Sequence
atgc intronic sequence ATGC exonic sequence...atcacctatggggtaatcataaattagtttgtttctgagaatataattgtaatgtaaagtctagcttattctaaacatcaaatttatcttgtggatgtagGAAGCTTTGAAGTGGGTGACTGATCAACCTGCATGGAAACGGTCTGAAGGGAGGGACCACATACTTCCAGTTCATCATCCATGGTCTTTCAAGACTGTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0014g00560.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g59630.1 (Oryza sativa), 3'ss of exon 2
atcacctatggggtaatcataaattagtttgtttctgagaata--taattgtaatgtaaagtctagcttattctaaacatcaaatttatcttgtggatgt-agGAAGCTTTGAAGTGGGTGACTGATCAACCTGCATGGAAACGGTCTGAAGGGAGGGACCACATACTTCCAGTTCATCATCCATGGTCTTTCAAGACTGTTC
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-gtggcta-ggtttatttacagaaggatattgtcatgaaatttcttcacccaagtttatttgcaagaggacagtattgat-attgttgttttgttggtgttagGAAGCTTTGAAATGGGTTACTGATCAACCTGCTTGGCAACGTTCAGAAGGCAGAGATCATGTAATTCCCGTTCATCACCCATGGTCGTTTAAGTCAGTTC
upper sequence: Vv19s0014g00560.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G139691_T01 (Zea mays), 3'ss of exon 2
atcacctatggggtaatcataaattagtttgtttctgagaatataattgtaatgtaaagtctagcttattctaaac--atcaaatttatcttgtggatgtagGAAGCTTTGAAGTGGGTGACTGATCAACCTGCATGGAAACGGTCTGAAGGGAGGGACCACATACTTCCAGTTCATCATCCATGGTCTTTCAAGACTGTTC
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atcattta--agatctttatctctgtgtatggaaattactttattgttattcacttcaatttattccaagaggaacttatcatcattacatcttgatgttagGAAGCTTTGAAATGGGTCACAGATCAGCCTGCTTGGCAACGTTCAGAAGGCAGGGATCATGTCATTCCTGTTCATCATCCATGGTCATTTAAGTCAGTCC
upper sequence: Vv19s0014g00560.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G11550.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------------------------------atcacctatggggtaatcataaatt--agtttgtttctgagaat-ataattgtaatgtaaagtcta-gcttattctaaacatcaaatttatcttgtggatgtagGAAGCTTTGAAGTGGGTGACTGATCAACCTGCATGGAAACGGTCTGAAGGGAGGGACCACATACTTCCAGTTCATCATCCATGGTCTTTCAAGACTGTTC
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gtgtgagtgctcttctaacgctctctgttctttgcttctacttctaaattaactattacagtgggaattggatcaaattgaggctttgttctttaattaattatttattaacaacacttttaaccttgcttttttcaatgactgctgtaatgtgatgtgaataattatgctta-tgccttatgt-tgttgtgggtgtagGAAGCTTTGAAGTGGATCACTGATCAACCTGCATGGAAGCGCTCTGGTGGCAGAGATCACATACTCCCCGTGCATCATCCCTGGTCTTTCAAGTCTGTTC
upper sequence: Vv19s0014g00560.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G02010.1 (Glycine max), 3'ss of exon 2
----atcacctatggggtaatcataaattagt-ttgtttctgagaatataattgtaatgtaaagtctagcttattctaaacatcaaatttatcttgtggatgtagGAAGCTTTGAAGTGGGTGACTGATCAACCTGCATGGAAACGGTCTGAAGGGAGGGACCACATACTTCCAGTTCATCATCCATGGTCTTTCAAGACTGTTC
| || |||| | || | | |||||| | | | | | || | | | | | ||| | | | | || |||||| |||||||||||||||||||| | |||||||| ||||| ||||| || |||| || || || |||||||| || || |||||||| |||||||| ||| | ||||
gtttgttctttaattagtaacaacaattgaaccttgtttttctgtttttcaatgactgctgtaatgtggacaattatg--ccttatgttg---ttgtgggtgtagGAAGCTTTGAAGTGGATCACTGATCAGCCTGCTTGGAAGCGCTCTGGTGGCAGAGATCACATACTCCCCGTGCATCATCCCTGGTCTTTTAAGTCCGTTC
upper sequence: Vv19s0014g00560.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G16890.1 (Arabidopsis thaliana), 3'ss of exon 2
atcacctatggggtaatcataaattagtttgtttctgagaatataattgtaatgtaaagtctagcttattctaaacatcaaatttatcttgtggatgtagGAAGCTTTGAAGTGGGTGACTGATCAACCTGCATGGAAACGGTCTGAAGGGAGGGACCACATACTTCCAGTTCATCATCCATGGTCTTTCAAGACTGTTC
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attcaggttaagcctgcctcaatgggagatgtattagttgaaaaacatgagatgccagattttactggtaatatattttttaactctttttaaactgtagGAAGCTTTGAAGTGGGTCACTGATCAGCCTGCTTGGAAGAGGTCCGAGGGAAGGGATCACATATTTCCTATTCATCATCCTTGGTCCTTCAAGTCTGTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtaatgtaaagtctagcttattctaaacatcaaatttatcttgtggatgtagGAAGCTTTGAAGTGGGTGACTGATCAACCTGCATGGAAACGGTCTGAAGGGAGGGACCACATACTTCCAGTTCATCATCCATGGTCTTTCAAGACTGTTC
ttctaaa putative branch site (score: 2)
ttattctaaacatcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcacctatggggtaatcataaattagtttgtttctgagaatataattgtaatgtaaagtctagcttattctaaacatcaaatttatcttgtggatgtagGAAGCTTTGAAGTGGGTGACTGATCAACCTGCATGGAAACGGTCTGAAGGGAGGGACCACATACTTCCAGTTCATCATCCATGGTCTTTCAAGACTGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - aatgtaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcaaat