Sequence
atgc intronic sequence ATGC exonic sequencegtaataattactgtcattaaaataacctaacatgatcaaactggtcttagccaaagttttaagttaaaatcattttaagttttgataatgtgggcttgtctctgtatagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0047g00870.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g11540.1 (Oryza sativa), 3'ss of exon 9
gtaataa-ttactgtcattaaaataacctaacatgatc----aaactggtcttagccaaagttttaagttaaaatcattttaagttttgataatgtgggcttgtctctgtatagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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gtaaaatcttggaatctttgaaagaaaatggaattgttcttgatgtttagtttattagcactttctagttgtgattgtcctaaatttacttgttatg---------ttttgcagCCTGTGTTCTTCAGTCTGAATGCCTATATTAGCCTTATCAAGCCTGACCAAACCATGTGGTACCGAGCTTGCAAGACCTGCAACAAGAAGGTGACTGAGG
upper sequence: Vv13s0047g00870.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G08660.2 (Glycine max), 3'ss of exon 9
------------------------------gtaataattactgtcattaaa----ataacctaacatgatca--aactggtcttagccaaagttttaa----gttaaaatcattttaagttttgataatgtgggcttgt----ctctgtatagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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gtatttggttgcaaattttcctgaatgttgggcattgctaatacgattccatctgcttgtttgatataaacattcattggaactcttagaaatttcaatggattttcattagtttctagtttaacttgtagtctcttatgttgctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
upper sequence: Vv13s0047g00870.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G00370.2 (Glycine max), 3'ss of exon 9
----------------------------------------------------gtaataattactgtcattaaaata-acctaacatgatcaaactggtcttagccaaagttttaagttaaaatcattttaagttttgat--aatgtgggcttgt-----ctctgtatagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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gtatttggttattaattttcctgaatgttggacattgctaatacagttccatgtggttgtt--tgatataaacattcattagacatgtt---attggaactcctgcaaattttaatggattttcatccgagtttctagtctaacttgtctcttctgttgctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
upper sequence: Vv13s0047g00870.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G61000.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaataattactgtcattaaaataacctaacatgatcaaactggtcttagccaaagttttaagttaaaatcattttaagttttgataatgtgggcttgtctctgtatagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
||| ||| |||| ||| |||| | ||| | || | |||| | || ||| | || | ||| | | || ||| | ||| ||||| |||||| |||| || || ||||||||||||||||| || || ||||||||||||||||| ||||||||||| || ||||||||||| ||||| |
gtactaaacactgaaattcaaat-------cctgaaccaaaagtgcttaattatagagtta---tgaacttattatgaacttggattttctggatc-----------agCCTGTATTTTTCAGCACTAGGGCTTACATAAGCTTCATCAAACCAGACCAAACAATGTGGTACCAAGCTTGTAAGACTTGTAACAAGAAAGTGACAGAAG
upper sequence: Vv13s0047g00870.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaataattactgtcattaaaataacctaacatgatcaaactggtcttagccaaagttttaagttaaaatcattttaagttttgataatgtgggcttgtctctgtat---agCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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-----------------------------gtact-tcaaaacacttttaac----atattaagatatggaaaaaagaaaagttgatttatgagtctcgtatatatattgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttaagttaaaatcattttaagttttgataatgtgggcttgtctctgtatagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
ttttgat putative branch site (score: 4)
cttgtctct putative PPT
taagttaaaatcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataattactgtcattaaaataacctaacatgatcaaactggtcttagccaaagttttaagttaaaatcattttaagttttgataatgtgggcttgtctctgtatagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG