Sequence
atgc intronic sequence ATGC exonic sequence...aagtttatgctgcttaagtatcatctctcataatatatatttttttttcaaggctcccatgatcaccgagtatcaccttatataattttcttaattccagGCTAGTGAGATGATCAGAAGGGATTATGACATGAAGTGTAAAATTCTAAGACAACTGGAATCAAAGGGAGAAAGTACTAACAAGATTGATAAAACTCGGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0009g01610.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G44190.1 (Glycine max), 3'ss of exon 6
aagtttatgctgcttaagtatcatctctcataatatatatttttttttcaaggctcccatgatcaccgagtatcaccttatataattttcttaattcc------agGCTAGTGAGATGATCAGAAGGGATTATGACATGAAGTGTAAAATTCTAAGACAACTGGAATCAAAGGGAGAAAGTACTAACAAGATTGATAAAACTCGGG
|||||| || | || | | ||| || || | | || | || || | | | | || |||| || | ||| ||| ||||||||||||| |||||| ||| |||||||||||||||||| | |||| |||||||||||||| ||||||| || || ||||||||||||| |
--ttttatgttgac--aataagtttttaataaattggtacttgtaatagaatatggctatt-tctctgtctgtttgctaatatcgttgt-ttacttctgcgagtagGCTAGTGAGATTGTCAGAAAGGAATATGACATGAAGTGTAAATTCTTAAGGCAACTGGAATCAAAAGGAGAAAAGACCTCCACAGTTGATAAAACTCGTG
upper sequence: Vv06s0009g01610.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA14G04590.1 (Glycine max), 3'ss of exon 4
aagtttatgctgcttaagtatcatctctcataatata-tatttttttttcaaggctcccatgatcaccgagtatcaccttatataattttcttaattcc------agGCTAGTGAGATGATCAGAAGGGATTATGACATGAAGTGTAAAATTCTAAGACAACTGGAATCAAAGGGAGAAAGTACTAACAAGATTGATAAAACTCGGG
|||| || | || | | | |||| | || | | || | || || | | | | || |||| ||| | ||| ||| ||||||||||||| |||||| ||| |||||||||||||||||| | |||| |||||||||||||| ||||||| || | ||||||||||||| |
-----tatgttgacaattaattttttttaataaattggtacacataatagaatatggctatt-tctctgtctgtttgctaatatcattgt-ttacttctgcgagtagGCTAGTGAGATAGTCAGAAAGGAATATGACATGAAGTGTAAATTCTTAAGGCAACTGGAATCAAAAGGAGAAAAGACCTCTACAGTTGATAAAACTCGTG
upper sequence: Vv06s0009g01610.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G03740.1 (Glycine max), 3'ss of exon 5
aagtttatgctgcttaagtatcatctctcataatatatatt----tttttttcaaggctcccatgatca--ccgagtatcaccttata-taattttcttaattccagGCTAGTGAGATGATCAGAAGGGATTATGACATGAAGTGTAAAATTCTAAGACAACTGGAATCAAAGGGAGAAAGTACTAACAAGATTGATAAAACTCGGG
| | ||| | |||| || || || || ||| | | | |||| | || ||| | | || |||| ||||| ||||||||||| |||||| ||| ||| |||||||||||||||||| | || | | ||||||||||| ||||||| ||| | ||||||||||| || |
-------tcttatgaaagatttgcctctatcaagattacttctgattccttttatattgttcttaatcagtttcaatagatcctcaaactattttttctaattgcagGCTAGTGATATGATCCGAAAGGAATATGACATGAAGTGTAAATTCTTACGGAATCTGGAATCAAAAGGAGAAAAGACTTCTAGAATTGATAAAACGCGCG
upper sequence: Vv06s0009g01610.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G12290.1 (Glycine max), 3'ss of exon 3
--------aagtttatgctgcttaagtatcatctctcataatatatatttttttttcaaggctcccatgatcaccgagtatcaccttatataattttcttaattccagGCTAGTGAGATGATCAGAAGGGATTATGACATGAAGTGTAAAATTCTAAGACAACTGGAATCAAAGGGAGAAAGTACTAACAAGATTGATAAAACTCGGG
||| || || | | || | ||| || | ||| || || | || | | | | | ||| | ||| || | ||||| ||||||||||| ||||||||| ||| |||||||||||||| ||| | || | | ||||||||||| ||||||| ||| | |||||||||| || |
tcttatgaaagatttgtctatatcaaaattagttctgattccttttatattgttcttaa----tcagttttagtaaattctcaacctat----ttctgctaattgcagGCTAGTGATTTGATCAGAAAGGAATATGACATGAAGTGCAAATTCTTACGGAATCTGGAATCAAAAGGAGAAAAGACTTCTAGAATTGATAAAATGCGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcaaggctcccatgatcaccgagtatcaccttatataattttcttaattccagGCTAGTGAGATGATCAGAAGGGATTATGACATGAAGTGTAAAATTCTAAGACAACTGGAATCAAAGGGAGAAAGTACTAACAAGATTGATAAAACTCGGG
tcttaat putative branch site (score: 3)
ttttctt CT-rich tract
accttatataattttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagtttatgctgcttaagtatcatctctcataatatatatttttttttcaaggctcccatgatcaccgagtatcaccttatataattttcttaattccagGCTAGTGAGATGATCAGAAGGGATTATGACATGAAGTGTAAAATTCTAAGACAACTGGAATCAAAGGGAGAAAGTACTAACAAGATTGATAAAACTCGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - -tatgctg
- - - - - - - - - - tcatctc
- - - - - - - - - - - - - - - - - - - - - - - - - - gctccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacctta