Sequence
atgc intronic sequence ATGC exonic sequence...gattttctggatttgttgaagtttttattcattacttttcctgtcatgctttatttccaatctttagttgtaacggttaaatcatgttctcattatgcagGTTGGGCTTCTCGAACTTTCTTTTCGGATAATGGATCTACAGCAATTGAAGTTGCTCTTAAGATGGCATTTCGAAAATTCTCTCTTGATCATGGCATCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0052g01390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os08g14770.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------gattttctggatttgt-tgaagtttttattcattacttttcctgtcatgctttatttccaatctttagttgtaacggttaaatcatg-------ttctcat-tatgc-agGTTGGGCTTCTCGAACTTTCTTTTCGGATAATGGATCTACAGCAATTGAAGTTGCTCTTAAGATGGCATTTCGAAAATTCTCTCTTGATCATGGCATCAT
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gtatgtgctgtaacttcactatgattttgcataattattatcactgacaaattctaagtacagctgttgtttaatgttacttttatgttactatacaagtcacgttgttgagaaacacttcattcattagacaccttctcttgtatgttagATTGGGCTTCTCGAGTTTATTTTTCAGACAATGGATCTACTGCAATTGAAATTGCTTTGAAGATGGCATTTCGTAAATATGCATGTGACCATGGGATTAT
upper sequence: Vv11s0052g01390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G102156_T01 (Zea mays), 3'ss of exon 5
-gattttctggatttgttg-aagtttttattcattacttttcctgtcatgctttatttccaatctttagttgtaacggttaaatcatgttctcattatgcagGTTGGGCTTCTCGAACTTTCTTTTCGGATAATGGATCTACAGCAATTGAAGTTGCTCTTAAGATGGCATTTCGAAAATTCTCTCTTGATCATGGCATCAT
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tttatttctttatttcttgcaactctatccacatcgctgatagcatcgttcctttttgcgtgcctatcatatttgtg-tcacaacttcccctttttct-cagGATGGGCTTCTCGAGTCTATTATTCAGACAATGGATCCACTGCAATTGAAATTGCTCTGAAGATGGCATTTCGTAAATTTTCTCTTGATCATGGAATTAT
upper sequence: Vv11s0052g01390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G01170.1 (Glycine max), 3'ss of exon 5
---gattttctggatttgttg--aagtttttattcattacttttcctgtcatgctttatttccaatctttagttgtaacggttaaatcatgttctcattatgcagGTTGGGCTTCTCGAACTTTCTTTTCGGATAATGGATCTACAGCAATTGAAGTTGCTCTTAAGATGGCATTTCGAAAATTCTCTCTTGATCATGGCATCAT
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gatgtttgccaatgctcattgttatctattgaatgatgatacattattttatgagcagtttgaagttctttgc-atagtagctaactcatttt----ttgtgcagGCTGGGCTTCTCGGACATATTTTTCGGACAATGGATCTACAGCAATTGAAATTGCTCTCAAGATGGCGTTTCGTAAATTTTCTGTTGATCATGGACTTAT
upper sequence: Vv11s0052g01390.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G57590.1 (Arabidopsis thaliana), 3'ss of exon 5
gattttctggatttgttgaagtttttattcattacttttcctgtcatgctttatttccaatctttagttgtaacggttaaatcatgttctcattatgcagGTTGGGCTTCTCGAACTTTCTTTTCGGATAATGGATCTACAGCAATTGAAGTTGCTCTTAAGATGGCATTTCGAAAATTCTCTCTTGATCATGGCATCAT
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--------------------gtttctaaacttgctctgtcacat--tgtttaattttcaaacattgg--gggatggttaatt---attttatgcatgcagGCTGGGCTTCTCGAGTATACTTCTCGGATAATGGATCCACAGCAATCGAAATTGCCTTGAAGATGGCATTTCGTAAGTTTTGTGTCGATCATAATTTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgctttatttccaatctttagttgtaacggttaaatcatgttctcattatgcagGTTGGGCTTCTCGAACTTTCTTTTCGGATAATGGATCTACAGCAATTGAAGTTGCTCTTAAGATGGCATTTCGAAAATTCTCTCTTGATCATGGCATCAT
ttgtaac putative branch site (score: 2)
ttctcatt putative PPT
ttaaatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gattttctggatttgttgaagtttttattcattacttttcctgtcatgctttatttccaatctttagttgtaacggttaaatcatgttctcattatgcagGTTGGGCTTCTCGAACTTTCTTTTCGGATAATGGATCTACAGCAATTGAAGTTGCTCTTAAGATGGCATTTCGAAAATTCTCTCTTGATCATGGCATCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- -tttctgg
- - - - - - - - - - - - - - - - - - - -cctgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgttc