Sequence
atgc intronic sequence ATGC exonic sequence...tgaaatgatttctcttttcaaactctaacttgaaaagacaggtgtgtatgtcactgtcttggtgcaacttgcaattcatattgttacttcgattgtgcagTACTCAAGAAATGTGAGTCAAACACGTTGGATCATTGATGATGAAAGAATGGGTGAAGCATCTGTTGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g00500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g47380.1 (Oryza sativa), 3'ss of exon 6
-------tgaaatgatt-tctcttttcaaactctaacttgaaaagacaggtgtg-tatgtcactgtcttggtgcaacttgcaattcatattgttacttcgattgtgcagTACTCAAGAAATGTGAGTCAAACACGTTGGATCATTGATGATGAAAGAATGGGTGAAGCATCTGTTGAG
|| | | | ||||| || | |||| || || | |||| ||| |||| ||| | | | | | | ||| || ||| | ||| ||||| ||||| || || || ||||||| ||||||||||| |||||||| |||||||| ||||||
atagaagcaaactaaaggtttctttgcatgtttgcactttaattgat-gctgtgctattcaactgagttgtt-----tccctcatgacaacgttcctc--attat-cagCTTTCAAGGAATGTCAGCCAGTCATGTTGGATAATTGATGATGAGAGAATGGGGGAAGCATCAGTTGAG
upper sequence: Vv18s0001g00500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G39890.2 (Glycine max), 3'ss of exon 5
tgaaatgatttctcttttca-aactctaacttgaaaag--acaggtgtgtatg---tcactgtcttggtgcaacttgcaattc-atattgttacttcgattgtgcagTACTCAAGAAATGTGAGTCAAACACGTTGGATCATTGATGATGAAAGAATGGGTGAAGCATCTGTTGAG
|| | | | | |||| || ||| || | || || ||| | | | | |||||| || |||| || |||||| | |||||| ||| | ||||||||||||||||| |||||||||||||||||||||||||| |||||||| ||||||
-----tgttctggatataagtaactacaatttgcaaggtaacgattgacaatgagttaatttatcttgtgcaaattcaaattttatgcctttacttt--cttggcagTATTCACGGAATGTGAGTCAAACACGCTGGATCATTGATGATGAAAGAATGGGAGAAGCATCAGTTGAG
upper sequence: Vv18s0001g00500.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G20410.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------------------------tgaaatgatttctcttttcaaa----ctctaacttgaaaagacaggtgtgtatgtcactgtcttggtgcaacttgcaattcatattgttacttcgattgtgcagTACTCAAGAAATGTGAGTCAAACACGTTGGATCATTGATGATGAAAGAATGGGTGAAGCATCTGTTGAG
| || || | | | |||| || | ||| ||| | | || | || || ||| || ||||| || | | | | |||||||||| |||||||| |||||| |||| ||||| |||||||||||||||||||| ||||| |||||||||
gtaagtcactgttttcatgttcttggggcagtgtattgtatttgtaaccttcatttctgtgtaaactgtagtttggtaacaaatgaattcgcagatgaccgagcagatctttaacctcttatcgaggatcaattt-caattgatggttcgatcttatctttgcagTACTCCAGAAATGTTAGTCAATCACGATGGATTATTGATGATGAAAGAATGGGGGAAGCGTCTGTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtatgtcactgtcttggtgcaacttgcaattcatattgttacttcgattgtgcagTACTCAAGAAATGTGAGTCAAACACGTTGGATCATTGATGATGAAAGAATGGGTGAAGCATCTGTTGAG
aattcatattgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaaatgatttctcttttcaaactctaacttgaaaagacaggtgtgtatgtcactgtcttggtgcaacttgcaattcatattgttacttcgattgtgcagTACTCAAGAAATGTGAGTCAAACACGTTGGATCATTGATGATGAAAGAATGGGTGAAGCATCTGTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-gaaatga
- - - - - - - - - caaactc
- - - - - - - - - - - - - - - -gaaaaga
- - - - - - - - - - - - - - - - - - - - - - -gtatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgcaa