Sequence
atgc intronic sequence ATGC exonic sequence...agtggctcagtgctcaagattattttatttttaattttctcgttctttactttgaatgatagttaataatggttttccattgttgttcgaatttctacagGCACATGCTGCTTCAGCTGTGCTCAACTTCAGTGAGAACTGCACTCCAGATATTTTAACGCCATATTTAGATGGAATTGTTGGCAAATTACTAGTACTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G033619_T01 (Zea mays), 3'ss of exon 1
agtggctca---gtgctcaagattattttatttttaattttctcgttctttactttgaatgat-agttaataatggttttccattgttgttcgaatttctacagGCACATGCTGCTTCAGCTGTGCTCAACTTCAGTGAGAACTGCACTCCAGATATTTTAACGCCATATTTAGATGGAATTGTTGGCAAATTACTAGTACTTC
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--tggtttacataaagtcgagggcttgctatatctgctcttc--atcaaacacaccagctgaccaataaggcattctctcatattttatttcctacatgttcagGCACATGCTGCATCAGCTATTCTGAACTTCAGTGAAAACTGCAGACCTGATATTTTGACACCATACTTGGATGTAATAGTTGGGAAACTTCTATTGTTAC
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G12120.1 (Glycine max), 3'ss of exon 2
agtggctcagtgctcaagattatttt-atttttaatt---ttctcgttctttactttgaatgatagttaataatggttttccattgttgttcgaatttctacagGCACATGCTGCTTCAGCTGTGCTCAACTTCAGTGAGAACTGCACTCCAGATATTTTAACGCCATATTTAGATGGAATTGTTGGCAAATTACTAGTACTTC
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---cttttattctttgtagtcattatgatttatgattgaagtcatgctatttaaattaaataa-gctttctattgtaattattttcaaaatattgtctacacagGCACATGCTGCTTCAGCAGTTCTCAACTTCAGCGAGAACTGCACACCTGATATCTTAACGCCATACTTGGATGGAATAGTTAGCAAACTACTTGTACTTC
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G28950.2 (Glycine max), 3'ss of exon 4
agtggctcagtgctcaagattattt-tatttttaattttctcgttctttactttgaatga--tagttaataatggttttccattgttgttcgaatttctacagGCACATGCTGCTTCAGCTGTGCTCAACTTCAGTGAGAACTGCACTCCAGATATTTTAACGCCATATTTAGATGGAATTGTTGGCAAATTACTAGTACTTC
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ctattctttatagtcattatgatttataattgaagtcgtcttgctattttaattaaataagctatctggtgtaattattctcaaaatatt---gtctacacagGCACATGCTGCTTCAGCAGTTCTCAACTTCAGCGAGAACTGCACACCTGATATCTTAACGCCATACTTGGATGGGATAGTTAGCAAACTACTTGTACTTC
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G19820.1 (Arabidopsis thaliana), 3'ss of exon 2
agtggctcagtgctcaagattattttatttttaattttctcgttctttactttgaatgatagttaataatggttttccattgttgttcgaatttctacagGCACATGCTGCTTCAGCTGTGCTCAACTTCAGTGAGAACTGCACTCCAGATATTTTAACGCCATATTTAGATGGAATTGTTGGCAAATTACTAGTACTTC
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---------------------gtaagatcccctgtttctctgtgaatataatcttctaacactttctaaagcagtacc-ttgtgacctt--ttcatgtagGCTCATGCTGCTTCAGCAGTACTCAACTTCAGTGAAAATTGTACTCCTGAAATATTGTCACCTTATTTAGACGGAGTAGTGAGCAAGTTACTTGTGCTAC
upper sequence: Vv06s0004g00500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S207_33V6.1 (Physcomitrella patens), 3'ss of exon 3
agtggctcagtgctcaagattattttatttttaattttctcgttctt-tactttgaatgatagttaataatggttttccattgttgttcgaatttctacagGCACATGCTGCTTCAGCTGTGCTCAACTTCAGTGAGAACTGCACTCCAGATATTTTAACGCCATATTTAGATGGAATTGTTGGCAAATTACTAGTACTTC
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-gtggtcggatttattatgctacttaaatataatcactcaaatcgagatactgcggtaccatgttatcgatttcgtagtaatggtgtggatatgcgagcagGCACATGCTGCCGCTGCTGTGCTTAACTTCAGTGAGAGCTGCACGCCTGAGATCTTGACCCCATATTTAGATGGAGTCATCTCTAAGCTTTTGATTCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttactttgaatgatagttaataatggttttccattgttgttcgaatttctacagGCACATGCTGCTTCAGCTGTGCTCAACTTCAGTGAGAACTGCACTCCAGATATTTTAACGCCATATTTAGATGGAATTGTTGGCAAATTACTAGTACTTC
agttaat putative branch site (score: 4)
tttctac putative PPT
aatgatagttaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtggctcagtgctcaagattattttatttttaattttctcgttctttactttgaatgatagttaataatggttttccattgttgttcgaatttctacagGCACATGCTGCTTCAGCTGTGCTCAACTTCAGTGAGAACTGCACTCCAGATATTTTAACGCCATATTTAGATGGAATTGTTGGCAAATTACTAGTACTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttccatt