Sequence
atgc intronic sequence ATGC exonic sequencegtctgcacattcttcactctctctctatacgtctttttgtatatatttatgatttttaatttaaatgctcgtgcctttgcagATTGTTGTTGGAAGAAGTGGGACTGAAATGCTCACAAATGAGGCTGGCGAAGTTACTAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0060g00210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G28200.1 (Glycine max), 3'ss of exon 2
-------------------------------gtctgcacattcttcactctctctctata-cgtctttttgtatatatttatgatttttaatttaaatg-ctcgtgcctt--tgcagATTGTTGTTGGAAGAAGTGGGACTGAAATGCTCACAAATGAGGCTGGCGAAGTTACTAG
|| | | | || | || | || || ||| ||| | | | ||| || || | || |||||||||| || ||||||||||| |||||||||||||| ||||||||||| |||||||| ||
gtcagtgctaatcttcacaacacatgacgtagtttcaatttcaaccatgatactaatacagtgtgattatgttaataacttaatgtcacatgttatttgtcttggattttggtgcagATTGTCGTGGGAAGAAGTGGAACTGAAATGCTCACTAATGAGGCTGGTGAAGTTACCAG
upper sequence: Vv14s0060g00210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G22190.1 (Glycine max), 3'ss of exon 2
---------------gtctgcacattcttcactctctctctatacgtctttttgtatatatttatgatttt--taatttaa------atgctcgtgcctt---------tgcagATTGTTGTTGGAAGAAGTGGGACTGAAATGCTCACAAATGAGGCTGGCGAAGTTACTAG
| |||| | || | || | | | || | || || || || ||| |||| || | || ||| ||||||||||||| |||||||| || |||||||||||||| ||||||||||| |||||||| ||
gtcagtactaatcttcccaacacagcgtagtttcaatttcaaccacgatactaatacagtttaattatgttaataacttaatgtcacgtgtttttgtcttggattttggtgcagATTGTTGTGGGAAGAAGCGGAACTGAAATGCTCACTAATGAGGCTGGTGAAGTTACCAG
upper sequence: Vv14s0060g00210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G26680.1 (Arabidopsis thaliana), 3'ss of exon 2
gtctgcacattcttcactctctctctatacgtctttttgtatatatttatgatttttaatt-taaatgctcgtgcctttgcagATTGTTGTTGGAAGAAGTGGGACTGAAATGCTCACAAATGAGGCTGGCGAAGTTACTAG
|| | | |||| || | ||| ||| || |||| || ||| ||||| | || ||| | ||||||||||||||||||| |||||||||||||||||| ||||| ||||| ||||| |||||
gttcgtgc-cccttcttctcctttgtatcaatctcaatgagtatagtt----tttgtaattgtggttgaatgtgac---acagATTGTTGTTGGAAGAACTGGGACTGAAATGCTCACTAATGAAGCTGGTGAAGTCACTAG
upper sequence: Vv14s0060g00210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ19284 (Selaginella moellendorffii), 3'ss of exon 1
gtctgcacattcttcactctctctctatacgtctttttgtatatatttatgatttttaatttaaatgctcgtgcctttgcagATTGTTGTTGGAAGAAGTGGGACTGAAATGCTCACAAATGAGGCTGGCGAAGTTACTAG
| || | | ||| | | | | | | | || | ||| || |||||||||| ||| ||| ||| |||||||||||||| ||||||||||| ||| |||| ||
--------------------------gtgagt-tctagatatctttgcgttgtgtctcacacaagaagccttgcattc-tagATTGTTGTGGGACGAACTGGCACTGAAATGCTCACGAATGAGGCTGGAGAAATTACAAG
upper sequence: Vv14s0060g00210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ10540 (Selaginella moellendorffii), 3'ss of exon 1
gtctgcacattcttcactctctctctatacgtctttttgtatatatttatgatttttaatttaaatgctcgtgcctttgcagATTGTTGTTGGAAGAAGTGGGACTGAAATGCTCACAAATGAGGCTGGCGAAGTTACTAG
| || | | ||| | | | | | | || ||||| || |||||||||| ||| ||| ||| |||||||||||||| ||||||||||| ||| |||| ||
--------------------------gtgagt-tctagatatctttgcgttgcgtctcacacaagaagccgtgcattc-tagATTGTTGTGGGACGAACTGGCACTGAAATGCTCACGAATGAGGCTGGAGAAATTACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacgtctttttgtatatatttatgatttttaatttaaatgctcgtgcctttgcagATTGTTGTTGGAAGAAGTGGGACTGAAATGCTCACAAATGAGGCTGGCGAAGTTACTAG
ttttaat putative branch site (score: 3)
tgccttt putative PPT
tttttgtatatattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgcacattcttcactctctctctatacgtctttttgtatatatttatgatttttaatttaaatgctcgtgcctttgcagATTGTTGTTGGAAGAAGTGGGACTGAAATGCTCACAAATGAGGCTGGCGAAGTTACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT