Sequence
atgc intronic sequence ATGC exonic sequence...ttttgtggagaaattgttgttgttctgagctctggcatgcattatgatttattttaacctttgctaatcataagttactgaaaatgttttttctgtgcagGAAATGGGATTGTTGGAGGTGAAGCATGGTCTGCTCCAGGTTTCAGAAACCTTGGAATTTCTTCATAACAATGCTCGTCTTATTCATCGGGCTATATCAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0089g00030.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G00470.1 (Glycine max), 3'ss of exon 1
--ttttgtggagaaattgttgttgttctgagctctggcatgcattatgatttattt-taacctttgctaatcataa-gttactgaaaatgttttttctgtgcagGAAATGGGATTGTTGGAGGTGAAGCATGGTCTGCTCCAGGTTTCAGAAACCTTGGAATTTCTTCATAACAATGCTCGTCTTATTCATCGGGCTATATCAC
|| | | | ||| | | | || ||| ||| |||| || ||| | | | | | | ||||| | ||| || |||||||||||||| | |||||||||||||||||| | || || | ||||| || | || ||||| || ||| |||||| |||| ||||||| ||||||||||
gtccctgaatttagaataatgtcaat-taaatccttgca---attgaaatttgttagtaaaataaattgagtaggttgctgatgaaagagcctttgctttgcagGAAATGGGAATTTTGGAGGTGAAGCATGGTTTACTTCAAATAGCAGAATCCCTCGACTTTCTCCACAACCATGCTCATCTTCTTCATCGAGCTATATCAC
upper sequence: Vv18s0089g00030.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G37070.1 (Glycine max), 3'ss of exon 1
ttttgtggagaaattgttgttgttctgagctctggcatgcattatgatttattttaacc--tttgctaatcataagttac---tgaaaatgttttttctgtgcagGAAATGGGATTGTTGGAGGTGAAGCATGGTCTGCTCCAGGTTTCAGAAACCTTGGAATTTCTTCATAACAATGCTCGTCTTATTCATCGGGCTATATCAC
| || |||| | | | | | || | || ||| | || | | || |||||| | ||||| | | | || |||||||||||||| | |||||||| ||||||||| | || ||| | ||||| || | || ||||| || ||| |||||| |||||||||||| |||||||||
--tagtccctgaatttaggaaaatgtcaaat---aaataccttgcaattgaaatttgttagtcaaatgatagtaagtttctcatgaaagagcctatgctttgcagGAAATGGGAATTTTGGAGGTAAAGCATGGTTTACTTCAGATAGCAGAATCCCTCGACTTTCTCCACAACCATGCTCATCTTATTCATCGATCTATATCAC
upper sequence: Vv18s0089g00030.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G22870.1 (Arabidopsis thaliana), 3'ss of exon 1
ttttgtggagaaattgttgttgttctgagctctggcatgcattatgatttattttaacctttgctaatcataagttactgaaaatgttttttctgtgcagGAAATGGGATTGTTGGAGGTGAAGCATGGTCTGCTCCAGGTTTCAGAAACCTTGGAATTTCTTCATAACAATGCTCGTCTTATTCATCGGGCTATATCAC
| || | | || | | || | | | || | ||| |||||| | | || | || |||| ||| | ||||||||||||||||||||||| ||||| || |||| || ||| | ||||||||||| || || | |||||||||||| ||| |||| |
--------------------------gtgcgttagaatttg--agcaattgagtgagcaaatggaag--atagtttactgtttcttataattgt-tgtagGAGATGAGCTTGTTGGAGGTGAAGCATGGTCTTCTCCAAATTGCAGAGACATTGAACTTTCTTCATAATAACGCCCATCTTATTCATCGTGCTGTATCTC
upper sequence: Vv18s0089g00030.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G71410.1 (Arabidopsis thaliana), 3'ss of exon 1
ttttgtggagaaattgttgttgttctgagctctggcatgcattatgatttattttaacctttgctaatcataagttactgaaaatgttttttctgtgcagGAAATGGGATTGTTGGAGGTGAAGCATGGTCTGCTCCAGGTTTCAGAAACCTTGGAATTTCTTCATAACAATGCTCGTCTTATTCATCGGGCTATATCAC
| | | | |||||||| | ||| | | ||| | || | || ||| ||| || || | ||||| || ||||| ||| | |||||||||||||||||||||||||||||| |||| || || || | || | || || || || ||| || ||||| || || || |
-gtaacatatataatgttgttgctgtga-ttaaaactcaatttaaggttgaccttggattttattaa--attgattgtttaaaat-------ttgatcagGAGATGAGCTTGTTGGAGGTGAAGCATGGTCTGCTCCAGATTTCTGAGACACTGAACTTCTTACACAATAACGCAAATCTCATCCATCGAGCCATTTCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttattttaacctttgctaatcataagttactgaaaatgttttttctgtgcagGAAATGGGATTGTTGGAGGTGAAGCATGGTCTGCTCCAGGTTTCAGAAACCTTGGAATTTCTTCATAACAATGCTCGTCTTATTCATCGGGCTATATCAC
tgctaat putative branch site (score: 2)
tgttttttct putative PPT
tgaaaatgtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgtggagaaattgttgttgttctgagctctggcatgcattatgatttattttaacctttgctaatcataagttactgaaaatgttttttctgtgcagGAAATGGGATTGTTGGAGGTGAAGCATGGTCTGCTCCAGGTTTCAGAAACCTTGGAATTTCTTCATAACAATGCTCGTCTTATTCATCGGGCTATATCAC
- - - ggagaaa
- - - - - - - - - - - - - - - - - gcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatg