Sequence
atgc intronic sequence ATGC exonic sequence...gccagtttcaagttcacaacttttccaccagttttgccattgggaactttgcttgttctaacaggaagtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os03g51020.1 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------gccagtttcaagttcacaact----tttccaccagttttgccattgggaactttgcttgt-tctaacaggaagtttcttatctcaatt----tctgtt--ttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
|| | || | | | | | || || | || | | |||| || | |||||| || ||| ||| ||| ||| ||| | | ||||||||| ||||| || |||||||| |||||||||||| | || || ||||| ||||| || || ||||| || || ||||| || ||||| ||||||||
gtgctctttttctggtccttaattacttggcatttctttattagttcatttgtattaaaatgatacttggtatcatgcttggtgtttgcgtttgttaatttgtttatctctaac--gatattttttaactccattatatcctgctgacaatataacagAACTGGTTTTGAAGAAGACAAAAATTTCCATGTTGTTCTCAACTCTGTCATTGCTGGACGTTACCATGTCACAGAATATCTGGGTTCAGCAGCATTCAGT
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------gccagtttcaagttcacaacttttcc-----accagttttgccattg-ggaactttgcttgttctaacaggaagtttcttatctcaatttctgttttgtggtg-----cagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
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gtaatgcatttaaatgtttgtcccatattttaatcttactaaagcataaaaaatgatgtggtgattttcagttatctattgtccttgtgtgcctgtgttcacagtgtggcacttaaacctttttataaagtattttgtgtattctaacattatctcctattaattatcagAACTGGCTTTGAAGAAGACAAAAACTTCCATGTTGTTCTCAATTCTGTCATTGCTGGGCGTTATCATGTATCAGAGTATTTGGGTTCAGCTGCATTCAGC
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------gccagtttcaagttcacaacttttcc-----accagttttgccatt--gggaactttgct-tgttctaacaggaagtttcttatct-caatttctgttttgtggtg-----cagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
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gtattttctttaaatgattgttccatctgttaatcttgttaaagcataaaaaaatgatatggtaatttccagttatctattgtccttgtgtgcctgtgttcacagtgtggcacctacgccgtatttttaaaagatattttatatcttctaacaccgtctcctgttaattaacagAACTGGCTTTGAAGAAGACAAAAATTTCCATGTTGTTCTCAATTCTGTCATTGCTGGGCGTTATCATGTATCAGAGTATTTGGGGTCAGCTGCTTTCAGC
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA16G34510.1 (Glycine max), 3'ss of exon 2
-------gccagtttcaagttcacaacttttccaccagttttgccattgggaactttgcttgttctaacaggaagtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
| | | | | ||| || | | | | ||| |||||| || || | || | | | | | |||| || |||||||| | ||||||||| |||||||||||||| || |||||||||||||||||||| || ||||||||||||||||||| ||||||||||| || ||||||||||| |||
tgtaggtactattgttatgttggaaagtctgt----attcttgtcattggt--ctgtgttccttttggccttgacatgcc-atctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACCGAGTATCTGGGATCAGCTGCATTTAGC
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA09G29970.1 (Glycine max), 3'ss of exon 2
-------gccagtttcaagttcacaacttttccaccagttttgccattgggaactttgcttgttctaacaggaagtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
| | | | | ||| || | || | | ||| |||||| || || | || | | | | || |||| || |||||||| | ||||||||| |||||||||||||| || |||||||||||||||||||| || ||||||||||||||||||| || |||||||| || || |||||||| |||
tgtaggtactattgttatgttgcaaagt----cagtattcttgtcattggt--ctgtgttccttttggccttgacatgct-atctgaacccatgttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTACTAGCTGGGCGCTATCATGTCACTGAGTATCTGGGATCTGCTGCATTTAGC
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 4
-------gccagtttcaagttcacaacttttccaccagttttgccattgggaactttgcttgttctaacaggaagtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
|| | | | | | || | || || | | | ||| || |||| | || | | || | |||||| | ||||||||| |||||||||||||| || |||||||||||||||||||| || ||||||||| | ||||||||||| |||||| | || || |||||||| |||
attttttgctatgctgtaaagtatgatttcttgactgtttctatgttc-------tccctttttttaacctttatagtccttcttaaactaagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGGAGGTATCATGTTACTGAGTATTTGGGATCTGCTGCATTTAGC
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 2
--gccagtttcaagttcacaacttttccaccagttttgccattgggaactttgcttgttctaacaggaagtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
| | | ||| || | | | | || | | | | | | || |||| | |||| | || || |||||| | ||||||||| |||||||||||||| || |||||||||||||||||||| || |||||||| | ||||||||||| || ||| | || || |||||||| |||
gattttttgttatgttgtaaagtatgatttcttgtctgtttctatg--ttctcccttttttaacctttatactctttcttaaacttagtttttgttgctcagAACTGGCTTTGAGGAGGACAAGAATTTCCATGTTGTTTTAAATTCTGTAATAGCTGGAAGGTATCATGTTACTGAATATTTGGGATCTGCTGCATTTAGC
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT3G17750.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------gccagtttcaagttcacaacttttccaccagttttg------ccattgggaactttgcttgttctaacaggaa--gtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
| | || |||| || | | || | | ||| ||| || | | ||| || || |||| | || ||| | ||| ||||| ||||||||||| || ||||||||||| ||||| ||||| ||||| ||||| || || ||||| || ||| ||||||| ||||| || || |||
gtctgttcccttacaatatcgtggtttattatgtattaaatgatgtttcgtacacattttgtttagaagggggatgaagtctgtcccgaatcttgtgaaccctcaggaaatttatttgtttcttctatttgtcttctgttgcccagGACTGGTTTTGAGGAGGATAAGAACTTCCATGTGGTTTTGAATTCTGTCATTGCTGGTCGTTACCATGTCACTGAGCATCTTGGATCAGCAGCTTTTAGC
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 2
gccagtttcaagttcacaacttttccaccagttttgccattgggaactttgcttgttctaacaggaagtttcttatctcaatttctgttttgtggt--gcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
||| ||| || | || || ||| ||| ||| | | || | | | || | | | | || ||| | | ||||| | | ||| ||||| || || ||||| || ||||| | || ||||||||||| ||||| |||||||| || ||||| || ||||| ||||| ||||| || |||||
accattttacttttgaaaagttatcc-ccaagattgaagtagtcaaaatatttcgacatagctgagtgctgctc-tcttattacttgtttggcatttatcagGACTGGTTTCGAAGAGGAAAAGAACTTTAACGTGGTTTTAAATTCGGTCATTGCTGGGCGGTACCATGTCACTGAGTACCTTGGATCAGCAGCCTTCAGT
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G73450.1 (Arabidopsis thaliana), 3'ss of exon 2
gccagtttcaagttcacaacttttccaccagttttgccattgggaactttgcttgttctaacaggaagt-ttcttatctcaatttctgttttgtggt--gcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
||| | | | | || |||| | || | ||| ||||| || | || | | ||| | | ||| | | ||||| | | ||| ||||| || || ||||| || ||||| | || ||||||||||| ||||| |||||||| || ||||| || ||||| ||||| ||||| || |||||
accaagattgaactaaaaaaatttc-atcatcgtcttaattttttacttttatt--tatagctgagagtgctgctctcttattacttgtttggcatttatcagGACTGGTTTCGAAGAGGAAAAGAACTTTAACGTGGTTTTAAATTCGGTCATTGCTGGGCGGTACCATGTCACTGAGTACCTTGGATCAGCAGCCTTCAGT
upper sequence: Vv01s0011g01590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S47_312V6.1 (Physcomitrella patens), 3'ss of exon 3
gccagtttcaagttcacaacttttccaccagttttgccattgggaacttt--gcttgttctaacaggaagtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
| | | || | || | | | | ||| ||| ||| || | | ||| || || | | ||||| |||||||||||||| |||||| |||| | ||||| | ||| |||| | ||||| ||||||||||| || |||||||| || || ||||| ||||||
acttttgacgaggttttaagggcacttttctgtactctactggatttttttagctagtcgttgtttcag--ttcacataatgccgagtgcctggatttgcagGACTGGGTTTGAGGAAGACAAAGACTTTCCAGTTGTAATTAATGCAGTTGTTGCTGGTCGCTATCATGTGACGGAGTATCTGGGTTCTGCTGCCTTCAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actttgcttgttctaacaggaagtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
ttctaac putative branch site (score: 1)
tttctgtttt putative PPT
tttcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccagtttcaagttcacaacttttccaccagttttgccattgggaactttgcttgttctaacaggaagtttcttatctcaatttctgttttgtggtgcagAACTGGGTTTGAGGAGGACAAAAACTTCCATGTTGTTTTAAATTCAGTCATAGCTGGGCGCTATCATGTTACCGAGTATCTTGGGTCAGCTGCATTCAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - -tcacaac
- - - - - - - - - - - ttccacc
- - - - - - - - - - - - - - - - -ttgccat
- - - - - - - - - - - - - - - - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacagga