Sequence
atgc intronic sequence ATGC exonic sequencegtagcaagtcagtgctgctttatgtagctcctttttaattttttttaatgtgcataagggaaagttggaaagattgtatatagttacttagagctttatgaatgttgatttaaccttattgtctttattagGTAATGGAGAAGCTTGTAGACATTGTGCATTTCTTACATTTGGAGATACATGATGCCTTTGCTACTGCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 6
--------------gtagca-agtcagtgct----gctttatgtagctcctttttaattttttttaatgtgcataagggaaagttggaaagattg--tatatagtt-acttaga----gctttatgaa----tgttgatttaacctta-----------ttgtctttattagGTAATGGAGAAGCTTGTAGACATTGTGCATTTCTTACATTTGGAGATACATGATGCCTTTGCTACTGCTG
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gttggtcattggttttattatagttcttgctatgagcaacatatagctatatggaagcatgctcacat-tgtcaattgtgaagttccactcattgattgtccaattgaactagaattcgttttgtgcaatcctgttcgtctaatttgaaaaaaaaacatttatttttcctagGTCATGGAAAAGCTCGTAGACATTGTGCATTTCTTACATTTGGAGATCCATAATGCCTTTGGGCGCTCAG
upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 7
------------------------------------gtagcaagtcagtgc-tgctttatgtagctcctttttaatttttttta-------atgtgcataagggaaagttggaa-agattgtatatagttacttagag------ctttatgaatgttgatttaaccttattgtctttattagGTAATGGAGAAGCTTGTAGACATTGTGCATTTCTTACATTTGGAGATACATGATGCCTTTGCTACTGCTG
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gtttgtagtagtttctttgtttataaaatgttggttcaaggaaggcattgggtactacaacgagtacatgtttgaacacaccgaccgcactacgcacatattctattgtcatatcattctttaaatttttagtaaaaaaaaccattctttaaatgctgaaa-aatattatgcttttccacagGTGATGGAAAAGCTCGTAGACATTGTTCATTTCTTACATTTGGAGATCAATAATGCCTTTGGCCTCGCTG
upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G148773_T02 (Zea mays), 3'ss of exon 6
gtagcaagtcagtgctgctttatgtagctcctttttaattttttttaatgtgcataagggaaagttggaaagattgtatatagttacttagagctttatgaatgttgatttaaccttattgtctttattagGTAATGGAGAAGCTTGTAGACATTGTGCATTTCTTACATTTGGAGATACATGATGCCTTTGCTACTGCTG
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-------------------------------tttttaccatataataaacggtgtgctgtcagcaacctgatgctctaggaatgcatccaatcctattctactatttcaaaaaaatatttatttctcctagGTCATGGGAAAGCTTGTGGACATTGTGCACTTCTTACATTTGGAGATCCATAATGCATTTGGGCTTTCAG
upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G046846_T01 (Zea mays), 3'ss of exon 7
gtagcaagtcagtgctgctttatgtagctcctttttaattttttttaatgtgcataagggaaagttggaaagattgtatatagttacttagagctttatgaatgttgatttaaccttattgtctttattagGTAATGGAGAAGCTTGTAGACATTGTGCATTTCTTACATTTGGAGATACATGATGCCTTTGCTACTGCTG
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------------------------cggtt--ttgaccatataatagactatgcactgtcagcaacttgtag--ctctaggaaaacattcaatcctgt-tgattcaaaaaataatatt--tgtttctcctagGTCATGGGAAAGCTTGTGGACATTGTGCACTTCTTACATTTGGAGATCCATAATGTATTTGGGCGTTCAG
upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G077621_T01 (Zea mays), 3'ss of exon 6
----------------gtagcaagtcagtgctgctttatgtagctccttttta--attttttttaatgtgcataagggaaagttggaa-------agattgtatatagttacttagagctt--tatgaatgt-------tgatttaaccttat-tgtctttattagGTAATGGAGAAGCTTGTAGACATTGTGCATTTCTTACATTTGGAGATACATGATGCCTTTGCTACTGCTG
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gttggtatgaggtgcctttgcacaa-aatgctgacaaggggaagacatttttaggatattgattactgtgtattaaacattttaggaccctgctcaagctgcaagcagccaagcatcctttcctatcattgtatttcaaggtttaaatattacatttttttctcagGTGGTGGTAAAGCTTGTAGATATTGTCCACTTCTTACATTTGGAGATATATAACGCCTTCGGTCATCCTG
upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 4
----------------------------gtagca--agtcagtgctgctttatgtag-ctcctttttaattttttttaatgtgcataagggaaagttggaaagattgtatatagttacttagagctttatgaatgttgatttaaccttattgtctttatt----agGTAATGGAGAAGCTTGTAGACATTGTGCATTTCTTACATTTGGAGATACATGATGCCTTTGCTACTGCTG
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gttggtatgaggtgccttgcacaaaaatgtcatactacaaaatgctggcaagggaagacatttttaggatattgatcaccaaacattttaggaccctgctcaaactgcaagcatcctttcctatccatcttatttccaatgttgaactattacattttttgctcagGTGATGGTAAAGCTTGTAGATATTGTCCACTTCTTATATTTGGAGATATATAATGCCTTCGGTCGTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatagttacttagagctttatgaatgttgatttaaccttattgtctttattagGTAATGGAGAAGCTTGTAGACATTGTGCATTTCTTACATTTGGAGATACATGATGCCTTTGCTACTGCTG
atttaac putative branch site (score: 3)
ttgtcttt putative PPT
ttattgtctttatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcaagtcagtgctgctttatgtagctcctttttaattttttttaatgtgcataagggaaagttggaaagattgtatatagttacttagagctttatgaatgttgatttaaccttattgtctttattagGTAATGGAGAAGCTTGTAGACATTGTGCATTTCTTACATTTGGAGATACATGATGCCTTTGCTACTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT