Sequence
atgc intronic sequence ATGC exonic sequence...gtttgctatagttttttcttaatttaataaatgcttgcaaattgagttacactgctacctccatggattgatcattgatattaaccagtgtattctgcagGACTACACTTGGCTTTTGGGCAGGCCATCGCAATTCAAAAATAAGAGTTATACTAGCACGTATTTGGGAGAATGACACAGAGCTTGATATAAAAAACAAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv03s0038g00680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g43160.1 (Oryza sativa), 3'ss of exon 2
gtttgctatagttttttcttaatttaataaatgc-ttgcaaattgagttacactgctacctccatggattgatcattgatattaaccagtgtattctgcagGACTACACTTGGCTTTTGGGCAGGCCATCGCAATTCAAAAATAAGAGTTATACTAGCACGTATTTGGGAGAATGACACAGAGCTTGATATAAAAAACAAC
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-gtcgaaatgagactttctaatttctgaaaatgcattatagttttgaacaagatgctgaaaatgccc-ttggtgttttttttttaaaaaaatggaa-acagGACAATACTTGGTTTTTGGGCTGGCCATCGCAATTCCAAAATAAGAGTTATTTTAGCACGAATCTGGGAGAATGATACTGAGCTTGCTATCAGCAACAAC
upper sequence: Vv03s0038g00680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g09430.1 (Oryza sativa), 3'ss of exon 2
---gtttgctatagtttt---ttcttaatttaataaatgcttgcaaattgagttacactgctacctccatggattgatcattgatattaaccagtgtattctgcagGACTACACTTGGCTTTTGGGCAGGCCATCGCAATTCAAAAATAAGAGTTATACTAGCACGTATTTGGGAGAATGACACAGAGCTTGATATAAAAAACAAC
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gaaagttgtcatgaccataaatttgtgacgatgctatggtttgaacatctatttgcactcctacaaa-atttgtcttttgttgcttttg-ccatggca----acagGACAATCCTTGGATTTTGGGCTGGCCATCGCAATTCTAAAATAAGAGTCATTTTGGCACAAGTCTGGGAGAATGATACAGAGCTTGCTATCAGTAACAAT
upper sequence: Vv03s0038g00680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G018962_T01 (Zea mays), 3'ss of exon 2
gtttgctatagttttttcttaatttaataaatgcttgcaaattgagttacactgctacctc--catggattgatcattgatattaaccagtgtattctgcagGACTACACTTGGCTTTTGGGCAGGCCATCGCAATTCAAAAATAAGAGTTATACTAGCACGTATTTGGGAGAATGACACAGAGCTTGATATAAAAAACAAC
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--cagaaaaagaactgaagggactacatcataaactatatttggtcttagcctaatagcctattactaattatattttattattgttttttaattcaatcagGACAACTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAGCTTGCTATCAGCAACAAC
upper sequence: Vv03s0038g00680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G000976_T01 (Zea mays), 3'ss of exon 2
--gtttgctatagttttttcttaatttaataaatgcttgcaaattgagttacactgctacctccatggattgatcattgatattaaccagtgtattctgcagGACTACACTTGGCTTTTGGGCAGGCCATCGCAATTCAAAAATAAGAGTTATACTAGCACGTATTTGGGAGAATGACACAGAGCTTGATATAAAAAACAAC
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atacacctcagaaaaagaactagagggactacatcgta--aactctatttgctcttagcctattactaattatattttattattgttttgcaattcaaccagGGTAATTCTTGGCTTTTGGGCTGGCCATCGCAATTCCAAAATAAGGGTTATCCTAGCACGAGTTTGGGAGAATGACACAGAACTTGCTATCAGCAACAAT
upper sequence: Vv03s0038g00680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G02630.1 (Glycine max), 3'ss of exon 3
-gtttgctatagttttttcttaatttaataaatgcttgcaaattgagttacactgctacctccatggattgatcattgatattaaccagtgtattctgcagGACTACACTTGGCTTTTGGGCAGGCCATCGCAATTCAAAAATAAGAGTTATACTAGCACGTATTTGGGAGAATGACACAGAGCTTGATATAAAAAACAAC
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atgatgcaataatatgtagtttgatctgtaagatcaacagacaaggattctacttgcatatttattgattctgaaaatttgataaatt-tgtgctttgcagAACTACTCTTGGATTTTGGGCCGGTCATCGTAACTCTAAAATCAGAGTTATTCTTGCACGTGTGTGGGAAAATGACACAGAACTTGATATTTCAAACAAT
upper sequence: Vv03s0038g00680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G33330.1 (Glycine max), 3'ss of exon 3
gtttgctatagttttttcttaatttaataaatgcttgcaaattgagttacactgctacctccatggattgatcattgatattaaccagtgta----ttctgcagGACTACACTTGGCTTTTGGGCAGGCCATCGCAATTCAAAAATAAGAGTTATACTAGCACGTATTTGGGAGAATGACACAGAGCTTGATATAAAAAACAAC
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actgatgatggtgcaatgata-cgtagtttgttctgtaagatcaatagacaatggt---tctacttattgattctgaaaatttgataattttatgcttttgcagGACTACTCTTGGATTCTGGGCTGGTCATCGGAACTCTAAAATCAGAGTTATTCTTGCACGTGTGTGGGAAAATGACACAGAACTTGATATTTCAAACAAT
upper sequence: Vv03s0038g00680.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G38040.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgctatagttttttcttaatttaataaatgcttgcaaatt---gagttacactgctacctccatggattgatcattgatattaaccagtgtattctgcagGACTACACTTGGCTTTTGGGCAGGCCATCGCAATTCAAAAATAAGAGTTATACTAGCACGTATTTGGGAGAATGACACAGAGCTTGATATAAAAAACAAC
|| ||| | | | | | || || | | || ||||| | || | ||| ||| | | | | | |||| ||| | | |||||| || ||||| |||||||| || ||||| ||||| || ||| | |||||||| || | | | ||||| || ||||||||||||||||| |||||||
gtaaactaagtcctccctcttttattaggaactctggtagatcctggagttgtattgttggctcaatg---ttactaatactgttaaatggtg-gtgttacagGACGACTCTTGGTTTTTGGGCTGGTCATCGAAATTCTAAGATACGGGTTATACTTGCTCATGTGTGGGAAAACGACACAGAGCTTGATATTTCAAACAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttacactgctacctccatggattgatcattgatattaaccagtgtattctgcagGACTACACTTGGCTTTTGGGCAGGCCATCGCAATTCAAAAATAAGAGTTATACTAGCACGTATTTGGGAGAATGACACAGAGCTTGATATAAAAAACAAC
tattaac putative branch site (score: 1)
atcattgatattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgctatagttttttcttaatttaataaatgcttgcaaattgagttacactgctacctccatggattgatcattgatattaaccagtgtattctgcagGACTACACTTGGCTTTTGGGCAGGCCATCGCAATTCAAAAATAAGAGTTATACTAGCACGTATTTGGGAGAATGACACAGAGCTTGATATAAAAAACAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - -aataaat
- - - - - - - - - - - - - - - - gcttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggattg