Sequence
atgc intronic sequence ATGC exonic sequence...caatttaatccatgatgttttaaaaaatatggtcaaataaacatcacataaattattgcttttcatattgcttcttccttatgattatgagttgtttcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os09g12800.1 (Oryza sativa), 3'ss of exon 4
------caatttaatccatgatgttttaaaaaatatggtcaaataaacatcacataaattattgcttttcatattgcttcttccttatgattatgagttgtttcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG
|| || ||| | | | || | ||||| | ||| || ||||| ||||| | | || ||| ||| || ||||||||||||||| || ||||||||||||| || || ||||| || ||||||| |||||| || || |||||||||||||||||
attgactaaattgatcaacagtaataaaagcatcatggttgtac---catgtactatattataaaaccgcatatg--tgatgataaataatttaatgtt-ttccagGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACTAAGCCAGGTCACAATGAAGGTGGTGTGAG
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g19560.2 (Oryza sativa), 3'ss of exon 4
caatttaatccatgatgttttaaaaaatatggtcaaataaacatcacataaattattgcttttcatattgcttcttccttatgattatgagttgtttcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG
|| || ||| | | || | ||||| | | | || | | || | || | | | | | | | | || ||||||||||||||| || ||||||||||||| || || ||||| || ||||||| ||||| || || |||||||||||||| ||
taaattgatctgcagtaataaaagcacaatggttatggttgtaccttgtacaatgttataaaaccgcttatgtgatgatacttcatttaatgttttccagGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACCAAGCCAGGTCACAATGAAGGTGGTGTTAG
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AC233865.1_FGT006 (Zea mays), 3'ss of exon 4
--caatt-taatccatgatgttttaaaaaatatggtcaaataaacatcacataaattattgcttttcatattgcttcttccttatgattatgagttgtttcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG
|| | | || |||| |||| ||| | | | | | | || || || || || || | | | | || || | ||||||||||||||| |||||||| |||||||| || || |||||||| |||||| |||||||| |||||||||||||||||
tttaactgccaccctctatgtcttaagcaatttttatgcttcattagtata-aacttgctgtcttatatgatgatatgaacccaacttcatttgtg--tccagGTGTGGCAACATCAACTGGGCTAAGCGGACCAAATGTAATATATGTAACACCTCCAAGCCTGGTACCAATGAAGGTGGTGTGAG
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 3
caatttaatccatgatgttttaaaaaatatggtcaaataaacatcacataaattattgcttttcatattgctt--cttccttatgattatgagttgtt--tcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG
|| ||| |||| | | | | || | | || |||| | || ||| || ||| || ||| || | || || | |||||||| || || || |||||||||||||| || |||||||| |||||||| ||||||||||| |||||||| |||||||| ||
----tttgcacatcatgtgtacacttttgttgtttatgcaggatttttaaaataaaaatttaatgtatgaattgactttctcatgtttttttttttttgcttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAACACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G11060.1 (Glycine max), 3'ss of exon 3
caatttaatccatgatgttttaaaaaatatggtcaaataaacatcacataaattattgctttt-catattgcttcttccttatgattatgagttgtttcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG
| || ||| | || | | | |||| | | || |||| | ||| ||| || || ||| || | || | |||||||| || || || |||||||||||||| || |||||||| ||||| || ||||||||||| |||||||| |||||||| ||
-gaatttgcacatcacgtgtacacttttgtggtttatgcaggatttttaaaataaaaaatttaatgtatgaattggctctcatgttttttttttcacttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAATACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G50300.1 (Arabidopsis thaliana), 3'ss of exon 4
caatttaatccatgatgttttaaaaaatatggtcaaataa--acatcacataaatt---attgcttttcatattgcttcttccttatgattatgagttgtttcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG
|| | ||| | | | | || || | ||| || | | |||| ||| || | | | || ||||||||||||||| | |||||||| || || ||| || ||||| |||||||||||||| ||||| || |||||||||||||||||
-----tatgctatgtgtcatcgagtagcttaactaagaggctgcactgtgtgaatgtgagttcttatgcataatgcactttttctttttgcgctaattctttcagGTGTGGCAATGTCAACTGGGCGAAACGTCTAAAATGTAATATCTGCAACACCAATAAACCTGGTCAGAATGAAGGTGGTGTGAG
upper sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S148_65V6.2 (Physcomitrella patens), 3'ss of exon 3
----caatttaatccatgatgttttaaaaaatatggtcaaataaacatcacataaattattgcttttcatattgcttcttccttatgattatgagttgtttcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG
| || | | | || | | | || | | |||| ||| | | | |||||||| || ||| | ||||||||||||||| || ||||||||||| ||||| || || || |||||||| || ||||| |||||||| |||| ||
ttcacgtcttcaaaggcattctcttgtgttgaaggattttctagat-ccgcatagtttaagggatcc---gccaagttttccttattttttatggttcatgcagGTGTGGCAACATAAATTGGGCAAAGCGCACAAAATGTAACATCTGCAACACTGCCAAACCTGGTTTCAATGAAGGCGGTGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acataaattattgcttttcatattgcttcttccttatgattatgagttgtttcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG
ttgtttc CT-rich tract
ttttcatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatttaatccatgatgttttaaaaaatatggtcaaataaacatcacataaattattgcttttcatattgcttcttccttatgattatgagttgtttcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG
- - - - -ccatgat
- - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - -acataaa