Sequence
atgc intronic sequence ATGC exonic sequencegtagcgccttgctccttcatgctttttttgagtcaaattaatgcttaatacttttgggtgttaaaaacttgtttgaatgcctctagagttgatgcctttgaaacacagGTAGGAGATGCAGGTCCTGCTCTTGACATGATGGCTGTGATGTTAGAAAACATCTCAAACATTACAGTTATGGCTAGAACCATGGTTTCTGCTGTTTACC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0064g00590.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os02g05040.1 (Oryza sativa), 3'ss of exon 9
-------------------------------------------------------------------------------gtagcgccttgctccttcatgctttttt--tgagtcaaattaatgcttaatacttttgggtgttaaaaacttgtttgaatgcctctagagttgatgcctttgaaacacagGTAGGAGATGCAGGTCCTGCTCTTGACATGATGGCTGTGATGTTAGAAAACATCTCAAACATTACAGTTATGGCTAGAACCATGGTTTCTGCTGTTTACC
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gtcctttactcttgaactgaaacttcttttgtgaattgtgacattctgcttgctgtactttgtcttcatcccttacagaattccaatcagatgcttcctagtgtggtaataggctgtataaat-ttcattgttattggattataatggtaggaacatacgccttacta--tgttggtattattacacagGTTGGTGATGCTGGACCTGTTCTTGACATGATGTCTGTGATGCTAGAGAACATCTCCCGCACTCCCCTTGTTGCTATAGCAACCACATCTGCCGTTTATC
upper sequence: Vv13s0064g00590.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G168449_T01 (Zea mays), 3'ss of exon 9
-------------------------------------------------------------------------------gtagcgccttgctccttcatgctttttttgagtcaaattaatgcttaatacttttgggtgtta-aaaacttgtttg-aatgcctctagagttgat---gcctttgaaaca-----cagGTAGGAGATGCAGGTCCTGCTCTTGACATGATGGCTGTGATGTTAGAAAACATCTCAAACATTACAGTTATGGCTAGAACCATGGTTTCTGCTGTTTACC
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gtgcatttgccattttctcacttgaaattttatgttaccttcatgcacaatataatggtgctacttcagtaaatctgtttttttaactgattcctccagtcctccttgcagtttggtctgtataatatgttgattagtttcatatgatctacacgcaatgcatataaggcttatcaagactttgttgtgttgatcagGTGTCTGATGCTGGGCCAGTTCTTGACATGATGGCTGTTATGCTAGAAAACATTGCGAGCACTCCTGTTGTAGCTAGATCAACTGCAGCTGCTGTTTATC
upper sequence: Vv13s0064g00590.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G431573_T02 (Zea mays), 3'ss of exon 1
gtagcgccttgctccttcatgctttttttgagtcaaattaatgcttaatacttttgggtgttaaaaacttgtttg-aatgcctctagagttgatgcctttgaaacacagGTAGGAGATGCAGGTCCTGCTCTTGACATGATGGCTGTGATGTTAGAAAACATCTCAAACATTACAGTTATGGCTAGAACCATGGTTTCTGCTGTTTACC
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--------ggtcatccttacattttggtctgtataatatgttgattggttccatgtgatctacacacaatgcatataaggattatcaaggctttgttgtgttgat-cagGTGTCTGATGCTGGGCCAGTTCTTGACATGATGGCTGTTATGCTAGAAAACATTGCGAGCACTCCTGTTGTAGCTAGATCAACTGCAGCTGCTGTTTATC
upper sequence: Vv13s0064g00590.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G36260.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------------gtagcgccttgctcctt---catgctttttttgagtcaaattaatgcttaatacttttgggtgttaaaaacttgtttgaatgcctctagagttgatgcctttgaaac---acagGTAGGAGATGCAGGTCCTGCTCTTGACATGATGGCTGTGATGTTAGAAAACATCTCAAACATTACAGTTATGGCTAGAACCATGGTTTCTGCTGTTTACC
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gtgacaacaaattcccccctaccgaagatgattttagttaatagtgtaacaaatcagataaacatatagatccatatgcacatttaattttaaacaaaccagaaacttggatgtttaattttaaatgatctaat---attcttttgtgcttactgactacaatattttgcagATTGCAGATGCAGGTCCTGTTATTGATACCATGGCTGTGTTGTTGGAAAACATGTCTAATATTACTGTTATGGCGAGAACCTTGATTGCTGCAGTCTATA
upper sequence: Vv13s0064g00590.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G01070.1 (Glycine max), 3'ss of exon 10
-------------------------gtagcgccttgctccttcatgctttttttgagtcaaa----ttaatgctta-atacttttgggtgttaaa----aacttgtttga-atgcctctagagttgatgcctttgaaa---cacagGTAGGAGATGCAGGTCCTGCTCTTGACATGATGGCTGTGATGTTAGAAAACATCTCAAACATTACAGTTATGGCTAGAACCATGGTTTCTGCTGTTTACC
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gtgacaacaaattccccactaccgaagatgattttagttaatagtgtaacaaatcagataaacatatagatctgtatgcatatttggatgtttaattttaagtgatctaatattcttttgtgcttactggctataatattttgcagATTGCAGATGCAGGTCCTGTTATTGATACCATGGCTGTGTTGTTGGAAAACATGTCTAATATTACTGTTATGGCCAGAACCTTGATTGCTGCAGTCTATA
upper sequence: Vv13s0064g00590.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G21080.1 (Arabidopsis thaliana), 3'ss of exon 9
gtagcgccttgctccttcatgctttttttgagtcaaattaatgcttaatacttttgggtgttaaaaacttgtttgaatgcctctagagttgat-gcctt-tgaaacacagGTAGGAGATGCAGGTCCTGCTCTTGACATGATGGCTGTGATGTTAGAAAACATCTCAAACATTACAGTTATGGCTAGAACCATGGTTTCTGCTGTTTACC
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---------------gtaacccctattttagccccaagaagctctaaaagctatacaattttcata-tgtacaaaaatgaataaatcgctgattgtctcacgaaatgtagGTAGGAGATGCAGGTCCTATCCTTGACATAATGGCTGTCATGTTGGAAAGCATGTCAAATATTACAGTCATGGCAAGAACCCTAATCGCCGCAGTTTTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgggtgttaaaaacttgtttgaatgcctctagagttgatgcctttgaaacacagGTAGGAGATGCAGGTCCTGCTCTTGACATGATGGCTGTGATGTTAGAAAACATCTCAAACATTACAGTTATGGCTAGAACCATGGTTTCTGCTGTTTACC
agttgat putative branch site (score: 5)
tgccttt CT-rich tract
ttaaaaacttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcgccttgctccttcatgctttttttgagtcaaattaatgcttaatacttttgggtgttaaaaacttgtttgaatgcctctagagttgatgcctttgaaacacagGTAGGAGATGCAGGTCCTGCTCTTGACATGATGGCTGTGATGTTAGAAAACATCTCAAACATTACAGTTATGGCTAGAACCATGGTTTCTGCTGTTTACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT