Sequence
atgc intronic sequence ATGC exonic sequence...ctgtatccaattatctaattcttgtttacatactctttttaatattcaattacaatgaagattgtccttgaatttatctcagttgggaaatgaggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g02960.1 (Oryza sativa), 3'ss of exon 1
--------ctgtatccaattatctaattcttgtttacatactctttttaatattcaa--ttacaatgaagattgt--ccttgaatttatctcagttggga---aatgaggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
|| | || | | || || | | |||| | | ||| | ||| | ||| || ||| | | ||| || ||||||| | ||| |||||||| ||||||||||| || |||||||||||||||||||| ||| |||||||||| ||||||||||| || ||
aatggtgtctctttcggttcttgtagcaattactaatgtactactctagatagcaagatttatagcctgacttgcagttttaaatgaccttgaattgaagGTGAACAAGGTGCAATCGGAAACGAGGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG---------------
upper sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g50360.1 (Oryza sativa), 3'ss of exon 2
--ctgtatccaatta-----tctaattcttgtttacata-ctctttttaatattcaa--ttacaatgaagattgtc-cttgaatttatctcagttgggaaatgag----gtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
|| || ||| | || | ||| || | || ||||| | ||| | ||| | || | | || | | | |||| |||||| || ||| ||||||| ||||||||||| || |||||||||||||||||||| ||| |||||||||| ||||||||||| || ||
gtttggatttcgttaacggttttaccttcggttcttgtagcaattactaatagctagatttatagcctgatttgccgtttttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAACAAGGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG---------------
upper sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g22450.1 (Oryza sativa), 3'ss of exon 1
---ctgtatccaattatc-----taattcttgtttacata-ctctttttaatattcaa--ttacaatgaagattgtccttgaatttatctcagttgggaaatgag----gtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
|| || ||| | || | ||| || | || ||||| | ||| | ||| || | | || | | | |||| |||||| || |||| | ||||| ||||||||||| || |||||||||||||||||||| ||| |||||||||| ||||||||||| || ||
tgtttggatttcgttaacggtgttaccttcagttcttgtagcaattactaatagctagatttatagcctgatttgcagttttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAATAAAGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG---------------
upper sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G171466_T01 (Zea mays), 3'ss of exon 1
-----------ctgtat-ccaattatctaattct-tgttta-catac---tctttttaatattcaattac--aatgaagattgtccttgaatt----tatctcagttgggaaatg-aggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
||| | | | | |||| ||| | || | |||||| | || | | | | || || |||| | | |||| | || || ||| || || |||| |||||| | ||||||||| | || |||||||||||||||||||| ||| |||||||||| ||||||||||| || || || ||
gtaacgacgacgtgtgtgttatctgttcccttctgcgttcagcacgcagacagatttaatttgcacgtgccagacgtggactgat-ttgagctgcggtgtctcgctctgggcgtgtagGCGCCGGCGCAACCGAGGGCACCAAGCAGAGCCGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACCGGCGTCACCAG------
upper sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G40550.1 (Glycine max), 3'ss of exon 2
-ctgtatccaattatctaattcttgtttacatactctttttaatattcaattacaatgaagattgtccttgaatttatctcagttgggaaatgaggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
|| | || | | | | || || ||| | | | | | | |||| | | |||| | | | ||| |||| | |||||| |||||| |||||||||||||||||||||||||||||||| || |||||||||||||| || ||||||| |||||||||||| | ||||||||
tttgccctctgttgctgcagccatttctatgctctatttgtttggcttgttatctgttgaccttgttcataaattcgttttatttgactt-tgagattcagGTGGTGCTGAGGGTTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGAAAAGCAATGTTGAAGCTGGGACTGAAACCTGTTACTGGTGTTAGTAGGGTCAC
upper sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G14260.1 (Glycine max), 3'ss of exon 2
---ctgtatccaat---tatctaattcttgtttacatactctttttaatattcaattacaatgaagattgtccttgaatttatctcagttgggaaatgaggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
|| |||| |||| || |||| | | | ||| || | | || | ||| | | |||| | | | ||| | || |||||||| |||||| ||||||||||||||||||||||||||||| || |||||||||||| | || ||||||| |||||||| ||| | ||||||||
aagaaaaatgcaatgtacatctttttattgtgtgcgtcttctattgcaaaaccatatctgttgatttgttttcttggact------aaatggactttaagatgcagGTGGTGCTGAGGGTGGGAAGCAGAGCAGAAGTGAGAAGAAGAGCCGAAAAGCAATGTTGAAGTTGGGACTGAAACCTGTTACTGGCGTTAGTAGGGTCAC
upper sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G40540.1 (Glycine max), 3'ss of exon 2
ctgtatccaattatctaattcttgtttacatactctttttaatattcaattacaatgaa-gattgtccttgaatttatctcagttgggaaatgaggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
|| | || | | | | ||| || | | | |||| | || || | || || | || | ||| | || ||||||||| |||||| ||||||||||||||||||||||||||||| || |||||| ||||| | || ||||||| |||||||||||| | ||||||||
-tgaagaaaaatgcaatgtacatcttttaattgttcgtcttctattgcaacaccatatctgtttatctgttttcttggactaaatggattttaagatgcagGTGCTGCTGAGGGTGGGAAGCAGAGCAGAAGTGAGAAGAAGAGCCGAAAAGCAATGCTGAAGTTGGGACTGAAACCTGTTACTGGTGTTAGTAGGGTCAC
upper sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G14250.1 (Glycine max), 3'ss of exon 2
-------ctgtatccaattatctaattcttgtttacatactctttttaatattcaattacaatgaagattgtccttgaatttatctcagttgggaaatgaggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
|||| || | || | | | || || | || ||| | | | |||| | | |||| | | ||||| | |||| |||||||| |||||| ||||||||||||||||||||||||||||| || || |||||||||||||| || | ||||| || || |||||| | ||||||||
ttgccctctgtttctgctgccatatctatgctctatttatttggcttgttatctgttgatcttc----ttgttcataaattcgtttt-gttgg--actgagatgcagGTGGTGCTGAGGGTTCAAAGCAGAGCAGAAGTGAGAAGAAGAGTCGAAAAGCAATGTTGAAGCTGGGACTAAAACCTGTCACCGGTGTTAGTAGGGTCAC
upper sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G49470.1 (Arabidopsis thaliana), 3'ss of exon 2
---ctgtatccaattatctaattcttgtttacatactctttttaatat-tcaattacaatgaagattgtccttgaattt-atctcagttgggaaatgaggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
|| || | || |||| | | | | ||| | ||||| | || || | ||||| ||| || || | |||| | | || ||||| || || | ||||||||||| |||||||| |||||||| | ||||| |||||||||||||| |||||||| || ||||||||| | | || ||
tttatggatttacttgactaagtttcggaga-atagagatcccaatatgtttatagcatagtgaattgttcttaaaattgaatgaagttttgttgt----tgtagGTGTAAGTGGAAGTTCAAAGCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGGCGATGTTGAAGCTCGGTATGAAACCTGTCACTGGTGTTAGTCGAGTAAC
upper sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EDO97954 (Chlamydomonas reinhardtii), 3'ss of exon 1
------------ctgtatccaattatctaattcttgtttacat-actctttttaatattcaattacaatgaagattgtccttgaatttatctcagttgggaaatgaggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
| | | | || | | | | | | || | |||| || | | || | || | | || | |||||| | |||| || || ||||||||| | || |||||||||||||||||||| ||| |||||| |||||||| ||||| ||||| ||
gctcagcgtctggcgctgtcggctgggcgagcgatgccagctttagtttcgtcggcccacagggatgctgaacatggcgcatgtgtg-atgttggctgc-agATGAGGAG--GGTGGCGCTGGCCGCGGCAAGCAGAGCCGCAGCGAGAAGAAGAGCCGCAAGGCCATGCAGAAGCTGGGCATGAAGCCCGTCACTGGCGTGAC---------
upper sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 2
ctgtatccaattatctaattcttgtttacatactctttttaatattcaattacaatgaagattgtccttgaatttatctcagttgggaaatgaggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
|| | | | ||| | | ||| ||| | | || || | | || ||||| ||| | || |||||||||||||| ||||||||| ||||||||| ||||| ||||| ||||| || ||||| |
---------------------------------------------------------------gttcct-actttctttatgtttctt--ccaggcgagGATGGAACGGGGAAATCGAAGCAAAGCCGGAGCGAGAAGAAGAGCCGGAAGGCAATGCAGAAGCTCGGGATGAAGCCCGTGACTGGAGTAACGAGGGTGA- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaattacaatgaagattgtccttgaatttatctcagttgggaaatgaggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
ttgaatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgtatccaattatctaattcttgtttacatactctttttaatattcaattacaatgaagattgtccttgaatttatctcagttgggaaatgaggtgcagGTGCAAATGAGGGCTCAAAGCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- gtatcca
- - - - - - - - - - - - - - catactc
- - - - - - - - - - - - - - - - - - - - - - - - - - caatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagttgg