggtttctgatacaatgtttaagtttgctcctgaataattaatgtttaattggttatgctgaacaaatactcattgttatctatcatattcaatgttaaatgcagTTGAAACTTGGGTCTCAATACTATTTCTATATGGAGACACAAACTGCACTTGCTGTTCCAGATGAAGACAATTGCATTACAGTTTACTCCTCAAACCAAT
upper sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 4
------------------------------------------------------gtatttgtcattta-cttgttatacaaattttgttcctatttct-attagtgtttttctttta---ttttttggt--------tttgtgatgaataattgctgaatt-gtcctcatgtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
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gtacatgtaacatatccattgtttcctccttctactcctttcacatctttgtggccatctctactttagtttctgatgtgatgtttaagtttgtttctgaataatgaattttgatgagaatatattgatcaagcatattcattgtcatcatgtatcaaattcaatgtttaatgcagTTGACACTTGGGTCTCAATACTATTTCTACATGGAGACACAAGCTGCCCTTGCTGTACCCGACGAAGACAATTGCATTGTGGTTTACATTTCAAGTCAAA
upper sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatttgtcatttacttgttatacaaattttgttcctatttctattagtgtttttcttttattttttggttttgtgatgaataattgctgaattgtcctcatgtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
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gtattaaaattctctttctctctcttaatct-ttgatatattaaaaaaaaataaaaaaaaatacattc-ttacactatgtttg-ctgttgattt-tggttatg--cagTTGAGACTTGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCACTTGCCTTGCCAGATGAAGACAACTGTTTAGTGGTTTACAGTTCAACTCAAG
upper sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G20960.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatttgtcatttacttgttatacaaattttgttcctatttctattagtgtttttcttttattttttggttttgtgatgaataat-tgctgaattgtcctcat-gtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
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-----------------------------gtggttcttttccaagacatatacacctctaaagccgtgctcttttc-taaccatcatataaaatctttgtgattgtgtagATAAGTTTCGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCTCTTGCAGTGCCGGATGAAGACAACTGTATGGTGGTTTATAGCTCGACTCAAA
upper sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G43600.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatttgtcatttacttgttatacaaattttgttcctatttctattagtgtttttcttttattttttggt-tttgtgatgaataattgctgaattgtcctcatgtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
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-------------------------------gtatgtaata-tagtccttttttactgtaaaaattagatatatatgttcaaccgttg-taacttttgatgtgaaacagATAAGACTCGGATCGCAATACGTCTTCTACATGGAGACACAAACAGCTCTTGCAGTGGGAGATGAAGACAACTGCATTGTAGTCTATAGTTCAACACAGA
upper sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G27150.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatttgtcatttacttgttatacaaattttgttcctatttctattagtgtttttcttttattttttggttttgtgatgaataattgctgaattgtcctcatgtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
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------------------gtatctcaaaactgtttccagattt-tcaccgccaaagttgtgtagtgacatctcattttgtgtgtttga-aacttggttatttattcagTTGAGGCTAGGGTCACAGTACTTCTTCTATATGGAGCCACAAACAGCACTTGCCTTGCCAGACGAAGACAATTGTGTCAAGGTATTTAGTTCATCTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttttattttttggttttgtgatgaataattgctgaattgtcctcatgtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
ttgtcctc CT-rich tract
ttattttttggtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttgtcatttacttgttatacaaattttgttcctatttctattagtgtttttcttttattttttggttttgtgatgaataattgctgaattgtcctcatgtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA