Sequence
atgc intronic sequence ATGC exonic sequencegtgcgtaatttgggtttttctgttgtttgaccagacttgaatgtgaacatatgaatgcatttattttttgaactaaaaatgatcattacatttctcattttgaagAACTTTACCAGCAAATGCTTGCCAAGGCTTTAGCACACTATTTTGAAGCCAAGCTGTTGCTGCTAGATGTAACAGACTTTTCATTGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0025g00650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 2
gtgcgtaatttgggtttttctgttgtttgaccagacttgaatgtgaacatatgaatgcatttattttttgaactaaa--aatgatcattacatttctcattttgaagAACTTTACCAGCAAATGCTTGCCAAGGCTTTAGCACACTATTTTGAAGCCAAGCTGTTGCTGCTAGATGTAACAGACTTTTCATTGAAG
|||| | | ||| ||| ||| | || || | | || | ||||| || | | |||| || || || ||||||||||||||||||||||||||||||| || | || |||||||||||||| || || || |||||||| ||||| ||| | |||
----gtaaatca---tattccattgca----caggttaaggagttgctgaatcactcttcttctggccctgactaagttaaggctaattaagttcct-atcttgaagAACTTTACCAGCAAATGCTTGCCAAAGCGCTTGCCCACTATTTTGAAGCAAAATTGCTGTTGCTAGATCCTACAGATTTTCTCATAAAG
upper sequence: Vv02s0025g00650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G37290.1 (Glycine max), 3'ss of exon 3
gtgcgtaatttgggtttttctgttgtttgaccagacttgaatgtgaacatatgaatgcatttatt-----ttttgaactaaaaatgatcattacatttctcattttg--------aagAACTTTACCAGCAAATGCTTGCCAAGGCTTTAGCACACTATTTTGAAGCCAAGCTGTTGCTGCTAGATGTAACAGACTTTTCATTGAAG
|| | | |||| | | || || | | | | || | | | ||| |||||| | || | |||| || ||| || | ||| ||||||||||||| || |||||||||||||||||||| || || ||||| |||||| || | ||| ||||| |||| |||||||||||||||
gttaattacttggaatctgctattttctattgataagggatttcatattctttgatgtttttattgttactattaagctaactatatctcacacacctcccttttcatgtcttaaaagAACTTTACCAACAGATGCTTGCCAAGGCTTTAGCTCATTACTTTGAGGCCAAGTTGCTTCTGTTAGATTTAACTGACTTTTCATTGAAG
upper sequence: Vv02s0025g00650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G02260.1 (Glycine max), 3'ss of exon 3
-----gtgcgtaatttgggtttttctgttgtttgaccagacttgaatgtgaacatatgaatgcatttattttt-----tgaactaaaaatgatcattacatttctcatttt--------gaagAACTTTACCAGCAAATGCTTGCCAAGGCTTTAGCACACTATTTTGAAGCCAAGCTGTTGCTGCTAGATGTAACAGACTTTTCATTGAAG
| | ||||| || | | ||||| | | | | || | | | ||| |||||| || | | |||| || ||| || | ||| ||||||||||||| || |||||||||||||||||||| || || ||||| |||||| || | ||| ||||| |||| |||||||||||||||
gttaattacttaatt-ggaatctgctgttttctattgataagggatttgatattctttgatgtttttattgttactgttaagctaactatatctcacacacctcccttttcatgtcttaaaagAACTTTACCAACAGATGCTTGCCAAGGCTTTAGCTCATTACTTTGAGGCCAAGTTGCTTCTGTTAGATTTAACTGACTTTTCATTGAAG
upper sequence: Vv02s0025g00650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G43230.1 (Glycine max), 3'ss of exon 2
gtgcgtaatttgggtttttctgttgtttgaccagacttgaatgtgaacatatgaatgcatttatttt--ttgaactaa--aaatgatcattacatttctca--ttttgaagAACTTTACCAGCAAATGCTTGCCAAGGCTTTAGCACACTATTTTGAAGCCAAGCTGTTGCTGCTAGATGTAACAGACTTTTCATTGAAG
|| | |||| | | ||||| | ||| || | | | | | | | ||| | |||| | |||| | | | || | | || |||||||||||| ||| ||||||||||||||||||| ||||| ||||| || ||| || | ||
----gttagttggactatgctgttttctgatgag-cctaacctaatgtttctactttctactatcgccatcaaactcattaaatttttctccccttcacgatgtcttacagAACTTTACCAACAAGTGCTTGCCAAGGCTTTAGCTCACTACTTTGAGGCAAAGTTGCTTCT---------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaatgcatttattttttgaactaaaaatgatcattacatttctcattttgaagAACTTTACCAGCAAATGCTTGCCAAGGCTTTAGCACACTATTTTGAAGCCAAGCTGTTGCTGCTAGATGTAACAGACTTTTCATTGAAG
aactaaa putative branch site (score: 2)
tttctcatttt putative PPT
atttattttttgaact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgtaatttgggtttttctgttgtttgaccagacttgaatgtgaacatatgaatgcatttattttttgaactaaaaatgatcattacatttctcattttgaagAACTTTACCAGCAAATGCTTGCCAAGGCTTTAGCACACTATTTTGAAGCCAAGCTGTTGCTGCTAGATGTAACAGACTTTTCATTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG