Sequence
atgc intronic sequence ATGC exonic sequence...atttttgtggaatctatttattatcttttctcccatttattgatgcccatatatagtcctgccatgcccacttcaagtgtctgattttgaactgcaccagAACCTGTTTCAAGGCACATGGAGGAGCAAGGGCTTGAGTTTCTTCAATTTGCTTTCCGTTGGTTCAACTGTCTTCTAATACGAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0094g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 7
atttttgtggaatctatttattatcttttctcccatttattgatgcccatatatagtcc--tgccatgcccac-ttcaagtgtctg--attttgaactgcaccagAACCTGTTTCAAGGCACATGGAGGAGCAAGGGCTTGAGTTTCTTCAATTTGCTTTCCGTTGGTTCAACTGTCTTCTAATACGAGAG
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-----cagaatagttatgtgttgtttgtagaagaaaaaaagaacagttttgcctagtacattaaaattccaatgtttaaccatctggcatcttctggttatacagAACCTGTGTCAAAGCACATGGAGGAACAAGGATTGGACTTTCTTCAGTTTGCGTTTCGTTGGTTCAATTGTCTTATGATTCGTGAG
upper sequence: Vv05s0094g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G142806_T01 (Zea mays), 3'ss of exon 8
atttttgtggaatctatttattatcttttctcccatttattgatgcccatatatagtcctgccatgcccacttcaagtgtctgattttga--actgcac-cagAACCTGTTTCAAGGCACATGGAGGAGCAAGGGCTTGAGTTTCTTCAATTTGCTTTCCGTTGGTTCAACTGTCTTCTAATACGAGAG
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--cgtcatgggatctgctcataagactagagttc-ctaattcttccatatatcagggaaaaacacttcatcttttacctcgtattttttgctgttgtatgcagAACCTGTTTCCAAGCACATTGAAGAGCAAGGATTAGAGTTTCTTCAGTTTGCCTTCCGCTGGTTCAACTGCCTTCTGATACGAGAG
upper sequence: Vv05s0094g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G13330.1 (Glycine max), 3'ss of exon 7
atttttgtggaatctatttattatcttttctcccatttattgatgcccatatatagtcctgccatgcccacttcaagtgtctga---ttttgaactgcaccagAACCTGTTTCAAGGCACATGGAGGAGCAAGGGCTTGAGTTTCTTCAATTTGCTTTCCGTTGGTTCAACTGTCTTCTAATACGAGAG
|| | || | |||| ||| ||| || ||| | ||| | || | | |||| |||||| |||||||||| ||||||||| ||||||| ||||| || || ||||| |||||||| ||||||||||| ||||||||||||||||| || || |||
-gaattaccaagccttctccttatttttgttcctat--attattatttgtatgtgttcaaatgtaatctgatgtgccctactgaaacttttgagctgcaccagAGCCTGTTTCACGGCACATTGAGGATCAGGGACTTGAATTTCTTCAGTTTGCTTTCCGCTGGTTCAACTGTCTTCTCATCCGTGAG
upper sequence: Vv05s0094g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G05350.1 (Glycine max), 3'ss of exon 8
atttttgtggaatctatttattatcttttctcccatttattgatgcccatatatagtcctgccatgcccacttcaagtgtctga--ttttgaactgcaccagAACCTGTTTCAAGGCACATGGAGGAGCAAGGGCTTGAGTTTCTTCAATTTGCTTTCCGTTGGTTCAACTGTCTTCTAATACGAGAG
|| || || | |||| ||| | | || ||| || || | || | | | | | | || | |||||| |||||||||| |||||||| ||||||| ||||| || || ||||| |||||||| ||||||||||| ||||||||||||||||| || || |||
tgaattaccaaaccttctccttatttttgttgctatatat--atagttatttgtatgtattcaaatgtaatctgatgtagtgaaacttttgagctgcaccagAGCCTGTTTCGCGGCACATCGAGGATCAGGGACTTGAATTTCTTCAGTTTGCTTTCCGCTGGTTCAACTGTCTTCTCATCCGTGAG
upper sequence: Vv05s0094g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA13G42180.1 (Glycine max), 3'ss of exon 7
at-ttttgtggaatctatttattatcttttctcccatttattgatgcccatatatagtcctgccatgcccacttcaagtgtctgattttgaactgcaccagAACCTGTTTCAAGGCACATGGAGGAGCAAGGGCTTGAGTTTCTTCAATTTGCTTTCCGTTGGTTCAACTGTCTTCTAATACGAGAG
|| | || | || | | ||| || | || | || | || || | | | | | | ||||||| | | ||||| |||||||||| || |||||||||||||| | || |||||||||||||||||||| |||||||||||||||||||| || |||
atatcttataaaaaacaactgatattttgaaatgtagggatataatattatttgtatgtctccta-attgaatctgatactgaaattttgagttcccccagATCCTGTTTCAAACCATATGGAGGAGCAAGGATTGGAATTTCTTCAATTTGCTTTCCGCTGGTTCAACTGTCTTCTAATCCGCGAG
upper sequence: Vv05s0094g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA15G03200.1 (Glycine max), 3'ss of exon 7
at-ttttgtggaatctatttattatcttttctcccatttattgatgcccatatatagtcctgccatgcccacttcaagtgtctgattttgaactgcaccagAACCTGTTTCAAGGCACATGGAGGAGCAAGGGCTTGAGTTTCTTCAATTTGCTTTCCGTTGGTTCAACTGTCTTCTAATACGAGAG
|| | || || | | ||| || | || || || | || || | | | | | | || |||| | | ||||| |||| ||||| || |||||||||||||| | || |||||||||||||||||||| |||||||||||||||||||| || |||
atatcttacaaaaaaaaactgatattttgaaatgtagggatatattattatttgtatatct-cgaaattgaatctgatactgaaatattgagttccgccagATCCTGCTTCAAACCATATGGAGGAGCAAGGATTGGAATTTCTTCAATTTGCTTTCCGCTGGTTCAACTGTCTTCTAATCCGCGAG
upper sequence: Vv05s0094g00070.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 7
----atttttgtggaatctatttattatcttttctcccatttattgatgcccatatatagtcctgccatgcccacttcaagtgtctgattttgaactgcaccagAACCTGTTTCAAGGCACATGGAGGAGCAAGGGCTTGAGTTTCTTCAATTTGCTTTCCGTTGGTTCAACTGTCTTCTAATACGAGAG
||| | |||||| || ||| || |||||| | | |||||| | ||| ||| || |||| ||| | || ||||||||||||||| |||||||| ||||| ||||| ||||||||||||||||||||||| |||| || |||||||| || || |||
cataattaaccaaccacctattttccat-tttaggcctgattattgttttata-atatagagttaacattgtcacatctt-catctg-ccttgttatatactagAACCTGTTTCAAGACACATGGAAGAGCATGGGCTAGAGTTTCTTCAATTTGCTTTCCGGTGGTATAATTGTCTTCTGATTCGTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccatatatagtcctgccatgcccacttcaagtgtctgattttgaactgcaccagAACCTGTTTCAAGGCACATGGAGGAGCAAGGGCTTGAGTTTCTTCAATTTGCTTTCCGTTGGTTCAACTGTCTTCTAATACGAGAG
gtctgat putative branch site (score: 4)
attttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttttgtggaatctatttattatcttttctcccatttattgatgcccatatatagtcctgccatgcccacttcaagtgtctgattttgaactgcaccagAACCTGTTTCAAGGCACATGGAGGAGCAAGGGCTTGAGTTTCTTCAATTTGCTTTCCGTTGGTTCAACTGTCTTCTAATACGAGAG
- - ttgtgga
- - - - - - - - - - - - - -ttctccc
- - - - - - - - - - - - - - - - - - - - - -tgcccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tcctgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtctga