Sequence
atgc intronic sequence ATGC exonic sequence...ctacaagtcaaatatgctcatatatattcccactgtgaatagtagagcattatggaactttatttaagtgctcatttttattagggttgatatttcatagGTGTGGAGAAATCTGGAAGGAATGCTGAAGGGGATTCATGGTGGGAAACATGGCAAGAAGTTCTTCATCAAGATGAATGGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g00110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g04100.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------ctacaagtcaaatatgctca-tatatattcccact-gtgaatagtagagcattatggaactttatttaagtgctcatt--tttattagggttgatatttca---tagGTGTGGAGAAATCTGGAAGGAATGCTGAAGGGGATTCATGGTGGGAAACATGGCAAGAAGTTCTTCATCAAGATGAATGGAG
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gtatgaacatatctttataatgaaggctctggtagcaaatggtctttgtaatttgttgttaaatttcctaagaattcagttaattttcttatttatgtgtgcccttttccttttgcatatctgatcagccgtcgttgacttttcattacaaatctctcacattagGTGCGGAGAAGTCTGGAAAGAATGGTGAAGGTGATTCTTGGTGGGAGAAATGGAAAGAAGTTCTTTACCAAGATGAATGGAG
upper sequence: Vv18s0001g00110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G110345_T01 (Zea mays), 3'ss of exon 4
ctacaagtcaaatatgctcatatatattcccactgtgaatagtagagcattatggaactttatttaagtgctcatttttattagggttgatatttca------tagGTGTGGAGAAATCTGGAAGGAATGCTGAAGGGGATTCATGGTGGGAAACATGGCAAGAAGTTCTTCATCAAGATGAATGGAG
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----aagacctttattttttt-tgtcctttcaatgtatgcttatttcttgcatctgtcacaaactcatgactgatttttcaatgcgctaa-attacaaaacattagGTGCGGAGAAATCTGGGAGGAATGCTGAAGGAGATTCTTGGTGGGAGAAATGGAAAGAAGTTCTGTACCAAGACGAATGGAG
upper sequence: Vv18s0001g00110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G126812_T01 (Zea mays), 3'ss of exon 4
-ctacaagtcaaatatgctcatatatattcccactgtgaatagtagagcattatggaactttatttaagtgctcatttttattagggttgatatttcatagGTGTGGAGAAATCTGGAAGGAATGCTGAAGGGGATTCATGGTGGGAAACATGGCAAGAAGTTCTTCATCAAGATGAATGGAG
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aatgtctttgtttctttgttctttaaattatgtttattccttgcatc-tgtcacagactcgtgacttacttttcaatgtaataataattataaaacattagGTGCAGAGAAATCTGGGAAGAATGCTGAAGGTGATTCTTGGTGGGAGAAGTGGAAAGAAGTACTGTACCAAGATGAATGGAG
upper sequence: Vv18s0001g00110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G42430.1 (Arabidopsis thaliana), 3'ss of exon 4
ctacaagtcaaatatgctcatatatattcccactgtgaatagtagagcattatggaacttt-atttaagtgctcat-ttttattagggttgatatttcatagGTGTGGAGAAATCTGGAAGGAATGCTGAAGGGGATTCATGGTGGGAAACATGGCAAGAAGTTCTTCATCAAGATGAATGGAG
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--ttgccccttatcccttgttactgatgattaatgagtgtgtcaaagttctgttttttttttgtttacgaattctcatttcagtggagtgtactttttgtagGTGTGGAGAAATCTGGTAAAAATTCTGAGGGTGACTCTTGGTGGGAAACTTGGCAAGAAGTCCTTCATCAAGATGAGTGGAG
upper sequence: Vv18s0001g00110.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ19379 (Selaginella moellendorffii), 3'ss of exon 2
------------------------ctacaagtcaaatatgctcatat--atattcccactgtgaatagtagagcattatggaactttatttaagt------gctcatttttattagggttgatatttcat---------agGTGTGGAGAAATCTGGAAGGAATGCTGAAGGGGATTCATGGTGGGAAACATGGCAAGAAGTTCTTCATCAAGATGAATGGAG
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gttttagcctttttcaacttaatagcatagcttgctttttctaatagtggtgggaaaaatgcgactggacgggctataaggaacttggtaaactttgtttcgcttattttttcttgttttacactcttgtggatagtgcagGTGCTGAAAAGTCCGGCAAAAATGCTGAAGGCGATGCCTGGTGGGAAACCTGGCAGGAAATTCTGCGTCAAGATGAATTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcattatggaactttatttaagtgctcatttttattagggttgatatttcatagGTGTGGAGAAATCTGGAAGGAATGCTGAAGGGGATTCATGGTGGGAAACATGGCAAGAAGTTCTTCATCAAGATGAATGGAG
ggttgat putative branch site (score: 5)
aactttatttaagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctacaagtcaaatatgctcatatatattcccactgtgaatagtagagcattatggaactttatttaagtgctcatttttattagggttgatatttcatagGTGTGGAGAAATCTGGAAGGAATGCTGAAGGGGATTCATGGTGGGAAACATGGCAAGAAGTTCTTCATCAAGATGAATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - tatgctc
- - - - - - - - - - - - - ttcccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggttga