Sequence
atgc intronic sequence ATGC exonic sequencegtaataattactgtcattaaaataacctaacatgatcaaactggtcttagccaaagttttaagttaaaaccattttaagttttgataatgtgggcttgtctctgtacagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv03s0088g00230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g11540.1 (Oryza sativa), 3'ss of exon 9
gtaataa-ttactgtcattaaaataacctaacatgatc----aaactggtcttagccaaagttttaagttaaaaccattttaagttttgataatgtgggcttgtctctgtacagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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gtaaaatcttggaatctttgaaagaaaatggaattgttcttgatgtttagtttattagcactttctagttgtgattgtcctaaatttacttgttatg---------ttttgcagCCTGTGTTCTTCAGTCTGAATGCCTATATTAGCCTTATCAAGCCTGACCAAACCATGTGGTACCGAGCTTGCAAGACCTGCAACAAGAAGGTGACTGAGG
upper sequence: Vv03s0088g00230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G08660.2 (Glycine max), 3'ss of exon 9
------------------------------gtaataattactgtcattaaa----ataacctaacatgatca--aactggtcttagccaaagttttaa----gttaaaaccattttaagttttgataatgtgggcttgt----ctctgtacagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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gtatttggttgcaaattttcctgaatgttgggcattgctaatacgattccatctgcttgtttgatataaacattcattggaactcttagaaatttcaatggattttcattagtttctagtttaacttgtagtctcttatgttgctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
upper sequence: Vv03s0088g00230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G00370.2 (Glycine max), 3'ss of exon 9
----------------------------------------------------gtaataattactgtcattaaaata-acctaacatgatcaaactggtcttagccaaagttttaagttaaaaccattttaagttttgat--aatgtgggcttgt-----ctctgtacagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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gtatttggttattaattttcctgaatgttggacattgctaatacagttccatgtggttgtt--tgatataaacattcattagacatgtt---attggaactcctgcaaattttaatggattttcatccgagtttctagtctaacttgtctcttctgttgctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
upper sequence: Vv03s0088g00230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G61000.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaataattactgtcattaaaataacctaacatgatcaaactggtcttagccaaagttttaagttaaaaccattttaagttttgataatgtgggcttgtctctgtacagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
||| ||| |||| ||| |||| | ||| | || | |||| | || ||| | || ||| | | || ||| | ||| |||||| |||||| |||| || || ||||||||||||||||| || || ||||||||||||||||| ||||||||||| || ||||||||||| ||||| |
gtactaaacactgaaattcaaat-------cctgaaccaaaagtgcttaattatagagtta---tgaacttattatgaacttggattttctggat-----------cagCCTGTATTTTTCAGCACTAGGGCTTACATAAGCTTCATCAAACCAGACCAAACAATGTGGTACCAAGCTTGTAAGACTTGTAACAAGAAAGTGACAGAAG
upper sequence: Vv03s0088g00230.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaataattactgtcattaaaataacctaacatgatcaaactggtcttagccaaagttttaagttaaaaccattttaagttttgataatgtgggcttgtctctgta---cagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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-----------------------------gtact-tcaaaacacttttaac----atattaagatatggaaaaaagaaaagttgatttatgagtctcgtatatatattgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttaagttaaaaccattttaagttttgataatgtgggcttgtctctgtacagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
ttttgat putative branch site (score: 4)
cttgtctct putative PPT
attttaagttttgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataattactgtcattaaaataacctaacatgatcaaactggtcttagccaaagttttaagttaaaaccattttaagttttgataatgtgggcttgtctctgtacagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG