Sequence
atgc intronic sequence ATGC exonic sequence...gttgaggctgagcagtatagacaaacaaattttccttttattaagtttattttattcaactatcttgttaatgttgatcaccaacatttgctaaatgcagTAACACCTCGTGTTGGAATCATAATGGGCTCTGATTCAGATCTTCCTGTTATGAAGGATGCTGCAGGGATTTTGAATCACTTTGGTGTGCCTCATGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0081g00240.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g10280.1 (Oryza sativa), 3'ss of exon 11
gttgaggctgagcagtatagac----aaacaaattttccttttattaagt----ttattttattca-actatcttgttaatgttgatcaccaacatt-tgctaaatgcagTAACACCTCGTGTTGGAATCATAATGGGCTCTGATTCAGATCTTCCTGTTATGAAGGATGCTGCAGGGATTTTGAATCACTTTGGTGTGCCTCATGAG
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----atgctttgttgtgccaccttctgacccactttactttctaaaaagtcctttcatgttcttcataccaatgggctgacaaagtataataatattgtactagTTGCAGTTAAACCTCGTGCTGCAATAATAATGGGTTCTGATTCTGATCTTCCTGTCATGAAAGATGCTGCAGTAGTATTGAAGAAATTCAACATACCTTT----
upper sequence: Vv14s0081g00240.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g10280.4 (Oryza sativa), 3'ss of exon 11
gttgaggctgagcagtatagacaaacaaattttccttttattaagt----ttattttattca-actatcttgttaatgttgatcaccaacatt-tgctaaatgcagTAACACCTCGTGTTGGAATCATAATGGGCTCTGATTCAGATCTTCCTGTTATGAAGGATGCTGCAGGGATTTTGAATCACTTTGGTGTGCCTCATGAG
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-----tgttgtgccaccttc-tgacccactttactttctaaaaagtcctttcatgttcttcataccaatgggctgacaaagtataataatattgtactagttgcagTTAAACCTCGTGCTGCAATAATAATGGGTTCTGATTCTGATCTTCCTGTCATGAAAGATGCTGCAGTAGTATTGAAGAAATTCAACATACCTTTTGAG
upper sequence: Vv14s0081g00240.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G30620.1 (Glycine max), 3'ss of exon 10
--------gttgaggctgagcagtatagacaaacaaattttccttttattaagtttattttattcaactatcttgttaatgttgatcaccaacatttgctaaatgcagTAACACCTCGTGTTGGAATCATAATGGGCTCTGATTCAGATCTTCCTGTTATGAAGGATGCTGCAGGGATTTTGAATCACTTTGGTGTGCCTCATGAG
|| | || | | || | | | | | |||| || | |||||| | || | | ||| | ||| ||| || ||| | || |||| || ||||||||||| |||||||||||||| ||||||||||| ||| || | || ||| | |||||||||||||| |||
accattctcttataattaagaaaactggagagg-agctgtatttgaagttaaaattttgttattctcacactttat--actttgttt-----tgttttataattgtagTTGCTCCATGTGTGGGGATCATAATGGGTTCTGATTCAGATCTACCTGTTATGAAAAGTGCCGCTGAAATCTTGGAGATGTTTGGTGTGCCTCACGAG
upper sequence: Vv14s0081g00240.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G36930.1 (Glycine max), 3'ss of exon 11
----gttgaggctgagcagtatagacaaacaaattttccttttattaagtttattttattcaactatcttgttaatgttgatcaccaacatttgctaaatgcagTAACACCTCGTGTTGGAATCATAATGGGCTCTGATTCAGATCTTCCTGTTATGAAGGATGCTGCAGGGATTTTGAATCACTTTGGTGTGCCTCATGAG
|| ||| | | | | || || | ||| || | ||||| | || | | | || | | || | ||||| ||| || ||| |||| | ||| || ||||||||||| |||||||||||||| ||||||||||| |||||| | || ||| | |||||||||||||| |||
tataattaagg--aaactggagaggagcactatatttgaaattttgaagttaaaattttgttattctcacact--ttatgctttgttttatttgataactgtagTTGCACCACATGTGGGGATCATAATGGGTTCTGATTCAGATCTACCTGTTATGAAAAGTGCTGCTGAAATCTTGGAGATGTTTGGTGTGCCTCACGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttattttattcaactatcttgttaatgttgatcaccaacatttgctaaatgcagTAACACCTCGTGTTGGAATCATAATGGGCTCTGATTCAGATCTTCCTGTTATGAAGGATGCTGCAGGGATTTTGAATCACTTTGGTGTGCCTCATGAG
tgctaaa putative branch site (score: 2)
tttattcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgaggctgagcagtatagacaaacaaattttccttttattaagtttattttattcaactatcttgttaatgttgatcaccaacatttgctaaatgcagTAACACCTCGTGTTGGAATCATAATGGGCTCTGATTCAGATCTTCCTGTTATGAAGGATGCTGCAGGGATTTTGAATCACTTTGGTGTGCCTCATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaccaa