Sequence
atgc intronic sequence ATGC exonic sequence...ctattttatgtgtttgccttccaatcttagtgctcacaattcttttagtttgatatgaagttattgtgcctgaagatattactgcaattgcatcaggaagAAGGATGGGTCGTTTGTAGGGTATTCAAGAAGAGAATGGCAACAATGCGGAAAGTGGGTGAACATGGGTCACCATGTTGGTATGATGACCAAGTTTCATT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0154g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G14700.1 (Glycine max), 3'ss of exon 2
-ctattttatgtgtttgccttccaatctta---gtgctcacaattcttttagtttgatatgaagttattgtgcctgaagatattactgcaattgcatcaggaagAAGGATGGGTCGTTTGTAGGGTATTCAAGAAGAGAATGGCAACAATGCGGAAAGTGGGTGAACATGG---GTCACCATGTTGGTATGATGACCAAGTTTCATT
||| | | ||| | || | | | | | | || | | | | ||||| | || | || | |||||||||||| ||||| || ||||| || ||||||||||||||| ||||||||| ||||||||| || ||| ||||| |||||||| ||||| ||||
aacattcttaatttttacattgtgctttcatgtggaattttagttgaaaaaatcaggccagggtttatttaatttttttttaacgttttaaccgtttcagGAAGAAGGCTGGGTTGTGTGTAGAGTGTTCAAGAAGAGAATGACAACAATGCAGAAAGTGGGAGAGTATGATCAATCACCCTGTTGGTACGATGAGCAAG-------
upper sequence: Vv02s0154g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G03340.1 (Glycine max), 3'ss of exon 2
---ctattttatgtgtttgccttccaat---cttagtgctcacaattcttttagtttgatatgaagttattgtgcctgaagatattactgcaattgcat--caggaagAAGGATGGGTCGTTTGTAGGGTATTCAAGAAGAGAATGGCAACAATGCGGAAAGTGGGTGAACATGGGTCACCATGTTGGTATGATGACCAAGTTTCATT
|||| | | ||||| | ||| | | | | | | |||| | | || ||| ||| || ||| ||| || ||| | ||||||||||| ||||| || ||||| || ||||| || ||||| ||||| || ||||| |||| || ||| ||||||||||||||||||||||| || |
ttatatttttgtttatttgcgctgtaatatattcactatgcgggagtgaaatagtaacctcttaa-ttagagtgt---aattaatttctgtaaatgctttccagGAAGAAGGCTGGGTTGTATGTAGAGTGTTCAAAAAACGAATGACAACAGTGAGGAAAATGGGGGAGTATGAGTCACCATGTTGGTATGATGACCCAGCTG----
upper sequence: Vv02s0154g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G04250.1 (Glycine max), 3'ss of exon 2
ctattttatgtgtttgccttcc-aatcttagtgctcacaattcttttagttt--gatatgaagttattgtgcc--tgaagatattactgcaattgcatcaggaagAAGGATGGGTCGTTTGTAGGGTATTCAAGAAGAGAATGGCAACAATGCGGAAAGTGGGTGAACATGG---GTCACCATGTTGGTATGATGACCAAGTTTCATT
| | | ||| | ||| ||| | | | || ||||| || | || | | | || | | | || | || ||||||||||| ||||| || ||||| || ||||||||||| ||| |||||| || ||||||||| || ||| ||||| |||||||| ||||| ||||
-agatatttttgtcaacattcttaatttctacacactttgttgttttatttcagaaaatcaggccagggtttcattattaactttttaattactgttccagGAAGAAGGCTGGGTTGTGTGTAGAGTGTTCAAGAAGAGGATGACAACAACGCAGAAAGTGGGAGAGTATGATCAATCACCCTGTTGGTACGATGAGCAAG-------
upper sequence: Vv02s0154g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 2
---------ctattttatgtgtttgccttccaatct-tagtgctcacaattcttttagtttgatatgaagttattgtgcctgaagatattactgcaattgcatcaggaagAAGGATGGGTCGTTTGTAGGGTATTCAAGAAGAGAATGGCA---ACAATGCGGAAAGTGGGTGAACATGGGTCACCATGTTGGTATGATGACCAAGTTTCATT
||| | | | |||| | || || | | | | |||| ||| || | |||| | || || || || |||||||||||||||| || ||||||||||||||||||| | ||||| ||| || ||||| |||| || | ||| || | | | || | |
cattggtcactactcactacacacaagaactcatctgtgatggaca-agtgttgtgcatttgcgatgttgtaaatgtg-----atatttttatgtgatgtgtgtagGAAGAAGGATGGGTAGTATGTAGGGTATTCAAGAAGAAATTGGCAGCGACAGTGAGGAAAATGGGAGATTACCATTCATCACCATCGCAGCATTGGTACG-------
upper sequence: Vv02s0154g00020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G12260.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------ctattttatgtgtttgccttccaatcttagtgc-tcacaatt-cttttagtttgatatgaagttattgtgcctgaagatatt--actgcaattgcat--caggaagAAGGATGGGTCGTTTGTAGGGTATTCAAGAAGAGAATGGCAACAATGCGGAAAGTGGGTGAACATGGGTCACCATGTTGGTATGATGACCAAGTTTCATT
|| |||| | | | |||||| | | | | | || | | || | | || | ||| | | ||| | | ||| | |||||||||||||||| || |||||||| |||||||||||| |||| || | | | |||| || | | ||| | || || || | | |
gtattaatataacaaccctaaaacattacttctctataaaagttagttgcatgtttatactaaacaatctcattatatgatagttgcatatatgatctcctaaaatcatttgaggtaatctcattaaatgatatttgggttgtagGAAGAAGGATGGGTTGTGTGTAGGGTTTTCAAGAAGAGATTGGCTGCAGTTAGACGAATGGGAGATTACGACTCATCCCCTTCACATTGGTACGATGATC---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtttgatatgaagttattgtgcctgaagatattactgcaattgcatcaggaagAAGGATGGGTCGTTTGTAGGGTATTCAAGAAGAGAATGGCAACAATGCGGAAAGTGGGTGAACATGGGTCACCATGTTGGTATGATGACCAAGTTTCATT
gtttgat putative branch site (score: 5)
aagatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctattttatgtgtttgccttccaatcttagtgctcacaattcttttagtttgatatgaagttattgtgcctgaagatattactgcaattgcatcaggaagAAGGATGGGTCGTTTGTAGGGTATTCAAGAAGAGAATGGCAACAATGCGGAAAGTGGGTGAACATGGGTCACCATGTTGGTATGATGACCAAGTTTCATT
- - - - - - - - ccttcca
- - - - - - - - - - - - - - - -gctcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcaat