Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgatcttgagtgttttgttttgtgatcttttccacagttttggtcttttagatgagagttgaacctaaacaagttataatttcttctcatgatcatgcagTGATGTCTTCTCATGATTCAATTAGCATGGTTTTGAAATGCATGTTGAAAGGGGCCGCTGACTTTCTTGTCAAGCCTGTTAGGAAGAATGAGCTGAGGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0048g02540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g36220.2 (Oryza sativa), 3'ss of exon 2
gtatgtgatcttgagtgttttgttttgtgatcttttccacagttttggtcttttagatgagagttgaacctaaacaagttataatttcttctcatgatcatgcagTGATGTCTTCTCATGATTCAATTAGCATGGTTTTGAAATGCATGTTGAAAGGGGCCGCTGACTTTCTTGTCAAGCCTGTTAGGAAGAATGAGCTGAGGAA
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gtatgtatccaacttgactctatgccatg-cctttctcata-------tctttctaatcccatt---actccatctgatgcttcatttttctattggtct--cagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGGGTGCTGCAGATTTCCTTGTTAAGCCAATACGGAAGAATGAATTAAGGAA
upper sequence: Vv15s0048g02540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G179024_T01 (Zea mays), 3'ss of exon 2
gtatgtgatcttgagtgttttgttttgtgatcttttccacagttttggtcttttagatgagagttgaacctaaacaagttataatttcttctcatgatcatgcagTGATGTCTTCTCATGATTCAATTAGCATGGTTTTGAAATGCATGTTGAAAGGGGCCGCTGACTTTCTTGTCAAGCCTGTTAGGAAGAATGAGCTGAGGAA
| ||| | || | ||| | ||| || | | | || || | | |||| | || | ||||| ||||||||||||| ||||| ||| | ||||||||||| ||||||||| | || || || || || || ||||| || || | || |||||||| | |||||
----------------------gtatgtcactcttgtcgtgttttcgctctcttt--ttaatctaatgccactactaagtctaatgtttttt----atcatccagTGATGTCTTCGCATGACTCAGTAAGCATGGTTTTCAAATGCATGCTAAAGGGTGCAGCAGATTTCCTTGTTAAACCGATAAGAAAGAATGAATTAAGGAA
upper sequence: Vv15s0048g02540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G44970.1 (Glycine max), 3'ss of exon 3
gtatgtgatcttgagtgttttgttttgtgatcttttccacagttttggtcttttagatgagagttgaacctaaacaagttataatttcttctcatgatcatgcagTGATGTCTTCTCATGATTCAATTAGCATGGTTTTGAAATGCATGTTGAAAGGGGCCGCTGACTTTCTTGTCAAGCCTGTTAGGAAGAATGAGCTGAGGAA
||||||| ||| | | | | |||| ||| | || | || | || || || ||| || || | ||| ||| | ||||||||||||||||||||||||| | |||||||| || ||||||||||| ||||| || ||||| |||||| | || |||||| | ||||||||||| || ||
gtatgtg---ttgtat-tggtactgtgtggccttaatta----ttagtagttacatgtggctaatggactcaaatttgtctcaactcctt---atggttttgcagTGATGTCTTCTCATGATTCAGTAAGCATGGTGTTTAAATGCATGTTAAAAGGTGCAGCTGATTTTCTTATAAAACCTGTTCGCAAGAATGAGCTAAGAAA
upper sequence: Vv15s0048g02540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G05530.1 (Glycine max), 3'ss of exon 3
gtatgtgatcttgagtgttt-tgttttgtgatcttttccacagttttggtcttttagatgagagttgaacctaaacaagttataatttcttctcatgatcatgcagTGATGTCTTCTCATGATTCAATTAGCATGGTTTTGAAATGCATGTTGAAAGGGGCCGCTGACTTTCTTGTCAAGCCTGTTAGGAAGAATGAGCTGAGGAA
| |||| || ||| | | | | ||| | | | || |||| | | | |||| || | || | | |||||||| |||||||||||||||||||||||| ||||||||| |||||||||||||| |||||||| | ||| |||||| | || || || ||||||||||||| |||||
------------gtatgttgacattatgtatttgtattcttagtctcgatgtt--agatcgaaatgg---ctaatgaactcatg-tctattctcatgggtgtgcagTGATGTCTTCTCATGATTCGGTTAGCATGGCATTGAAATGCATGTTAAAAGGGGCAGTTGATTTTCTTATAAAACCCATTCGGAAGAATGAGCTTAGGAA
upper sequence: Vv15s0048g02540.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G02050.1 (Glycine max), 3'ss of exon 2
gtatgtgatcttgagtgttttgttttgtgatcttttccacagttttggtcttttagatgagagttgaacctaaacaagttataatttcttctcatgatcatgcagTGATGTCTTCTCATGATTCAATTAGCATGGTTTTGAAATGCATGTTGAAAGGGGCCGCTGACTTTCTTGTCAAGCCTGTTAGGAAGAATGAGCTGAGGAA
|||||| |||| || || ||| | || | ||| | || | |||| | | | | || || | | ||| |||||||| |||||||||||||||||||||||| ||| ||||| |||||||||||||| || ||||| | ||| |||||| | || || || | ||||||||||| |||||
gtatgttgacttg------ttattatgtatttgttatcttagtctcagtgta--agatcgaaatgg----ttaatgagct-cattttattctcatgggtgtgcagTGATGTCTTCTCATGATTCGGTTAACATGGCGTTGAAATGCATGTTAAACGGGGCAGTTGATTTTCTTATAAAACCCATTCGCAAGAATGAGCTTAGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttagatgagagttgaacctaaacaagttataatttcttctcatgatcatgcagTGATGTCTTCTCATGATTCAATTAGCATGGTTTTGAAATGCATGTTGAAAGGGGCCGCTGACTTTCTTGTCAAGCCTGTTAGGAAGAATGAGCTGAGGAA
acctaaa putative branch site (score: 3)
taaacaagttataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgatcttgagtgttttgttttgtgatcttttccacagttttggtcttttagatgagagttgaacctaaacaagttataatttcttctcatgatcatgcagTGATGTCTTCTCATGATTCAATTAGCATGGTTTTGAAATGCATGTTGAAAGGGGCCGCTGACTTTCTTGTCAAGCCTGTTAGGAAGAATGAGCTGAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA