Sequence
atgc intronic sequence ATGC exonic sequencegttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagtaataatgtttataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccatatttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 2
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcaga-tggcatgagtaataatgtttataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccatatttctttaattcttt--tgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
| || || |||| | | | || | | | | | ||| | || ||| | | || | |||| ||| || ||| || ||||||||| ||||| || ||||| |||||||| || || || ||||||||||| || || ||||| || ||||| ||||| ||||||||||| || || |
-----------------------------------------------------------------------------agtagcctgatatgactgctccatctcattattcaatatattttgtt--atact-agaattttactgatatgacagctgtctttcattatttgtttactgcagCAAATGTGTTTCACCGAGATCTTAAACCAAAAAATATTTTGGCAAATGCTGATTGTAAGCTCAAAATATGTGATTTTGGCCTTGCAAGAGTTGCTTTCAG
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 2
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagtaataatgtttataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccatatttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
| |||| | || | || | | | | ||| ||||| | | | || || | ||| | ||| |||| || | | ||| ||||||||| |||||||| ||||| |||||||| || || | ||||||||||| || || ||||| || ||||||||||| | ||||||||||| || ||
------------------------------------------------------------------tcattactaggggctcctaatctgtctgtttccgctgtgtccttttagtgg---------cact-aacatgcctgatatgactgatgcatctttcaatagct-tattgcagCAAATGTATTTCATCGAGATCTCAAACCAAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGACTTTGGCTTAGCAAGAGTAGCTTTCAA
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G017351_T01 (Zea mays), 3'ss of exon 1
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagtaataatgtttataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccatatttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
| | | | || | | | | | || ||| | | | || || | ||| | ||| |||| || | | ||| ||||||||| || ||||| ||||| |||||||| || || | ||||||||||| || || ||||| || ||||| ||||| || ||||||||||| || |
----------------------------------------------------------------------------taggggcttctcttcttactgttttccagtgagttctgttagtggcagtggcactaacatgcctgatatgactgatgcatctttcaatagct-tattgcagCAAATGTATTCCATCGAGATCTCAAACCAAAAAATATTCTGGCAAATGCTGATTGTAAGCTCAAAATATGTGATTTTGGCCTAGCAAGAGTAGCTTTCAG
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 2
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagtaataatgtttataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccat--atttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
| ||| | | | | ||| | || ||| || | ||| ||| || | | || ||||| ||||||||||||| ||||| || ||||| || ||||| ||||| ||||||||||||||||||||||| ||||| ||||||||||||||||| ||||| || || ||
---------------------------------------------------------------------------------------gttagttagggaatcttt--cttagattgcttgctgtagcatatattatatgatcactgtggctgattttgaatttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTTGGTCTTGCCAGAGTGGCTTTCAA
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 2
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagta-ataatgtttataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccatatttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
|| ||| | | |||| ||| | | ||||| | |||| || ||| | |||| | | || || | || | | | ||||||||| | | ||||| ||||||||||||| ||||| || ||||| || ||||| ||||| ||||||||||||||||||||||| ||||| || |||||||||||||| ||||| || || ||
---------------------------------------gttagttagggaatctttcttagatt-------gcttgct---gtagcatatatatatatttgttattgcataaaactagtagcaaaattatatgatcactatggctgattttg----aacttcttaatggacttgtagCAAATGTTTTTCACCGTGATCTAAAGCCAAAAAACATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGCGACTTTGGTCTTGCCAGAGTGGCTTTCAA
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 2
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagtaataatgtttataacttgaagtgggtgcccggatat-tcagtattccggtcctgattttgccatatttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
|| | | | ||| || | |||| || ||| | | ||||| | || | |||| | |||| | || | | | | | ||| || |||||||| | | |||||| |||||||||||||| ||||| || ||||| || ||||| || || ||||||||||||||||||||||| ||||| |||||||| |||||||| ||||| || || ||
------------------gttatgatcactatatttagc--tagtttt---tatttttagattcctaaggcagctttttca-------tagttaatgtt--ttattataagagctaattattaaatcacatgatcattgtgg--ctgatttta----aactttttaatgggtttgtagCAAATGTTTTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 1
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagtaataatgtttataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccatatttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
|| | | ||| | | ||| |||||| | || | || ||||| | | | |||||||| | ||| | | || | | |||||||| | | |||||| |||||||||||||| ||||| || ||||| || ||||| || || ||||||||||||||||||||||| ||||| |||||||| |||||||| ||||| || || ||
-----------------------gttatgatctttatatttag--ctagt---ttttatt----tttagattcctaatgcagctttt-tcatagttaatgttttattataaaagctaattattgaatcacatgatcattgtggctgatttta----aactttttaatgggtttgtagCAAATGTATTTCACCGAGATCTAAAGCCAAAAAATATTTTAGCAAATGCTGACTGCAAACTGAAGATTTGTGACTTCGGTCTTGCCAGAGTGGCTTTCAA
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 2
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagtaataatgttt-ataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccatatttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
|| || | || ||| ||||| ||| || || | || | ||| | |||| | | | ||| | | | |||| ||| |||||||||||||||||||| ||||| || ||||| || ||||||||||| |||||||||||||||||||| ||||| ||||||||||| || || ||
----------------------------------------------------------------------------gttaagctagc--gagcaataaaatttcattgattagtataagtttatgattatct----------ttctgaaaatactttttttttctcttcctttc--agCTAATGTCTTTCATCGGGATCTTAAACCCAAAAACATATTGGCAAATGCTGATTGCAAACTCAAGATCTGTGATTTTGGACTTGCAAGAGTCGCATTCAA
upper sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 2
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagtaataatgtttataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccatatttct-ttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
|| | || | || | || || || | |||| ||| || | | ||| ||| | | || | || || | ||| ||||| |||||||| || ||||| ||||||||| | || ||||| |||||||| ||||| || || ||||||||||| ||||| |||| |||||||
----------------------------------------------------------------------------tcacaactctcactgtacaaaagactgatgggatgtggtcc-tttttggat-ttctgtctgtttttgtggatgttgacgtcttcatgtttgggattgttcagCTAATGTGTTTCATCGCGACCTGAAGCCAAAGAACGTGTTGGCAAACGCTGACTGTAAACTGAAAATTTGTGACTTTGGACTTGCTCGAGTGGCCTTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cggatattcagtattccggtcctgattttgccatatttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
tttctttaattctttt CT-rich tract
atatttctttaattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatatgatgctacaatattgtattttaactttttggccttggtttagcatactttattacaatctaattagcttgtgcagatggcatgagtaataatgtttataacttgaagtgggtgcccggatattcagtattccggtcctgattttgccatatttctttaattcttttgtagCAAATGTCTTTCATCGGGATCTGAAACCAAAGAACATCTTAGCAAATGCTGACTGCAAACTCAAGATCTGTGACTTTGGTCTTGCAAGAGTAGCCTTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA