Sequence
atgc intronic sequence ATGC exonic sequencegtaataattactgtcattagaataacctaacatgatcaacctggtcttagccaaagttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0065g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g11540.1 (Oryza sativa), 3'ss of exon 9
gtaataa-ttactgtcattagaataacctaacatgatcaacctggtcttagccaaagttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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gtaaaatcttggaatctttgaaagaaaatggaattgtt--cttgatgtttagtttattagcactttctagttgtgattgtcctaaatttacttgttatgtttt---gcagCCTGTGTTCTTCAGTCTGAATGCCTATATTAGCCTTATCAAGCCTGACCAAACCATGTGGTACCGAGCTTGCAAGACCTGCAACAAGAAGGTGACTGAGG
upper sequence: Vv11s0065g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G098714_T01 (Zea mays), 3'ss of exon 9
--gtaataattactgtcattagaataacctaacatgatcaacctggtcttagccaaagttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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gtataatcgtcaatatccactgaacga--tgatattatttatatcttgaattgaaaaattgtaaatttggagaacccccaatttgaccctttta--tttgttgcattgcagCCTGTTTTCTTCAGTTTGTATGCCACCATAAGCCACATCAAGCCTGACCAGAACATGTGGTACCGTGCTTGCAAGACCTGCAACAAGAAGGTGACTGAAA
upper sequence: Vv11s0065g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G468475_T01 (Zea mays), 3'ss of exon 8
gtaataattactgtcattagaataacctaacatgatcaacctggtcttagccaaagttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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gta-cgaccctgaatattc-actaaaataacactgttcgtatcttcaatggaagagttgcaaatctggagaagctccaattcaact--tcttgttttttcctt-tgcagCCTGTTTTCTTCAGTCTGTACGCCATCATAAGCCACATCAAGCCTGATCAGATTATGTGGTACCGTGCTTGCATGACCTGCAACAAGAAGGTGACTGAAG
upper sequence: Vv11s0065g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G08660.2 (Glycine max), 3'ss of exon 9
------------------------gtaataattactgtcattagaataac-ctaacatgatcaacctggtc-ttagccaaagttttgag----ttaaaagcatattc---agttttga---taa--tgtgggcttgt------ctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
| | | || | || || | | || | | | | || | | | || || || | || ||| ||||| | ||| ||| | || | ||||| ||||| | ||||| || | |||| | | ||||||||||| ||||||||||| |||||||||| || || |||||||||||||| |||||||| || ||
gtatttggttgcaaattttcctgaatgttgggcattgctaatacgattccatctgcttgtttgatataaacattcattggaactcttagaaatttcaatggattttcattagtttctagtttaacttgtagtctcttatgttgctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
upper sequence: Vv11s0065g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA05G00370.2 (Glycine max), 3'ss of exon 9
---------------------------------gtaataattactgt-cattagaataacctaacatgatcaacc--tggtc---ttagccaaagttttg---agttaaaagcatattca-----gttttga---taatgtgggcttgt-----ctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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gtatttggttattaattttcctgaatgttggacattgctaatacagttccatgtggttgtttgatataaacattcattagacatgttattggaactcctgcaaattttaatggattttcatccgagtttctagtctaacttgtctcttctgttgctttgggcagCCTGCTTTTTTCAGTCTTAGAGGACATATAACCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
upper sequence: Vv11s0065g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaataattactgtcattagaataacctaacatgatcaacctggtcttagccaaagttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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-------------------gtacttcaaaacacttttaacatatt-------aagatatggaa--aaaagaaaagttgattt--atgagtctcgtatatatat-tgcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
upper sequence: Vv11s0065g00990.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G61000.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaataattactgtcattagaataacctaacatgatcaacctggtctt--agccaaagttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
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----------------------gtactaaacactgaaattcaaatcctgaaccaaaagtgcttaattatagagttatgaacttattatgaacttggattttctggat-cagCCTGTATTTTTCAGCACTAGGGCTTACATAAGCTTCATCAAACCAGACCAAACAATGTGGTACCAAGCTTGTAAGACTTGTAACAAGAAAGTGACAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
ttttgat putative branch site (score: 4)
cttgtcttt putative PPT
ttttgataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataattactgtcattagaataacctaacatgatcaacctggtcttagccaaagttttgagttaaaagcatattcagttttgataatgtgggcttgtctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG