Sequence
atgc intronic sequence ATGC exonic sequencegtgctgatgctcatccaccaggcaaccaccctatcaaacccccatattttctttgatcaatttaattaaattaataatcagagttttcgagttgtattcctgtgcggaatagtcacagCATGTTGTGGTGTTGCTGCAGTTCATCACCTTTGGATTCGCATGCACACCTCTGTACTTCGTGTGGGAGAAAGCGATAGGGATGCACGAGTGCAAGAGCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 6
gtgctgatgctcatccaccaggcaaccaccctatcaaacccccatattttctttgatcaatt-taattaaattaataatcagagttttcgagttgtattcctgtgcggaatagtca--cagCATGTTGTGGTGTTGCTGCAGTTCATCACCTTTGGATTCGCATGCACACCTCTGTACTTCGTGTGGGAGAAAGCGATAGGGATGCACGAGTGCAAGAGCC---------------------
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------------------------------gtatataattat-atatatacgtacaacgatgatagtgagaaaaataacacga----tcgaattaatccctagctaataaagaccaataatcgccatgcatcatatgtgcagTTCATCACGTTCGGGTTCGCGTGCACGCCACTCTACTTCGTGTGGGAGAAGCTGATCGGCGTGCACGAGACGGGGAGCGTGGCCCTGCGCGCCGCCGCGC
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 6
gtgctgatgctcatccaccaggcaaccaccctatcaaacccccatattttctttgatcaatttaattaaattaataatcaga---gttttcgagttgtattcctgtgcggaat--agtcacagCATGTTGTGGTGTTGCTGCAGTTCATCACCTTTGGATTCGCATGCACACCTCTGTACTTCGTGTGGGAGAAAGCGATAGGGATGCACGAGTGCAAGAGCC---------------------
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-------------gcaagcaagcatatata-tatgctatatatacaattattacattacgattaataatatgcatgcttgcatgcagttaatatatatactccattgaatgattaaattaactaatattgggatggaattgcagTTTATAACATTCGGGTTTGCATGCACCCCATTATACTTCGTGTGGGAGAAAGCAATAGGGATGCACGAGTGCAAGAGCCTATGCAAGCGTGCATTGGTGA
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 6
---gtgctgatgctcatccaccaggcaaccaccctatcaaacccccatattttctttgatcaatttaattaaattaataatcagagttttcgagttgtattc---ctgtgcggaatagtcacagCA-TGTTGTGG-TGTTGCTGCAGTTCATCACCTTTGGATTCGCATGCACACCTCTGTACTTCGTGTGGGAGAAAGCGATAGGGATGCACGAGTGCAAGAGCC---------------------
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gtcattttaatgctcatccaccaggcaagcatgcc------cattcatttttcatctatataat---attacatatgtattacaatgccttttgttgtatcctaattggattgaatgattaaattaatattgggaatttcattgcagTTTATAACATTCGGGTTTGCATGCACCCCATTATATTTCGTGTGGGAGAAAGCAATAGGGATGCACGAGTGCAAGAGCCTATGCAAGCGTGCATTGGTGA
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 6
gtgctgatgctcatccaccaggcaaccaccctatcaaacccccatattttctttgatcaatttaattaaattaataatcagagttttcgagttgtattcctgtgcggaatagtcacagCATGTTGTGGTGTTGC-TGCAGTTCATCACCTTTGGATTCGCATGCACACCTCTGTACTTCGTGTGGGAGAAAGCGATAGGGATGCACGAGTGCAAGAGCC---------------------
|| | || | | || | || | | | || ||| | | |||| | ||||| | | || | | || ||| |||| ||||||| || || ||||| || |||||||| || || || || |||||||||||||| |||||||| |||||||| | |||||
-------------------------gtacgtacttaatactataagttactagtaataactgtttcattatccatatttatcatttttca--tgtatagtaattgaaattaattt--ggatattgc----ttgcatgcagTTTATAACATTTGGGTTTGCATGCACGCCACTATATTTGGTGTGGGAGAAAGCAATAGGGATACACGAGTGTAGGAGCCTGTGCAAGCGTGCTTTGGCGA
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ36050 (Selaginella moellendorffii), 3'ss of exon 6
gtgctgatgctcatccaccaggcaaccaccctatcaaacccccatattttctttgatcaatttaattaaattaataatcagagttttcgagttgtattcctgtgcggaatagtcacagCATGTTGTGGTGTTGCTGCAGTTCATCACCTTTGGATTCGCATGCACACCTCTGTACTTCGTGTGGGAGAAAGCGATAGGGATGCACG--AGTGCAAGAGCC-------------------
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----------------------------------------------------gtaagaaagatcatcgttcttctcactatgaactatgatcttcgttcctggagctaaacttcccatcgtctcg-----------cagTTTATTACGTTTGGATTCGCTTGCACGCCCTTGTACTTCGTGTGGGAGAAGATAATTGGCGTTCATAGAAGTCCAAGGTTCCTACTTCGAGCAGCTGCCC
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 6
---gtgctgatgctcatccaccaggcaaccacccta------tcaaaccc--ccatattttctttgatcaatttaatt-----------------aaattaataatcagagttttcgagttgtattcctgtgcggaatagtcacagCATGTTGTGGTGTTGCTGCAGTTCATCACCTTTGGATTCGCATGCACACCTCTGTACTTCGTGTGGGAGAAAGCGATAGGGATGCACGAGTGCAAGAGCC---------------------
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gtcattctcatgctcatccatcaggcaagcttttttctttcctcgagctcttctttacttcttcttcttcttcttcttcttcttcttcccgagaagaaagaaagaggaaagtttgccaagtttttctttcttctgattcctcgattctcgcgatggaaa----acagTTCATCACGTTTGGATTCGCATGCACGCCGCTGTACATCGTGTGGGAGAAGATTCTGGGCATTCACAAGACGGCCAATCTCCCCGTGCGAGCGCTGGCCA
upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 6
gtgctgatgctcatccaccaggcaaccacccta------tcaaacccccatattttctttgatcaatttaatt-------aaattaataatcagagttttcgagttgtattcctgtgcggaatagtcacagCATGTTGTGGTGTTGCTGCAGTTCATCACCTTTGGATTCGCATGCACACCTCTGTACTTCGTGTGGGAGAAAGCGATAGGGATGCACGAGTGCAAGAGCC---------------------
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gttctcatgctcatccatcaggcaagcttttttctttcctcgagctcttctttacttcttcttcttcttcttcccgagaagaaagaaagaggaaagtttgccaagtttttctttcttctgattcctcgattctcgcgatggaaa----acagTTCATCACGTTTGGATTCGCATGCACGCCGCTGTACATCGTGTGGGAGAAGATTCTGGGCATTCACAAGACGGCCAATCTCCCCGTGCGAGCGCTGGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattaaattaataatcagagttttcgagttgtattcctgtgcggaatagtcacagCATGTTGTGGTGTTGCTGCAGTTCATCACCTTTGGATTCGCATGCACACCTCTGTACTTCGTGTGGGAGAAAGCGATAGGGATGCACGAGTGCAAGAGCC
aattaat putative branch site (score: 3)
aattaataatcaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctgatgctcatccaccaggcaaccaccctatcaaacccccatattttctttgatcaatttaattaaattaataatcagagttttcgagttgtattcctgtgcggaatagtcacagCATGTTGTGGTGTTGCTGCAGTTCATCACCTTTGGATTCGCATGCACACCTCTGTACTTCGTGTGGGAGAAAGCGATAGGGATGCACGAGTGCAAGAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA