Sequence
atgc intronic sequence ATGC exonic sequence...tttttttatgttattaatcaatgtggcatgtcttttggcagattgattagtgtatctagaagaacagttttatttagtgattattgttattattttgcagTTGTATATCTTGATGCTGACACTATTGTTGTTAAAAGTATTGAGGATCTCTTTAAATGCGGGAAATTCTGTGCTAATTTGAAGCATTCTGAGAGGCTGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g41520.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------------tttttttatgttat-taatcaatgtggcatgtct--tttggcagattgattagtgtatctagaagaacagttttatt-tagtgattattgt-tattattttgcagTTGTATATCTTGATGCTGACACTATTGTTGTTAAAAGTATTGAGGATCTCTTTAAATGCGGGAAATTCTGTGCTAATTTGAAGCATTCTGAGAGGCTGAA
|| ||| || |||| || | | ||| | || | | | | | || |||| || || | | | ||| | | || |||| |||||| || || ||||| ||||| |||||||| ||||||||||||||| | || || || ||||| |||||||| || |||| |||||||| ||| ||||
gtatagttggatgatgtgttctgctttctatacatcatgggcattttgtttgttttggtttcatttgaattgcctaattgatctaactattctggtatgttttacccccacttttttttccgaggtcagtattgttctcatattcattttcttttgttttccagTTGCTTACCTCGATGCAGACACCATTGTTGTGAAAAGTATTGAGGATATTTTCAACTGTGGGAAGTTCTGTGCAAACCTGAAACATTCTGAAAGGATGAA
upper sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g43700.1 (Oryza sativa), 3'ss of exon 2
-------tttttttatgttattaatcaat-gtggcatgtcttttggcagattgattagtgtatctagaagaacagttttatttagtgattattgttattattttgc-agTTGTATATCTTGATGCTGACACTATTGTTGTTAAAAGTATTGAGGATCTCTTTAAATGCGGGAAATTCTGTGCTAATTTGAAGCATTCTGAGAGGCTGAA
| || | || | || || | |||| || | || ||| || | | |||||| | || || || || | |||| | ||| || ||||| |||||||| ||| | || || ||||||||||||||||| || || || ||||| ||||||| || ||||||||||||| || ||||
gtatgtttcaattaacatttccattctattaaagtatgttgttcctccatttcattt---catttttgttcattgtttta---aatgtttttttttttggttttcccagTCGTTTATCTCGATGCTGATACTGTGGTCGTGAAAAGTATTGAGGATCTTTTCAAGTGTGGGAAGTTCTGTGGCAACCTGAAGCATTCTGAAAGAATGAA
upper sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G43630.1 (Glycine max), 3'ss of exon 2
tttttttatgttattaatcaatgtggcatgtcttttggcagattgattagtgtatctagaagaacagttttatttagtgattatt-----gttattattttgcagTTGTATATCTTGATGCTGACACTATTGTTGTTAAAAGTATTGAGGATCTCTTTAAATGCGGGAAATTCTGTGCTAATTTGAAGCATTCTGAGAGGCTGAA
| | | | | || || || || | | ||| || || | |||||| || |||| | | | | ||||||||| || |||||||| ||||||||||| ||||||| |||||| ||||| || || || |||||||||||||||||||| ||||||||||||||| ||||
-----tggaggagacagtttaggtttcaggttttcagctttctatcttataagcggtacaatgtgtggtttattggttgtttatgcattgaatgtgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAAAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAATTTAAAGCATTCTGAGAGGTTGAA
upper sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G37000.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------tttttttatgttattaatcaa--tgtggcatgtcttttggcagattgattagtgtatctagaagaacagttttatttagtgattattgttattattttgcagTTGTATATCTTGATGCTGACACTATTGTTGTTAAAAGTATTGAGGATCTCTTTAAATGCGGGAAATTCTGTGCTAATTTGAAGCATTCTGAGAGGCTGAA
| | | | || | | | | | || | || ||| | | | || | | || | |||||| || | | ||| | ||||||||| |||||||||||||| |||||||| ||||| | |||||| || || || ||||| || ||||||||||||||||| ||||||||||||||| ||||
gtatagtatttatgttttttgtgtcgggttatggaagttgtggaggatgctctaaactttccatttaggttattgcctttcaaatgggatgtagcttctcatgtttatgccctatgatttattggctgtct-tgaatatgtatgtgcagTTGTTTATCTTGATGCTGATACTATTGTGGTTAAGAATATTGAAGAACTTTTCAAATGTGGAAAATTCTGTGCTAATTTAAAGCATTCTGAGAGGTTGAA
upper sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 2
tttttttatgttattaatcaatgtggcatgtcttttggcagattgattagtgtatc-tagaagaacagttttatttagtgattat-tgt----tattattttgcagTTGTATATCTTGATGCTGACACTATTGTTGTTAAAAGTATTGAGGATCTCTTTAAATGCGGGAAATTCTGTGCTAATTTGAAGCATTCTGAGAGGCTGAA
| | | | | || || || ||| || | | | | || || | |||||| || |||| || | | | | ||||||||| || |||||||| ||||||||||| |||| || |||||| ||||| || || || ||||||||||||||||| || ||||||||||||||| ||||
-----tgggggagacagtttaggtttcaagt-tttaagctttctatcttataagtggtacaatgtgtggtttattggttgtttatgcgttgaatgtgaatgtgcagTTGTTTACCTTGATGCGGACACTATTGTGGTTAGAAATATTGATGATCTTTTCAAGTGTGGGAAATTCTGTGCTAACTTAAAGCATTCTGAGAGGTTGAA
upper sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 2
tttttttatgttattaatcaatgtggcatgtcttttggcagattgattagtgtatctagaagaacagttttatttagtgattattgttattattttgcagTTGTATATCTTGATGCTGACACTATTGTTGTTAAAAGTATTGAGGATCTCTTTAAATGCGGGAAATTCTGTGCTAATTTGAAGCATTCTGAGAGGCTGAA
| | | ||| | |||| | ||| | | | |||| | | | | | || | || || || || |||||| |||||||||||||| |||||||| || || | ||||||||||| ||||| || || || || || || |||||||||||||||||||| ||
------------gtaggagatttcagcagtttttttcg----ttggattccggtttgagaacttaaatctcaaaagct--ttgtctttttttttgtgtagTTGTGTATCTTGATGCTGATACTATTGTGGTAAAGAACATTGAGGATCTGTTTAAGTGTTCTAAGTTTTGCGCAAACTTGAAGCATTCTGAGAGGCTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attagtgtatctagaagaacagttttatttagtgattattgttattattttgcagTTGTATATCTTGATGCTGACACTATTGTTGTTAAAAGTATTGAGGATCTCTTTAAATGCGGGAAATTCTGTGCTAATTTGAAGCATTCTGAGAGGCTGAA
gattgat putative branch site (score: 4)
ttatttt putative PPT
aacagttttatttagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttttatgttattaatcaatgtggcatgtcttttggcagattgattagtgtatctagaagaacagttttatttagtgattattgttattattttgcagTTGTATATCTTGATGCTGACACTATTGTTGTTAAAAGTATTGAGGATCTCTTTAAATGCGGGAAATTCTGTGCTAATTTGAAGCATTCTGAGAGGCTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - caatgtg
- - - - - - - - - - - - -gcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaac