Sequence
atgc intronic sequence ATGC exonic sequence...ggcttcttaaaatttaaaattagttcgatgaattaattgtgcatcattattgtttttaatgtccaattatattttcttaaacctttggttcttctcttagCCGCTCAGAACATCGATTACTTCTTCGATCTGATAATGCGGATAGTCGTCTCACACCTTTGGGGCGTGAAATTGGTTTGATAGATGATAGACGTTGGAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0044g01690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g72980.1 (Oryza sativa), 3'ss of exon 9
-----ggcttcttaaaatttaaaattagttcgatgaattaattgtgcatcattattgtttttaatgtccaattatattttcttaaacctttggttcttctcttagCCGCTCAGAACATCGATTACTTCTTCGATCTGATAATGCGGATAGTCGTCTCACACCTTTGGGGCGTGAAATTGGTTTGATAGATGATAGACGTTGGAAA
| ||| | | | | || || | | || ||||| | | || || | | || | |||| || || | | | ||||| |||||||| || || | |||||| |||||||||| |||||||| | || |||||||| || || ||||||||||||||||||||||| ||| |
ggtaagtggctttaccagtaggtactggtagcattatgatttcttgaatcataact-ttgttgacct----ttttttttttttgttgctacatacatacattcagCCGTTCAGAACACCGTCTATTGCTTCGAGCTGATAATGCTGATAGTCGGTTGACTCCTTTGGGACGAGATATTGGTTTGATAGATGATAGACGATGGGAG
upper sequence: Vv04s0044g01690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G481548_T01 (Zea mays), 3'ss of exon 9
ggcttcttaaaatttaaaattagtt--cgatgaattaattgtg-catcattattgtttttaatgtccaattatattttcttaaacctttggttcttctcttagCCGCTCAGAACATCGATTACTTCTTCGATCTGATAATGCGGATAGTCGTCTCACACCTTTGGGGCGTGAAATTGGTTTGATAGATGATAGACGTTGGAAA
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-gttctttgagtttttatgctgtctagtgtctaatcaaatatgactaaactcccccccccttttttcctttgtttttgttgggacattta--tggacatccagCCGTTCAGAACACCGGCTATTGCTTCGATCAGATAATGCTGATAGTCGTTTGACCCCTTTGGGACGAGAGATTGGTTTAATAGATGATAGACGTTGGGAG
upper sequence: Vv04s0044g01690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G440344_T01 (Zea mays), 3'ss of exon 3
-ggcttcttaaaatttaaaattagttcgatgaattaattgtgcatcatt--attgtttttaatgtccaattatattttcttaaacctttggttcttctcttagCCGCTCAGAACATCGATTACTTCTTCGATCTGATAATGCGGATAGTCGTCTCACACCTTTGGGGCGTGAAATTGGTTTGATAGATGATAGACGTTGGAAA
| ||||| ||||| | | || || |||| || | | | | | | | || | ||| || || ||| | | ||| | |||||||| || || | |||||||| |||||||| ||||||||| | || |||||||| || || |||||||| |||||||||||||||||| |
tgagttcttttaatttttatgttgtctagtgt-ctaatcaaatatgactaaactccccccttttttcctttgtttttgctgggacattta--tggacatccagCAGTTCAGAACACCGGCTATTGCTTCGATCAGATAATGCTGATAGTCGTTTGACCCCTTTGGGACGAGAGATTGGTTTAATAGATGATAGACGTTGGGAG
upper sequence: Vv04s0044g01690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA05G32720.1 (Glycine max), 3'ss of exon 6
-------------ggcttcttaaaatttaaaattagttc---gatgaattaattgtgcatcattattgt----ttttaatgtccaattatatttt--cttaaacctttggttcttctcttagCCGCTCAGAACATCGATTACTTCTTCGATCTGATAATGCGGATAGTCGTCTCACACCTTTGGGGCGTGAAATTGGTTTGATAGATGATAGACGTTGGAAA
| | | | | | | || |||| || || ||| |||| | ||| | | | |||||| | ||| | | | || | ||||||||||||| ||||| |||||| | ||||||| ||||| ||||| |||||||||||||| || ||||||||||| ||||| |||||||| || ||||||
gtaagctaaccaagataacagcatttctgctttctgctcatagatgcatatatgctgcttcatcctgacactcctttttcctttattgatatttaaattgaaatttgtcttcctcatgttagCCGCTCAGAGCATCGGTTACTTTTGAGATCTGACAATGCTGATAGCCGTCTCACACCTTTAGGTCGTGAAATTGGGTTGATCGATGATAGGCGCTGGAAA
upper sequence: Vv04s0044g01690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G00380.1 (Glycine max), 3'ss of exon 8
---ggcttcttaaaatttaaaattagttc---gatgaattaattgtgcatcat--tattgtttttaat----gtccaattatattttcttaaacctttggttcttctcttagCCGCTCAGAACATCGATTACTTCTTCGATCTGATAATGCGGATAGTCGTCTCACACCTTTGGGGCGTGAAATTGGTTTGATAGATGATAGACGTTGGAAA
|| || || | | | || |||| || || ||| |||| | || | | || || |||| | | ||| | | | || | ||||||||||||| ||||| ||||| | ||||||| ||||| ||||| |||||||||||||| || ||||||||||| ||||| ||||||||||| ||||||
gtaaactaaccaagataacatttctgctcatagatgcatatatgctgcttcatcctgttactccttattcctttcttgttatttaaattgaaatttgtcttcctcatgttagCCGCTCAGAGCATCGGTTACTCTTGAGATCTGACAATGCTGATAGCCGTCTCACACCTTTAGGTCGTGAAATTGGATTGATTGATGATAGACGCTGGAAA
upper sequence: Vv04s0044g01690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G13440.1 (Arabidopsis thaliana), 3'ss of exon 9
ggcttcttaaaatttaaaattagttcgatgaattaattgtgcatcattat-----tgtttttaatgtccaattatattttcttaaacctttggttcttctcttagCCGCTCAGAACATCGATTACTTCTTCGATCTGATAATGCGGATAGTCGTCTCACACCTTTGGGGCGTGAAATTGGTTTGATAGATGATAGACGTTGGAAA
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-----ttccacgtgaactattttgtgcatgtactaatagcctattactacttatgtgtgtttagtaacacggaataatcaaatgtgttttttttctcaacgacagCCGTTCAGAACATCGGCTTCTTCTTCGATTTGATAATGCGGATAGTCGACTAACGCCTCTGGGGCGTGAACTTGGATTGATAGATGATAGACGATGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attattgtttttaatgtccaattatattttcttaaacctttggttcttctcttagCCGCTCAGAACATCGATTACTTCTTCGATCTGATAATGCGGATAGTCGTCTCACACCTTTGGGGCGTGAAATTGGTTTGATAGATGATAGACGTTGGAAA
ttttaat putative branch site (score: 3)
cctttggttcttctct putative PPT
tttttaatgtccaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggcttcttaaaatttaaaattagttcgatgaattaattgtgcatcattattgtttttaatgtccaattatattttcttaaacctttggttcttctcttagCCGCTCAGAACATCGATTACTTCTTCGATCTGATAATGCGGATAGTCGTCTCACACCTTTGGGGCGTGAAATTGGTTTGATAGATGATAGACGTTGGAAA
- - -cttaaaa
- - - - - - - -aaaatta
- - - - - - - - - - - - - - - - - - - -tgcatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgtcc