Sequence
atgc intronic sequence ATGC exonic sequence...tcagttcaaacgtgtgattttttcatgtattaattcattgttgaaatatgcctttggtttatgtatgttttgttgctgatgtatgttctccttgttgcagAACTTTGTAGGTTTGTCTGTATCCGATGGTTACATTGCTACGGGCTCAGAAGCAAATGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0014g02660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g52640.3 (Oryza sativa), 3'ss of exon 4
--tcagttcaaacgtgtgatt-ttttcatgtattaattcattgttgaaatatgcctttggtttatgtatgttttgttgctgatgtatgttctccttgttgcagAACTTTGTAGGTTTGTCTGTATCCGATGGTTACATTGCTACGGGCTCAGAAGCAAATGAG
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ttctagtatagccctttcttcatattcctttagttgctttcaggcaaaagaatactttgttttatgcttaattta--gttatttcttgaacctgttga-acagAATTTTGTTGGACTTTCTATATCTGATGGTTACATTGCTACTGGCTCAGAGACAAATGAG
upper sequence: Vv19s0014g02660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G061602_T01 (Zea mays), 3'ss of exon 5
tcagttcaaacgtgtgatttttt--catgtattaattcat-tgttgaaatatgcctttggtttatgtatgttttgttgctgatgtatgttct---ccttgttgcagAACTTTGTAGGTTTGTCTGTATCCGATGGTTACATTGCTACGGGCTCAGAAGCAAATGAG
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-----tgcaacatagccttttgtatagtgagttgctttctgtgctgaaaggcactgatattttcattgggtgat-cgatttacttattttttaaaccttttgccagAACTTCGTTGGTCTTTCCATATCTGATGGTTACATTGCTACTGGCTCTGAAACAAATGAG
upper sequence: Vv19s0014g02660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G37080.1 (Glycine max), 3'ss of exon 7
tcagttcaaacgtgtgat--tttttcatgtattaattcat-tgttgaaatatgcctttggtttatgtatgttttgttgctgatgtatgttctccttgttgcagAACTTTGTAGGTTTGTCTGTATCCGATGGTTACATTGCTACGGGCTCAGAAGCAAATGAG
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---atgcaaattttgggccatttgtaattaatttctgcaaatttttatgtattgtatttaaatttctgcggcaatatgatgatgcaccttcgctttgttgcagAACTTCGTGGGGTTGTCTGTATCTGATGGTTACATTGCTACTG-----------------
upper sequence: Vv19s0014g02660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G25240.1 (Glycine max), 3'ss of exon 7
tcagttcaaacgtgtgat-tttttcatgtattaattcattgttgaaatatgcctttggtttatgtatgttttgttgctgatgtatgttctccttgttgcagAACTTTGTAGGTTTGTCTGTATCCGATGGTTACATTGCTACGGGCTCAGAAGCAAATGAG---------------------
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-tatgcaaaatttgggccatttgtaattaattactgcaaattttatatatggtatttaaatttctgcggcaatatgatgatgcaccttccttttgttgcagAATTTCGTGGGGTTGTCTGTATCTGATGGTTACATTGCTACTGGTTCAGAGACAAACGAGGCATTTCATTTTTCCTCTCTC
upper sequence: Vv19s0014g02660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G35190.1 (Glycine max), 3'ss of exon 10
tcagttcaaacgtg--tgattttttcatgtattaattcattgttgaaatatgcctttggtttat-gtatgttttgttgctgatgtatgttctccttgttgcagAACTTTGTAGGTTTGTCTGTATCCGATGGTTACATTGCTACGGGCTCAGAAGCAAATGAG
| |||| | |||||| | | || || | | | |||| ||| ||| | | |||||||| || ||| | || |||||||||||||| || || || ||||| |||||||||||||| || || ||||| ||||||||
-aggctcaattattattgatttccatacatttttatgtaa-gccatttttcaattttgaggtatcatataatatcctgctgatgcatcttc-ctttcttgcagAACTTTGTGGGGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAG
upper sequence: Vv19s0014g02660.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G35320.1 (Glycine max), 3'ss of exon 7
------tcagt-tcaaacgtgtgattttttcatgtattaattcattgttgaaatatgcctttggtttatgtatgttttgttgctgatgtatgttctcct-tgttgcagAACTTTGTAGGTTTGTCTGTATCCGATGGTTACATTGCTACGGGCTCAGAAGCAAATGAG
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gctcatttattatcaatttccaaacatttttatgta---agccatttttcaattttg-----aggaaccatagaatatcctgctgatgcatcttcctttgtcttgcagAACTTTGTGGGGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgcctttggtttatgtatgttttgttgctgatgtatgttctccttgttgcagAACTTTGTAGGTTTGTCTGTATCCGATGGTTACATTGCTACGGGCTCAGAAGCAAATGAG
tgctgat putative branch site (score: 3)
ttctccttgtt putative PPT
tttatgtatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcagttcaaacgtgtgattttttcatgtattaattcattgttgaaatatgcctttggtttatgtatgttttgttgctgatgtatgttctccttgttgcagAACTTTGTAGGTTTGTCTGTATCCGATGGTTACATTGCTACGGGCTCAGAAGCAAATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - tcatgta
- - - - - - - - - - - - - - - - - - - - -tgaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgct