Sequence
atgc intronic sequence ATGC exonic sequence...tcagttcaaacagagattaccttttgttttttattttttctgagagttaacagattttatggagtgcaataggggcaagccacaacctccttttgattagACAAAGCCTGCTCTTCCAGCTCTTGGGCGTCTTATTCACTCGAATGATGAAGATGTGCTAACTGATGCGTGTTGGGCACTGTCTTACCTTTCTGATGGTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0183g00210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 5
tcagttcaaacagagattaccttttgttttttattttttctgagagttaacagattttatggagtgcaataggggcaagccacaacctccttttgattagACAAAGCCTGCTCTTCCAGCTCTTGGGCGTCTTATTCACTCGAATGATGAAGATGTGCTAACTGATGCGTGTTGGGCACTGTCTTACCTTTCTGATGGTA
||| ||| || || ||||| | || | | | || || ||| ||| | || || | | | | | ||||| | ||||||||||||||| || | || ||||||||||| |||||||| || || || ||||||||||| ||||| || || || | |||||||| |
---gtttggacaaagttt---ctttgtactctactgtagttagtagggaa-agac-------agttccttaa---catgatgtttattgggtgtcaatagACTAGGCCTGCTCTTCCAGCACTGGCACGGCTTATTCACTCCAATGATGAGGAAGTTCTCACTGATGCGTGCTGGGCTCTTTCATATTTATCTGATGGCA
upper sequence: Vv00s0183g00210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G29000.1 (Glycine max), 3'ss of exon 5
-tcagttcaaacagagattaccttttgttttttattttttctgaga-gttaacagattttatggagtgcaataggggcaagccacaacctccttttgattagACAAAGCCTGCTCTTCCAGCTCTTGGGCGTCTTATTCACTCGAATGATGAAGATGTGCTAACTGATGCGTGTTGGGCACTGTCTTACCTTTCTGATGGTA
| || || ||| | || | |||| || | || | || |||||| || | || || | |||| | || || ||||| ||||| ||||||| |||||||| || ||||| |||||||| || | |||||||| |||||||||||||| || |||||||||||||
cattggtcttttgtttatgtcctgcttttactgatttattataagctgctattgtgttttattt--cacagttcatacattatactttgtttttttcttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCGAACGATGAAGAAGTTTTGACTGATGCATGTTGGGCACTGTCATATCTTTCTGATGGTA
upper sequence: Vv00s0183g00210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G39210.1 (Glycine max), 3'ss of exon 6
tcagttcaaaca-gagattaccttttgttttttattttttctgagagttaacagattt-tatggagtgcaataggggcaagccacaacctccttttgattagACAAAGCCTGCTCTTCCAGCTCTTGGGCGTCTTATTCACTCGAATGATGAAGATGTGCTAACTGATGCGTGTTGGGCACTGTCTTACCTTTCTGATGGTA
| | | | | || | ||| ||| | | ||| || | | | | | || || | | | ||| |||| || || ||||| ||||| ||||||| ||||||| || || ||||||||||| || || |||||||| ||||||||||| || || |||||||||||||
tgtgctgatatgtgaagcaaatgcaagttgtttttcccagtttagatttgctggctctgttttgactgaggattgattgatttttatccttttttta--cagGTTAAACCTGCACTTCCTGCTCTTGCCAGTCTTATCCAGTCAAATGATGAAGAAGTCCTGACTGATGCTTGTTGGGCACTTTCATATCTTTCTGATGGTA
upper sequence: Vv00s0183g00210.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G38320.1 (Glycine max), 3'ss of exon 5
-tcagttcaaacagagattaccttttgttttttattttttctgagagttaacagattttatggagtgcaataggggcaagccacaacctccttttgatt-agACAAAGCCTGCTCTTCCAGCTCTTGGGCGTCTTATTCACTCGAATGATGAAGATGTGCTAACTGATGCGTGTTGGGCACTGTCTTACCTTTCTGATGGTA
| ||| | | ||| | || | ||| || | || | || ||| || | || || | |||| || || || ||||| ||||| ||||||| |||||||| || || || |||||||| || | |||||||| |||||||||||||| || ||||||||||| |
atttgttttcttgtatgtgtcctgcttttactgattgatttaagctgctattattttctattt--cacagttcatacattatactgtttttttttccttcagGTTAAACCTGCACTTCCTGCTCTTGCCCGTCTTATCCATTCAAACGATGAAGAAGTATTGACTGATGCATGTTGGGCACTGTCATATCTTTCTGATGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttaacagattttatggagtgcaataggggcaagccacaacctccttttgattagACAAAGCCTGCTCTTCCAGCTCTTGGGCGTCTTATTCACTCGAATGATGAAGATGTGCTAACTGATGCGTGTTGGGCACTGTCTTACCTTTCTGATGGTA
agttaac putative branch site (score: 3)
cctcctttt putative PPT
agattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcagttcaaacagagattaccttttgttttttattttttctgagagttaacagattttatggagtgcaataggggcaagccacaacctccttttgattagACAAAGCCTGCTCTTCCAGCTCTTGGGCGTCTTATTCACTCGAATGATGAAGATGTGCTAACTGATGCGTGTTGGGCACTGTCTTACCTTTCTGATGGTA
- - - -aaacaga
- - - - - - - - - -ccttttg
- - - - - - - - - - - - - - - - - - - - - - - -taacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggggcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccacaa