Sequence
atgc intronic sequence ATGC exonic sequencegtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatttatttatttatttgttaatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
---------------------------------gtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttat-ttatttatttatttat-ttatttgt-taatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT
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gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttc--tcgtctgaatagc-gaggcgcatgcc-tgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
----------gtactatacatatatctcattcaa-ccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatt--tatttatttatttgttaatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT--
||| | | || || || | | | | || | | | || || | | | | | | | || ||||| |||| | || || ||||| ||||| || || ||||| ||||||| |||||||| ||||| ||||||||||||||||| ||||| || || ||||| || ||
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgtt-----gcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
----------gtactatacatatatctcattcaa-ccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttattt--atttatttatttgttaatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT
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gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgtt-----gcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 4
------------------------------------gtactatacatat-atctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatttatttatttatttgttaatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT
|| ||| ||| || |||| || || ||| || |||||| | | |||| || | | || | | | ||| | | || || | ||| ||||||||||||| || || || ||||| |||| |||| ||||| || || ||||| ||||||||||||||||||||||||||||||||||| |||||
gtgacaacaatattcataaattaagttacaaataatttattattattattatttcatacattaaattatt--aatgatatgaaactgtcattaata--tagtagtaatgctatgtttttccaattgttatt--atgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 4
-----------------------------gtacta-tacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatt-tatttatttatttatttatttgtta--atgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT
|||||| ||||| | | ||| | |||| ||| || ||| | | |||| | |||| | || | | | || | |||||| ||| ||||||||||||| || || || ||||| |||| |||| ||||| || || ||||| ||||||||||||||||||||||||||||||||||| |||||
gtaacaataataaatttacaaacagatacgtactactacattattattattattactgatattcaat-tattaattatatgcaattgtaattaatttagtagtaatgctatgcttttccgattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 4
------------------------gtactatacatatatctcattcaaccaaatatccaaa-acatatga--tattaaaattagtaaatg--attttatttatttatt-tatttatttatttgttaatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT
| || | |||| | || || | |||| | | | |||||| ||||| | ||| || | | | || | || | | || || | | | | || | || |||| || || || || || ||||| |||| |||| ||||| || || ||||| |||||||||||||||||||| ||||||||||| || |||||
gtaataacaatttagatttgcaaataaataaatgcatatat-atacatatatatatatatatatatatgaattattatatttattagtggctactataataatatgcgatcttgatgttactatgattgtgtagGTGGAGGGGGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTTGGGGGACATGCCGTTACTGT
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 4
------------------------gtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaa-attagtaa--atgattttatttatttatttatttatttatttgttaatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT
| || ||||||| | |||| | ||| | | || || || | | | | || || ||| | || || | ||| | | | || | || |||||||||| || || || || || |||| |||| ||||| || || ||||| |||||||||||||||||||| ||||||||||| || |||||
gtaataataatttagatttgcaaataaataatcatatatattattcctactgtgatctatgaatcattatgtttcttagtggctactataataatatgcgatc-ttgatgttactatatatgattgtgtagGTGGAAGGAGTTAAGCATTCGGGCCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTTGGGGGACATGCCGTTACTGT
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
gtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatttatttatttatttgttaatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT
|| | | | || | || | | | | | | || || || || | || | | || || || || | ||| || | ||||||||||| || ||||| ||| ||||||||| |||||||||||||||| ||||||||||| ||||||||||| ||||||||||| |||||
ttaatgcataaatgttatatacttgtagagttgtagataattgaattttcttatagaaggagaataatgta-atgtaccaat--gttggaataataa-aaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S279_43V6.2 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------gtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatt-tatttatttattt--atttatttgttaatggg---cagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT
|| | | | |||| || | | | | | | || | || ||| | || | | | | | | | | || | | | || | |||| | ||| || || | | |||||||| ||||||||||| |||||||| || |||||||| | |||||||| || ||
gtacccatcaattcttccttcatgccgtctctatgtaatgattccctgatcctccatgccaggctgcgtggtcttttggaataactagcgtctctctctctctctctcagcttttattctcgcttaggcgaggttgcgatgtgcatttgtagtactcactcagtgcaactgaaatggtgtttgagtttagGCGCCGGGAGCAACTCACGATGGGCCCAATTCATTACTCCTATACTTTACAGGGGCTACCAACATTCTGTATACATTCGGAAGTCATGCTGTCACAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaattagtaaatgattttatttatttatttatttatttatttgttaatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT
tgttaat putative branch site (score: 3)
taaatgattttattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatttatttatttatttgttaatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG