Sequence
atgc intronic sequence ATGC exonic sequence...aagccaacttagcatccttcccacattagtttctctgtcattacttgttgaaactacttcaatcaagttctgacaatttcagtcatggcatgatatgcagTTATGTCATGGGTATTGGTGAAGCTGAGGCCTTTTCTGAAAGGTTGAAGAGAGAACTTCTTGCCTTGGAAGCAGCAAATGTGCATGCCATTTTGGAATCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 6
aagccaacttagcatccttcccacattagtttctctgtcattacttgttgaaactacttcaatcaagttctgacaatttcagtc-atggcat---gatatgcagTTATGTCATGGGTATTGGTGAAGCTGAGGCCTTTTCTGAAAGGTTGAAGAGAGAACTTCTTGCCTTGGAAGCAGCAAATGTGCATGCCATTTTGGAATCT
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-ctttatcatactttttttctaatgtgaagtatgagatgttatcttatcctcacta-tccaa--aatttctgtttacgtcactttgtggtttttgaatgtgcagTTATATCATGGGTATTGGTGAAGCCGAGGCATTTTCTGAAAGGTTAAAAAGAGAGCTCCAGGCTCTGGAAGCAGCAAATGTGCATGCCATTTTAGAAAGT
upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G18840.1 (Glycine max), 3'ss of exon 6
aagccaacttagcatccttcccacattagtttctctgtca--ttacttgttgaaactacttca-atcaagttctga--caatttcagtcatggcatgatatgcagTTATGTCATGGGTATTGGTGAAGCTGAGGCCTTTTCTGAAAGGTTGAAGAGAGAACTTCTTGCCTTGGAAGCAGCAAATGTGCATGCCATTTTGGAATCT
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-tgctaagtca-tatc-ttgtaacat--atttcagtgtcaatttgacaaaaaaaggtatgttatgtgaatttcagaattgatttttttctttttgaattgtgcagTTATGTCATGGGTATTGGTGAAGCAGAGGAATTTTCTGAAAGGTTGAAGAGGGAGCTCCAGGCTCTGGAAGCAGCAAATGTGCATGCTCTTTTAGAAAGT
upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G36540.1 (Glycine max), 3'ss of exon 6
aagccaacttagcatccttcccacattagtttctctgtcattacttgttgaaactacttcaatcaagttctgacaatttcag------tcatggcatgat-atgcagTTATGTCATGGGTATTGGTGAAGCTGAGGCCTTTTCTGAAAGGTTGAAGAGAGAACTTCTTGCCTTGGAAGCAGCAAATGTGCATGCCATTTTGGAATCT
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--gtttgctaagtcatatcttataacttatttcagtatca--atttgaacaaaaaaatggtat---gttatgtcaatttcagattttttttttttttaattgtgcagTTATGTCATGGGTATTGGTGAAGCAGAGGAATTTTCTGAAAGGTTGAAGAGAGAGCTCCAGGCTCTGGAAGCTGCAAATGTGCATGCTCTTTTAGAAAGT
upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 6
aagccaacttagcatccttcccacattagtt-tctctgtcattacttgttgaaactacttcaatcaagttctgacaatttcagtcatggcatgatatgcagTTATGTCATGGGTATTGGTGAAGCTGAGGCCTTTTCTGAAAGGTTGAAGAGAGAACTTCTTGCCTTGGAAGCAGCAAATGTGCATGCCATTTTGGAATCT
| |||| ||| | || | || | | | || | || | || || | | | | | | | | |||| ||||||||| ||||| ||||||||||||||||| |||||||||||| ||||| |||| || | || | ||||| |||||||| ||||| ||| | |||
ttgagaact-agcttgctggggatatcgatagtgggagcagatatcttttccacttattttaccagaatattcagtcaactaatataaatgtcatatacagTTATGTAATGGGCATTGGTGAAGCTGAGGCATTTTCTGAAAGGCTGAAGCGAGAGCTCCAAGCGCTTGAAGCGGCAAATGTACATGCAATTCTTGAAAGC
upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 6
--aagccaacttagcatccttcccacattagtttctctgtcattacttgttgaaactacttcaatcaagttctgacaatttcagtcatggcatgatatgcagTTATGTCATGGGTATTGGTGAAGCTGAGGCCTTTTCTGAAAGGTTGAAGAGAGAACTTCTTGCCTTGGAAGCAGCAAATGTGCATGCCATTTTGGAATCT
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gagaactagcttgctggggataaaaagataatggaa--gcagatatctattccacttattttgtcagattattcactcaactaatataattgtcatatacagTTATGTGATTGGCATTGGTGAAGCTGAGGCATTTTCTGAAAGGCTGAAACGAGAGCTTCAGGCGCTTGAAGCGGCAAATGTACATGCAATTCTGGAAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgaaactacttcaatcaagttctgacaatttcagtcatggcatgatatgcagTTATGTCATGGGTATTGGTGAAGCTGAGGCCTTTTCTGAAAGGTTGAAGAGAGAACTTCTTGCCTTGGAAGCAGCAAATGTGCATGCCATTTTGGAATCT
ttctgac putative branch site (score: 2)
acaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagccaacttagcatccttcccacattagtttctctgtcattacttgttgaaactacttcaatcaagttctgacaatttcagtcatggcatgatatgcagTTATGTCATGGGTATTGGTGAAGCTGAGGCCTTTTCTGAAAGGTTGAAGAGAGAACTTCTTGCCTTGGAAGCAGCAAATGTGCATGCCATTTTGGAATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
aagccaa
- - - - - - - -ccttccc
- - - - - - - - - - - - - - - - - ctgtcat
- - - - - - - - - - - - - - - - - - - - - -cttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatggc