Sequence
atgc intronic sequence ATGC exonic sequence...aaattcaaatgttattttatctatatatcttctttgtttggaatgctttatcacttgtttccgagttccttggagcctgatgttcttgttcctaaggcagGTTAAGCTGTGGTGTAACTGCCCTTTTTGGCCTGATGATGGTATGTGCAAGCTGCGTGATTGCAGTGTTTGTGAATGTCCTGAAAGTGAATTTCCAGAAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0027g00090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g52340.1 (Oryza sativa), 3'ss of exon 2
aaattcaaatgttattttatctatatatcttctttgt--ttggaatgctttatcac-ttgtttccgagttccttggag------cctgatgttcttgttcctaaggcagGTTAAGCTGTGGTGTAACTGCCCTTTTTGGCCTGATGATGGTATGTGCAAGCTGCGTGATTGCAGTGTTTGTGAATGTCCTGAAAGTGAATTTCCAGAAC
|||||||| | | | || | | | ||| | ||| || ||| | | | | || | | | || || ||||||| |||||||| |||||||||| |||||||||||||| ||||| ||| | ||||| ||||| ||||| || || || | ||| ||||| || |
---------gactattttatttgttaactttgtgtatgattgcaccaaaatatgacattgaaaataaacactcaaaaaaattcacttgtttatttgctttcttgtttagGTTAAATTGTGGTGTGACTGCCCTTTCTGGCCTGATGATGGAATGTGTCGGCTTAGGGATTGTAGTGTCTGTGAGTGCCCAGAGAATGAGTTTCCTGAGC
upper sequence: Vv19s0027g00090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 2
--aaattcaaatgttattttatctatatatcttctttgtttggaatgctttatcacttgtttccgagttccttggagcctgatgttcttgttcctaaggcagGTTAAGCTGTGGTGTAACTGCCCTTTTTGGCCTGATGATGGTATGTGCAAGCTGCGTGATTGCAGTGTTTGTGAATGTCCTGAAAGTGAATTTCCAGAAC
| || ||| | | | || | | | ||| || | || | ||| |||| | | || ||||| | || | ||||||| |||||||| |||||||||||||||| |||||||| ||||||||||| | ||||| ||||||||||| ||||| || | ||| || || ||||
ctatatgtgaatatgactaccaaaatgctcatattaaaaataaaatttttaagcaatggttcatctgttctaagtcgtgtgttgttccttgtctttta--agGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGTCCGGAGAATGAGTTCCCTGAAC
upper sequence: Vv19s0027g00090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G521844_T01 (Zea mays), 3'ss of exon 2
----aaattcaaatgttattttatctatatatcttctttgtttggaatgctttatcacttgtttccgagttccttggagcctgatgttcttgttcctaaggcagGTTAAGCTGTGGTGTAACTGCCCTTTTTGGCCTGATGATGGTATGTGCAAGCTGCGTGATTGCAGTGTTTGTGAATGTCCTGAAAGTGAATTTCCAGAAC
| | || | || | || | | || | || | || | | |||| | | || ||||| | || | | ||||||| |||||||| |||||||||||||||| |||||||| ||||||||||| | ||||| ||||||||||| || | || | ||| || || ||||
tgtgatgccaccaaaatactcacattaaaaataaaaaatttctgcagtggccagtggctcatct----gttctaagtcacgtgctgttccttgtcttttgtaagGTTAAATTGTGGTGTGACTGCCCTTTTTGGCCCGATGATGGAATGTGCAAGCTTAGAGATTGTAGTGTTTGTGAGTGCTCAGAGAATGAGTTCCCCGAAC
upper sequence: Vv19s0027g00090.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G72280.1 (Arabidopsis thaliana), 3'ss of exon 2
-aaattcaaatgttattttatctatatatcttctttgtttggaatgctttatcacttgtttccg--agttccttggagcctgatgttcttgttcctaa-----ggcagGTTAAGCTGTGGTGTAACTGCCCTTTTTGGCCTGATGATGGTATGTGCAAGCTGCGTGATTGCAGTGTTTGTGAATGTCCTGAAAGTGAATTTCCAGAAC
| | | ||| | | ||| ||| | | | | | | | | | | ||| ||| || | |||| || || || || ||||||| || |||||| ||||||| || ||||| || ||||| ||||| |||||||||||||||| ||||||||||| || | ||| ||||||||||
gtcagtgagatgctttagaatccgattatgtcgaaaaactatgaagttgtgttctgtagtgtagttagtgacttttggctggctgttttttttttaaatgttgggtagGTTAAACTATGGTGTGACTGCCCATTCTGGCCAGACGATGGAATGTGTCGTTTGCGTGATTGCAGTGTCTGTGAATGTCCAGAGAATGAGTTTCCAGAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttatcacttgtttccgagttccttggagcctgatgttcttgttcctaaggcagGTTAAGCTGTGGTGTAACTGCCCTTTTTGGCCTGATGATGGTATGTGCAAGCTGCGTGATTGCAGTGTTTGTGAATGTCCTGAAAGTGAATTTCCAGAAC
gcctgat putative branch site (score: 4)
ttcttgttcct CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaattcaaatgttattttatctatatatcttctttgtttggaatgctttatcacttgtttccgagttccttggagcctgatgttcttgttcctaaggcagGTTAAGCTGTGGTGTAACTGCCCTTTTTGGCCTGATGATGGTATGTGCAAGCTGCGTGATTGCAGTGTTTGTGAATGTCCTGAAAGTGAATTTCCAGAAC
aaattcaa
- - - - - - - - - - - - - - - - - - - - gaatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcctga