Sequence
atgc intronic sequence ATGC exonic sequencegtcagtctttttcttttttctccctgttttttccttctcttttagtgcttcaattaattttcctcctcgtgtgtcctatcatctcgagttttgattgttgaactagagaaatttgtgggtctggaaatgacagATATGCCCGGCGTGGTCTCTGTGTTTCCCAATTTAAAAAGAAGGCTGCACACCACTCATTCGTGGGATTTCATGGGTCTCGTGGGCGAAGAAACCATGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0044g01970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os06g41880.1 (Oryza sativa), 3'ss of exon 7
gtcagtctttttcttttttctccctgttttttccttctcttttagtgcttcaattaattttcctcctcgtgtgtcctatcatctcga-gttttgattgttgaactagagaaatttgtgggtctggaaatgacagATATGCCCGGCGTGGTCTCTGTGTTTCCCAATTTAAAAAGAAGGCTGCACACCACTCATTCGTGGGATTTCATGGGTCTCGTGGGCGAAGAAACCATGGA
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-------------------------gtaatttccttgtatatgcatggctt--ctgatgtctttagcatcctgacacgtgatcctggtgtgatgatgactgaa--agctaactctgctgcac--acttctgcagATATGCCTGGTGTCATCTCAGTGTTCCCAAACACAAAGAGGAGCCTCCACACCACTCATTCATGGGATTTCATGGGCTTGTCCGTCGATGCAGCGGCTGA
upper sequence: Vv04s0044g01970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G09420.1 (Glycine max), 3'ss of exon 1
gtcagtctttttcttttttctccctgttttttccttctcttttagtgcttcaattaattttcctcctcgtgtgtcctatcatctcgagttttgattgttgaactagagaaatttgtgggtctggaaatga-cagATATGCCCGGCGTGGTCTCTGTGTTTCCCAATTTAAAAAGAAGGCTGCACACCACTCATTCGTGGGATTTCATGGGTCTCGTGGGCGAAGAAACCATGGA
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gtcagtgaaatttcaccccatttcttttctctttttttttgcaaataataaacacaatgatttcattcactccttaaactttaatatttataggctcttgtaatttcttttttcatg--ttcaaatttgatcagAAATGCCAGGGGTGGTATCTGTTTTTCCCAATGCTAAAAGAAAGCTTCACACCACTCATTCATGGGATTTCATAGGACTTTTGGGCAATGAATCAATGGA
upper sequence: Vv04s0044g01970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA01G36000.1 (Glycine max), 3'ss of exon 3
----gtcagtctttttcttttttctccctgttttttccttctcttttagtgcttcaattaattttcctcctcgtgtgtcctatcatctcgagttt--tgattgttg--aactagagaaatttgtgggtctggaaatga-cagATATGCCCGGCGTGGTCTCTGTGTTTCCCAATTTAAAAAGAAGGCTGCACACCACTCATTCGTGGGATTTCATGGGTCTCGTGGGCGAAGAAACCATGGA
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gtcagtgaaattctccccatttctttactctttttctttgcaaataaataaggtcaatgttcattcattcactcactccttaaactttaacatttataggctattgtaattttattttattttcatgttcaaatttgatcagAAATGCCAGGAGTGGTATCTGTTTTCCCCAATTCTAAAAGAAAGCTGCACACCACTCATTCATGGGACTTCATAGGACTTTTGGACAACGAAAGCATGGA
upper sequence: Vv04s0044g01970.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G22010.1 (Glycine max), 3'ss of exon 2
gtcagtctttttcttttttctccctgttttttccttctcttttagtgcttcaattaattttcctcctcgtgtgtcctatcatctcgagttttgattgttgaactagagaaatttgtgggtctggaaatgac-agATATGCCCGGCGTGGTCTCTGTGTTTCCCAATTTAAAAAGAAGGCTGCACACCACTCATTCGTGGGATTTCATGGGTCTCGTGGGCGAAGAAACCATGGA
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gtatgtcaggaagtttccggctgctattttctttttttctttttctcaacttctcagttttcacctcagaacttgttttaataatggttttttgttttttgact---------tgtgtgcccaaatttaaccagAAATGCCAGGAGTGGTTTCTGTTTTTCCCAATTCTAAAAGAAAGTTGCACACAACTCACTCATGGGATTTCATGGGACTTCTGGATGACCAAACCATGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatctcgagttttgattgttgaactagagaaatttgtgggtctggaaatgacagATATGCCCGGCGTGGTCTCTGTGTTTCCCAATTTAAAAAGAAGGCTGCACACCACTCATTCGTGGGATTTCATGGGTCTCGTGGGCGAAGAAACCATGGA
ttttgat putative branch site (score: 4)
ttttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtctttttcttttttctccctgttttttccttctcttttagtgcttcaattaattttcctcctcgtgtgtcctatcatctcgagttttgattgttgaactagagaaatttgtgggtctggaaatgacagATATGCCCGGCGTGGTCTCTGTGTTTCCCAATTTAAAAAGAAGGCTGCACACCACTCATTCGTGGGATTTCATGGGTCTCGTGGGCGAAGAAACCATGGA
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