Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgttttcatagtgtctggtgatatttatggatctgcagttgtttgtggctaaattttgcattgctgatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 9
--------gtatgtgttttcatagtgtctggtgatatttatggatctgcagttgtttgtggctaaattttgcattgctgatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT
| | | | ||| ||| | ||| | | || | | ||| || || || || ||| |||||||||||||||||||| |||||||| ||||| || |||||||||
gtaactgcctttttctcctcaggtcttctacaagttcatattactgcatatttatcttaatttaagttacgcttt-ctatatagGGTGCTGTATGTATGAGATGGCAGCTCATCGGCCTGCCTTCAAGGCTTTT
upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g64490.1 (Oryza sativa), 3'ss of exon 10
gtatgtgttttcatagtgtctggtgatatttatggatctgcagttgtttgtggctaaattttgcattgctgatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT
| || | | | | ||||| | | || || ||| | || | | ||| |||| || |||||||| ||||||||||||||||| ||||| || ||||| |||
--gtaatattcccttgctcatatggatatgtttaaatgtgtga--atttctaactgatatagatattta----cagGATGTTGTATGTACGAGATGGCTGCTCATCGGCCTGCCTTCAAGGCATTT
upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G074262_T01 (Zea mays), 3'ss of exon 10
gtatgtgttttcatagtgtctggtgatatttatggatctgcagttgtttgtggctaaattttgc--attgctgatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT
||| |||| | | | ||| ||| || | | || | || ||| | | || |||| || |||||||||||||||||||||||||| ||||| || |||||||||
gtaatagtttcttacatataaagagatgctta--aatatattaatattagatgcctcttttaactggtgtctttgcagGATGTTGTATGTATGAGATGGCTGCTCATCGACCTGCTTTCAAGGCTTTT
upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 10
-------------------gtatgtgttttcatagtgtctggtg-----atatttatggatctgcagttg-tttgtggctaaat---tttgcattgctgatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT
| | ||| || ||| | || ||| | ||| | | || || || || ||| |||| || | ||| || ||||||||||||||||| ||||| |||||||| || ||||| |||
gtattacgttttacctggttcaattctttcagtaatgtgagatgtttacataactggtgatttattataaattcctgacttaacatgttttcatt--tgcttagGATGTTGTATGTATGAGATGGCAGCTCACCGCCCTGCCTTCAAGGCATTT
upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 9
gtatgtgtttt-catagtgtctgg-tgatatttatggatctgcagttgtttgtggctaaattttgcatt-gctgatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT
|||| ||| || || | ||||| || | ||||| | |||||||| | | || | || |||||||| ||||| ||||||||||||||||||||||| || ||||| ||||||
gtatatgtcttatgcgatgaatatctgatagttgt---tctgc-------tatggctaaaatgtatttttgttgttcagGTTGTTGTATATATGAGATGGCTGCTCATCGCCCAGCTTTTAAAGCTTTT
upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 9
gtatgtgttttcatagtgtctgg-tgatatttatggatctgcagttgtttgtggctaaattttgcattgct-gatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT
|||| | || | | | | |||| || || || ||| | | |||||| || || || | ||||| |||||||| || ||||||||||||||||||||||| ||||| ||||||
gtatatattctaaaaccaagtatctgatgattgcacatttggctttgct-gcagctaaaattaatttttcttgttcagGGTGCTGTATATACGAGATGGCTGCTCATCGCCCTGCCTTTAAAGCTTTT
upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 9
gtatgtgttttcatagtgtctggtgatatttatggatctgcagttgtttgtggctaaattttgcattgct-gatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT
|||| ||| || | ||| |||| || || | | || | |||||| || | | |||||||| ||||| ||||||||||||||||||||||| || ||||| ||||||
gtatatgtcttagg------cgatga-atttctg-atattcgttttgctaccgctaaaaggcattttttttgttcagGTTGTTGTATATATGAGATGGCTGCTCATCGCCCAGCTTTTAAAGCTTTT
upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 9
--gtatgtgttttcatagtgtctggtgatatttatggatctgcagttgtttgtggctaaattttgcattgct-gatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT
| | |||| | | || | | ||| || ||| || ||| | | |||||| | || || | ||||| |||||||| || ||||||||||||||||||||||| ||||| ||||||
gtatgtatgttataaccaagtatc-taatacttgcagatttggttttgct-gcagctaaaatgaattttacttgttcagGGTGCTGTATATACGAGATGGCTGCTCATCGCCCTGCTTTTAAAGCTTTT
upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ20709 (Selaginella moellendorffii), 3'ss of exon 9
gtatgtgttttcatagtgt-ctggtgatatttatggatctgcag--ttgtttgtggctaaattttgcattgctgatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT
|| | ||| |||| || || | ||| || | | ||||| | |||| ||| || ||||||||||||||||||||||| || ||||| || || || ||
---------------gtatgctgatgatggttccaagcttgtcgcattgattttcttgatcttttgaaatgct----agGATGTTGTATGTATGAGATGGCTGCTCACCGACCTGCTTTCAAAGCCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtgatatttatggatctgcagttgtttgtggctaaattttgcattgctgatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT
ggctaaa putative branch site (score: 3)
taaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgttttcatagtgtctggtgatatttatggatctgcagttgtttgtggctaaattttgcattgctgatcagGTTGCTGTATGTATGAGATGGCTGCTCATCGCCCTGCATTTAAGGCTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT