Sequence
atgc intronic sequence ATGC exonic sequence...tgttttttcttaatgtagtgatagatgatagatgattaaacctttagagttatgctagtctttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 8
--tgttttttcttaatgtagtgatagatgatagatgattaaacctttagagttatgctagtctttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG
| ||| ||| | | || || | | | | || | | ||||||| | | | | || | || | || | | || || ||||||||| | || |||||||||||| |||| |||||||||||||||||||| |||||| | |
tggaatatttgttagt-tgttggcagctcactacttaatacttatgtc-agttatgattgccacaatgttgaggtgttcttattttttaatttattttgtagACTTGAGAACACGCTAAACTATGGTCTTGAACGAGTCTGGGCTGTTGGATACATGAAGGGTTCAAGAAG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G419984_T01 (Zea mays), 3'ss of exon 7
------tgttttttcttaatgtagtgatagatgatagatgattaaacctttagagttatgctagtctttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG
|||| | | |||| | | | | | || | ||||| | | || || || | | | | ||| | | || || || |||||||| | || ||||| ||||| ||||| |||||||||||||||||||| || || | |
ggaaaatgttctatactaatttc----tgaacgccacttgtgttgctctttataatctca-tatcctgagatgttctttgttttatatcttgaactatt-ctgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGGTCTAGAAG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 7
-tgttttttcttaatgtagtgatagatgatagatgattaaacctttagagttatgctagtctttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG
| | | | | | ||| || || | || | | ||||| | || | || | | | | || || | | | || || |||||||| | || ||||| ||||| ||||| |||||||||||||||||||| || ||| | |
atatcctatactggttgagtccgag-tgctgcttgtgttactctttataatttcataatcctaaggtgttctttgttttatactttgaactatttttgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGATCAAGAAG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G000645_T02 (Zea mays), 3'ss of exon 8
----tgttttttcttaatgtagtgatagatgatagatgattaaacctttagagttatgctagtctttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG
| |||| | | | | | | | || | ||||| | | | || || | | | | ||| | | || || || |||||||| | || ||||| ||||| ||||| |||||||||||||||||||| || || | |
ctggaaaatgttctatactgatttctgaacgccacttgtgttgctctttataatc---tcatcctgagatgttctttgttttatatcttgaactatt-ctgtagACTTGAGAACACACTAAACTATGGCCTTGAGAGAGTCTGGGCTGTTGGATACATGAAGGGGTCTAGAAG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 8
---tgttttttcttaatgtagtgatagatgatagatgattaaacctttagagttatgctagtc---tttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG
| |||| || | | | | | ||| | | | || ||| | |||| ||||| || | | | | ||| | | |||||| |||||||| ||||| |||||||||||||||||||||||| ||||||| |||| |||||||||||
ttacatgtttttaagatttcaccaaaattagtttgaaattgagattatggatatattccagtcatctttaaatttttatgg-tggtgcaatctgc-----ttgcagGCTTGAGAACACATTGAACTATGGTCTTGAAAGAGTTTGGGCTATTGGATATCTGAAGGGTTCACGCCG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 8
tgttttttcttaatgtagtgatagatgatagatgattaaacctttagagttatg--ctagtctttaatttccgacagactgaaccttcttcat-taactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG
|||||| ||| | || | | | | | ||||| ||| | |||| | | | | || | | |||||| |||||||| ||||| ||| |||||||||||||||||||| |||||||| |||| |||||||| ||
---tttttcataacatttctccttgaattattttgaaatatatctgagattatggatatatctgtcatttttaaatttttatggttgtgtaatatgcttgcagGCTTGAGAACACATTGAACTATAGTCTTGAAAGAGTTTGGGCTATTGGATACCTGAAGGGTTCACGTCG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 8
-tgttttttcttaatgtagtgatagat---gatagatgattaaacctttagagttatgctagtctttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG
| || |||| | | || || | | || | || | ||| ||| ||| | | |||| | | | | || | |||||| |||||||| || || ||||||||||||||||| |||||| |||||||| |||| |||| || ||
tttacagtttttaagctgttactaaatttagttggaagtatactttgtaagatatatactaattctccatttt----aatttttatggttcaatttgcttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 8
-tgttttttcttaatgtagtgatagatgatagatgattaaacct--ttagagttatgctagtctttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG
| |||| | | | || | | ||| | |||| | || || ||| | | | | || | | | || || | |||||| |||||||| || || ||||||||||||||||| |||||| |||||||| |||| |||| || ||
ctattttatttccgtttacagtttttaagctgat-actaaatgtagttggaagtatatt--ttggaagatatatactaattctccatttcaatgtatttgcagGCTTGAGAACACATTAAACTATGGTCTTGAAAGAGTCTGGGCTATTGGATACTTGAAGAGTTCTCGTCG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------------------------------------------------------------tgttttttcttaatgtagtgatagatgatagatgattaaacctttagagttatgctagtctttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG
| || | | || | | | | || ||| | |||| || | | | | | |||| || | || | | || || | |||||| |||||||| ||||||||||| ||||| ||||| ||||| |||| ||||| ||| ||||||||||
gtattataatattaaacagtttttttttgttggacatattatagtaaacgcttcttgtatgccttggctaaaccatctccactttggcttcattcttgtgcactttttcaccattaccaattt--cttttattgtccttcca-tttgtaatc-ccaatttcctaatgtctgttttttc-ttgcagGCTAGAGAACACATTGAATTATGGCCTTGAGAGAGTCTGGGCAATTGGTTACATTAAAAGTTCACGCCG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 12
----tgttttttcttaatgtagtgatagatgatagatgattaaacctttagag--ttatgctagtcttt----aatttccgacagactgaaccttcttcattaacta-----cagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG
| | || || | || || || || ||||| ||||| | || | | ||| ||| | | | || | || | | || | ||||| ||||| || ||||| ||||| ||||| || ||||||||| ||||| |||| ||||||||||||||
gtaactcgtatgctgtctgcattgg-agctgctat-tgattttgtctttaaaaacttccttcaatttttcaaaaatcttcatccaacagttttttacttaatacttgacatctagGCTTGAGAATACATTGAACTATGGCCTTGAGAGGGTTTGGGCTATTGGACACATTAAAGGTTCACGCCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagttatgctagtctttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG
cattaac putative branch site (score: 2)
ccttcttcatt CT-rich tract
tctttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttttttcttaatgtagtgatagatgatagatgattaaacctttagagttatgctagtctttaatttccgacagactgaaccttcttcattaactacagGCTCGAGAACACGTTGAATTATGGTCTTGAAAGAGTTTGGGCTGTTGGATACATGAAAGGTTCACGCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - gttatgc