Sequence
atgc intronic sequence ATGC exonic sequence...ttattcaaatgtgtggtgaagtagatatcttcaatgataagatgattattgttctcacttttgcctgtttatgtaatgaatgaattggatgattttccagATATATGGCTCCAGAGTATGCATCAAGTGGCAAGTTGACGGAAAAATCCGATGTTTATTCATTTGGGGTTGTGCTTTTAGAACTGATTACAGGTCGTAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0083g00330.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g01040.1 (Oryza sativa), 3'ss of exon 5
ttattcaaatgtgtggtgaagtagatatcttcaatgataagatgattattgttctcacttttgcctgtttatgtaatgaatgaattggatgattttccagATATATGGCTCCAGAGTATGCATCAAGTGGCAAGTTGACGGAAAAATCCGATGTTTATTCATTTGGGGTTGTGCTTTTAGAACTGATTACAGGTCGTAAA
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---------------gttagtgaagtactggcaattttcagaagcagatctgtcgtgatcttacagagataattaataaa--attcgtttttccttgcagGTACATGGCTCCAGAGTATGCATCAAGTGGGAAATTGACTGAGAGATCTGATGTGTTCTCTTTTGGTGTTGTTCTCTTAGAGCTTATCACTGGTAGAAAA
upper sequence: Vv14s0083g00330.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G458548_T01 (Zea mays), 3'ss of exon 7
ttattcaaatgtgtggtgaagtag-atatcttcaatgataagatgattattgttctcacttttgcctgtttatgtaatgaatgaattggatgattttccagATATATGGCTCCAGAGTATGCATCAAGTGGCAAGTTGACGGAAAAATCCGATGTTTATTCATTTGGGGTTGTGCTTTTAGAACTGATTACAGGTCGTAAA
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--------gtgggtgatgagccgtcatatctcacaaagtacatcaatatatgacataaccatacggaattcatg--gtagacatcttgttt--cttttcagGTACATGGCTCCAGAGTATGCATCGAGTGGCAAACTGACTGAGAGATCAGATGTGTTCTCTTTTGGTGTAGTTTTGTTAGAGCTTATTACTGGCCGGAAA
upper sequence: Vv14s0083g00330.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G28600.1 (Glycine max), 3'ss of exon 6
--ttattcaaatgtgtggtgaagtagatatcttcaatgataagatgattattgttctcacttttgcctgtttatgtaatgaatgaattgga-tgattttccagATATATGGCTCCAGAGTATGCATCAAGTGGCAAGTTGACGGAAAAATCCGATGTTTATTCATTTGGGGTTGTGCTTTTAGAACTGATTACAGGTCGTAAA
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acatgtgaaacttaagagtcttttggattttgatatcactcaagtatgaactgttcctattctga---gtatacctaatgggaataatggtctgaattgccagGTACATGGCACCAGAATATGCGACAAGTGGGAAACTTACTGAAAAATCTGATGTATATTCTTTTGGGGTTGTGCTGTTGGAACTAATTACAGGTCGGAAG
upper sequence: Vv14s0083g00330.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G51520.1 (Glycine max), 3'ss of exon 6
-ttattcaaatgtgtg-gtgaagtagatatcttcaatgataagatgattattgttctcacttttgcctgtttatgtaatgaatgaattgga-tgattttccagATATATGGCTCCAGAGTATGCATCAAGTGGCAAGTTGACGGAAAAATCCGATGTTTATTCATTTGGGGTTGTGCTTTTAGAACTGATTACAGGTCGTAAA
| | || || | || | ||||| || | | | | ||||| | | | || || ||||| | ||| ||| || |||| || ||||| ||||| ||||| ||||||| || | || ||||| || ||||| ||||| ||||||||||||||||| || || ||||||||||| ||
ttcacatgaagctgagagtcttttggatattgataacactcaagtatgaactgttcctattctaa---gtatacctaatgggaataatggtctgaattgccagGTACATGGCACCAGAATATGCGACAAGTGGAAAACTTACTGAAAAGTCTGATGTATATTCTTTTGGGGTTGTGCTTTTGGAGCTAATTACAGGTCGGAAG
upper sequence: Vv14s0083g00330.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G20300.1 (Glycine max), 3'ss of exon 9
ttattcaaatgtgtggtgaagtagatatcttcaatgataa-gatgattattgt-tctcacttttgcctgtttatgtaatgaatgaattggatgattttccagATATATGGCTCCAGAGTATGCATCAAGTGGCAAGTTGACGGAAAAATCCGATGTTTATTCATTTGGGGTTGTGCTTTTAGAACTGATTACAGGTCGTAAA
||| || || ||||| | | | |||| ||| | | | | | || | ||| || || | | | || || ||||| || || || ||||| ||||| ||||||| || | || ||||| || ||||| ||||| ||||||||||||||||| || || ||||||||||| ||
-aatttcgat-tgacatgaagctgggagtcttttggatattgataacactcaagtatgaattgttcctattccaagtatacctaatgggaataatggtccagGTACATAGCACCAGAATATGCGACAAGTGGAAAACTTACTGAAAAGTCTGATGTATATTCTTTTGGGGTTGTGCTTTTGGAGCTAATTACAGGTCGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattgttctcacttttgcctgtttatgtaatgaatgaattggatgattttccagATATATGGCTCCAGAGTATGCATCAAGTGGCAAGTTGACGGAAAAATCCGATGTTTATTCATTTGGGGTTGTGCTTTTAGAACTGATTACAGGTCGTAAA
ttctcac putative branch site (score: 2)
ttttcc putative PPT
tttatgtaatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattcaaatgtgtggtgaagtagatatcttcaatgataagatgattattgttctcacttttgcctgtttatgtaatgaatgaattggatgattttccagATATATGGCTCCAGAGTATGCATCAAGTGGCAAGTTGACGGAAAAATCCGATGTTTATTCATTTGGGGTTGTGCTTTTAGAACTGATTACAGGTCGTAAA
- - - - - -tgtggtg
- - - - - - - - - - - - - - - - - -gataaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgaat