Sequence
atgc intronic sequence ATGC exonic sequence...aagtttgctgaatccagcctgttgatctacttttctgtgtctcatttccatatttaagtttaaaacatctcttatttgctctaaatcttttgtgactaagGTACATTGAAGAAAGATCATTTAGGAGATTTGTTGAAGCTTGCCTGGAAGAAACTGTGGTTGTTTATGTTGATCACCTCCTGACACAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 19
aagtttgctgaatccagcctgttgatctacttttctgtgtctcattt-ccatatttaagtttaaaacatctcttatttgctctaaatcttttgtgactaagGTACATTGAAGAAAGATCATTTAGGAGATTTGTTGAAGCTTGCCTGGAAGAAACTGTGGTTGTTTATGTTGATCACCTCCTGACACAG
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gtgttccttgtggcatgtaaacggtcacttattcctgataatagttagtcatgtttctttctatacttgatttgaagacttccgggtctattttttcta-gATATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCCTGGAGCAAACAATTGTGGTATACGTTGATCATCTCCTTACTCAG
upper sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G161553_T01 (Zea mays), 3'ss of exon 2
---aagtttgctgaatccagcctgttgatctacttttctgtgtctcatttccatat--ttaagtttaaaacatctcttatttgctctaaatcttttgtgactaagGTACATTGAAGAAAGATCATTTAGGAGATTTGTTGAAGCTTGCCTGGAAGAAACTGTGGTTGTTTATGTTGATCACCTCCTGACACAG
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tcgaagttaaatgttaacagtctggagttttgcttacaatagttgtgtctttatgtgctttagtttaataccctttgtgtgtg-tgtgtgtgtgt----gtttagGTATATTGAAGAAAGACCATTTCGAAGATTTGTGGAGGCTTGCATAGAAGAAACAATCGTGGTCTATGTTGATCATCTCCTTTCCCAG
upper sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 15
-----aagtttgctgaatccagcctgttgatctacttttctgtgtctcatttccatatttaagtttaaaacatctcttatttgctctaaatcttttgtgacta-agGTACATTGAAGAAAGATCATTTAGGAGATTTGTTGAAGCTTGCCTGGAAGAAACTGTGGTTGTTTATGTTGATCACCTCCTGACACAG
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tctgtcaatttagtttatcgaatttaaacattaacactctagagtttgcttataatagttgtctt---aatgtgcttta---gtttaatactgtttgtgtgtgtagGTATATTGAAGAAAGATCATTTCGAAGATTTGTGGAGGCTTGCATAGAGGAAACAATTGTGGTCTATGTTGACCATCTCCTTTCTCAG
upper sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA03G03120.2 (Glycine max), 3'ss of exon 21
aagtttgc-tgaatccagcctgttgatctacttttctgtgtctcatttccatatttaagtt-taaaacatctcttatttgctctaaatcttttgtgactaagGTACATTGAAGAAAGATCATTTAGGAGATTTGTTGAAGCTTGCCTGGAAGAAACTGTGGTTGTTTATGTTGATCACCTCCTGACACAG
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ttgctggtgtgaattgcttctattgcatttatttgaagtttgattgttaaatatttagtttgttgaggaaaactaagtttcgaccatccatatat--tcaagGTACATTGAAGAACGATCTTTTAGGAGATTTGTTGAAGCCTGCCTGGAAGAAACAGTGGTTGTTTATGTTGATCATCTTTTAACACAG
upper sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT1G71820.1 (Arabidopsis thaliana), 3'ss of exon 21
aagtttgctgaatccagcctgttgatctacttttctgtgtctcatttccatattta-agtttaaaacatctcttatttgctctaaatctt-ttgtgacta--------agGTACATTGAAGAAAGATCATTTAGGAGATTTGTTGAAGCTTGCCTGGAAGAAACTGTGGTTGTTTATGTTGATCACCTCCTGACACAG
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------------------------gtaagtttttctttcccccttttgtttaacaagagccaaaaatgctacaagtctattgaagatgtcgtggtgaatactggatgcagGTATGTCGAAGAAAGATCATTTAGAAGATTTGTCGAAGCATGTTTGGAAGAAACAGTCGTTGTCTATGTTGACCATCTCCTAACTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccatatttaagtttaaaacatctcttatttgctctaaatcttttgtgactaagGTACATTGAAGAAAGATCATTTAGGAGATTTGTTGAAGCTTGCCTGGAAGAAACTGTGGTTGTTTATGTTGATCACCTCCTGACACAG
ctctaaa putative branch site (score: 3)
tcttttgt CT-rich tract
tatttaagtttaaaac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagtttgctgaatccagcctgttgatctacttttctgtgtctcatttccatatttaagtttaaaacatctcttatttgctctaaatcttttgtgactaagGTACATTGAAGAAAGATCATTTAGGAGATTTGTTGAAGCTTGCCTGGAAGAAACTGTGGTTGTTTATGTTGATCACCTCCTGACACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - -gaatcca
- - - - - - - - -cctgttg
- - - - - - - - - - - - - - - - - - - - - catttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaca