Sequence
atgc intronic sequence ATGC exonic sequence...ttctgcttgctcaaattgcaacttttcttcttatgttttgatgtttgaaccatttatgcgaagttattttgttaacagagtagatgcatggttttgacagGTTCATGGTGCTTTTGCTGGATATAGTGGAATTACAGTGGGTATATGCAACACTCACTATGTCTACCTTCCCATTCCTGAAGTCGTTTCTTACCCCAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0199g00240.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G38450.1 (Glycine max), 3'ss of exon 11
--ttctgcttgc-tcaaattgcaacttttcttcttatgttttgatgtttgaaccatttatgcgaagttat-tttgttaacagagtagatgcatggttttgacagGTTCATGGTGCTTTTGCTGGATATAGTGGAATTACAGTGGGTATATGCAACACTCACTATGTCTACCTTCCCATTCCTGAAGTCGTTTCTTACCCCAGAG
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aattcctccaacgtctaatagttacctgtatgtgtatctcagaagatgtg---tatttctgttattttctatctgatactgatccacagcttttgcattg-cagGTTCATGGTGCGTTTGCAGGATATAGTGGCATTACAGTAGGTTTATGTAACACCCACTATGCCTACTTTCCCATCCCCGAAGTGATATCTCATCCTAGGC
upper sequence: Vv00s0199g00240.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA18G21720.1 (Glycine max), 3'ss of exon 13
---ttctgcttgctcaaattgcaacttttcttcttatgttttgatgtttgaaccatttatgcgaagttat-tttgttaacagagtagatgcatggttttgacagGTTCATGGTGCTTTTGCTGGATATAGTGGAATTACAGTGGGTATATGCAACACTCACTATGTCTACCTTCCCATTCCTGAAGTCGTTTCTTACCCCAGAG
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aaatacaattcctctagcgcccaatacttacctgtatgt---gaatttcagaagatttcggttactttctatctgatactgatccacagcttttgcattg-cagGTTCATGGTGCGTTTGCAGGATATAGTGGCATTACAGTAGGTTTATGTAACACCCACTATGTTTACTTTCCCATCCCCGAAGTGATATCCCATCCTAGGT
upper sequence: Vv00s0199g00240.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA01G03040.1 (Glycine max), 3'ss of exon 12
ttctgcttgctcaaattgcaacttttcttcttatgttttgatgtt-tgaaccat-ttatgcgaagttattttgttaacagagtagatgcatggttttgacagGTTCATGGTGCTTTTGCTGGATATAGTGGAATTACAGTGGGTATATGCAACACTCACTATGTCTACCTTCCCATTCCTGAAGTCGTTTCTTACCCCAGAG
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-acaaattgcatacaattcaacatctccaattaaaagtacgtcttatgtgtagtgttgtacattagtcacttgatattgattcatagcttttgtattg-cagGTTCATGGTGCATTTGCTGGATTTAGTGGCATTACAGTAGGCTCTTGTAACACACACTATGCTTACTTTCCCATCCCCGAAGTGATATCTCATCCCAAAT
upper sequence: Vv00s0199g00240.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G04570.1 (Glycine max), 3'ss of exon 12
----ttctgcttgctcaaattgcaacttttcttcttatgttttgatgttt-gaaccatttatgcgaagttattttgttaacagagtagatgcatggttttgacagGTTCATGGTGCTTTTGCTGGATATAGTGGAATTACAGTGGGTATATGCAACACTCACTATGTCTACCTTCCCATTCCTGAAGTCGTTTCTTACCCCAGAG
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caagcacaaaatgcatacaatgcaacatctccaaaagtacatccatgtgtagtactgtatatttg----tcacttgatattgattcatagcttttgtattg-cagGTTCATGGTGCATTTGCTGGATTTAGTGGCATCACAGTAAGCACTTGTAACACACACTATGCTTACTTTCCCATCCCCGAAGTGATATCTCATCCCAAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaccatttatgcgaagttattttgttaacagagtagatgcatggttttgacagGTTCATGGTGCTTTTGCTGGATATAGTGGAATTACAGTGGGTATATGCAACACTCACTATGTCTACCTTCCCATTCCTGAAGTCGTTTCTTACCCCAGAG
tgttaac putative branch site (score: 2)
aagttattttgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctgcttgctcaaattgcaacttttcttcttatgttttgatgtttgaaccatttatgcgaagttattttgttaacagagtagatgcatggttttgacagGTTCATGGTGCTTTTGCTGGATATAGTGGAATTACAGTGGGTATATGCAACACTCACTATGTCTACCTTCCCATTCCTGAAGTCGTTTCTTACCCCAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - gcttgct
- - - - - - - -ttgcaac
- - - - - - - - - - - - - - - - - - - - - - - - -ccattta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcatg