Sequence
atgc intronic sequence ATGC exonic sequence...tgatcaaaacgttaatcaaattatgcttcttgctttttggtttaaaggtgttgtatcagtaggaaaatcacatctcacaagttgaatgcatagtctgcagATTGTTTTCACTCTGGAACTCTATGGGGTTAAGAAGATTGTTGGAATCCAGTATGGTTATCGTGGACTTTTTGATCGGGGCTTAGCTGAAATAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0108g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g24910.1 (Oryza sativa), 3'ss of exon 5
tgatcaaaacgttaatcaaattatgcttcttgctttttggtttaaaggtgttgtatcagtaggaaaatcacatctcacaagttgaatgcatag-----------tctgcagATTGTTTTCACTCTGGAACTCTATGGGGTTAAGAAGATTGTTGGAATCCAGTATGGTTATCGTGGACTTTTTGATCGGGGCTTAGCTGAAATAGAG----
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----------gtggagttcattacatgcttttatttaatgttgacagatattcagtaaattctggccat-cattttgcctgttgaataaccaagctttcctatattttcagATAGTATTTACATTGGAGATCTATGGGGTTAAGAACATTGTTGGAATTCAGTTTGGTTATCGTGGATTTTTTGAGAAAGGCTTAAAAGAAATGCCTGTAA
upper sequence: Vv14s0108g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g24910.2 (Oryza sativa), 3'ss of exon 5
tgatcaaaacgttaatcaaattatgcttcttgctttttggtttaaaggtgttgtatcagtaggaaaatcacatctcacaagttgaatgcatag-----------tctgcagATTGTTTTCACTCTGGAACTCTATGGGGTTAAGAAGATTGTTGGAATCCAGTATGGTTATCGTGGACTTTTTGATCGGGGCTTAGCTGAAATAGAG
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----------gtggagttcattacatgcttttatttaatgttgacagatattcagtaaattctggccat-cattttgcctgttgaataaccaagctttcctatattttcagATAGTATTTACATTGGAGATCTATGGGGTTAAGAACATTGTTGGAATTCAGTTTGGTTATCGTGGATTTTTTGAGAAAGGCTTAAAAGAAATGCCT
upper sequence: Vv14s0108g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os08g34050.1 (Oryza sativa), 3'ss of exon 4
--tgatcaaaacgttaatcaaattatgcttcttgctttttggtttaaaggtgttgtatcagtaggaaaatcacatctcacaagttgaatgcatag--tctgcagATTGTTTTCACTCTGGAACTCTATGGGGTTAAGAAGATTGTTGGAATCCAGTATGGTTATCGTGGACTTTTTGATCGGGGCTTAGCTGAAATAGAG
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ttttacttatgcctagaatatgtgctgattccttctgcaatttttagcaa----gaaataatgttgcatgtatgacttacaaatcgttttttccgcgtttgcagATAGTATTCACTCTAGAGACCTATGGGGTTAAGAATATTGTTGGGATTCCATTTGGTTATCGTGGATTTTTTGAAAAGGGCCTAAAAGAAATGCCA
upper sequence: Vv14s0108g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G127717_T02 (Zea mays), 3'ss of exon 5
tgatcaaaacgttaatcaaattatgcttcttgctttttggtttaaaggtgttgtatcagtaggaaaatcacatctcacaagt---tgaatgcat---agtctgcagATTGTTTTCACTCTGGAACTCTATGGGGTTAAGAAGATTGTTGGAATCCAGTATGGTTATCGTGGACTTTTTGATCGGGGCTTAGCTGAAATAGAG
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------agatgatttttgaattgtgaatccctcactttcaagtaaacactgaatagaataaccagagctgtagttggtatgtgactacatgtattaatatttccagATAGTATTTACTTTGGAGACTTATGGGGTGAAGAATATTGTTGGAATCCCATTTGGTTATCGTGGATTTTTTGAGAAAGGCTTAAAAGAAATGCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggtgttgtatcagtaggaaaatcacatctcacaagttgaatgcatagtctgcagATTGTTTTCACTCTGGAACTCTATGGGGTTAAGAAGATTGTTGGAATCCAGTATGGTTATCGTGGACTTTTTGATCGGGGCTTAGCTGAAATAGAG
atctcac putative branch site (score: 3)
aaaatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgatcaaaacgttaatcaaattatgcttcttgctttttggtttaaaggtgttgtatcagtaggaaaatcacatctcacaagttgaatgcatagtctgcagATTGTTTTCACTCTGGAACTCTATGGGGTTAAGAAGATTGTTGGAATCCAGTATGGTTATCGTGGACTTTTTGATCGGGGCTTAGCTGAAATAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- atcaaaa
- - - - - - -aatcaaa
- - - - - - - - - - - - - ttcttgc
- - - - - - - - - - - - - - - - - - - - - - - ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgca