Sequence
atgc intronic sequence ATGC exonic sequence...ctgattccttccaaattacattgacttagaaaataggaatcaagggtttattgcatatgtttgatatattttcctttcctatgctttgtctaatatgtagAGAAGAGGAAGAGCTGGCCGTGTTCAACCAGGAAAATGTTACCATCTCTATCCTCGATGTGTATATGATGCTTTTGCAGATTATCAATTGCCTGAAATTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0011g04360.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------------------------ctgattccttccaaattacattgacttagaaaa---------taggaatcaagggtttattgcatatgtttgatatattttcctttcctat-gctttgtctaata-tgtagAGAAGAGGAAGAGCTGGCCGTGTTCAACCAGGAAAATGTTACCATCTCTATCCTCGATGTGTATATGATGCTTTTGCAGATTATCAATTGCCTGAAATTT
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gtgtttttctcttgttggagtattactaattttatttttttcgtaacactttgaatgaatttgcattttctggaatcaatatgctaataaatatttttttttaactttaacacgcatatcatcaacttctatcatatcattttggctaattaaattgtataacaatttagAGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGTATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCC
upper sequence: Vv01s0011g04360.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G373175_T02 (Zea mays), 3'ss of exon 11
-----ctgattccttccaaatta-cattgacttagaaaataggaatcaagggtttattgcatatgtttgatat-attttcctttcctatgctttgtctaatatgtagAGAAGAGGAAGAGCTGGCCGTGTTCAACCAGGAAAATGTTACCATCTCTATCCTCGATGTGTATATGATGCTTTTGCAGATTATCAATTGCCTGAAATTT
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cgtggcttttaacctgaaaattgtcactgtctaagtcaattcta-tca------catcacttacctctaattttattttgctaattaaataaatgaatataatatagAGACGAGGACGAGCTGGCCGAGTCCAACCAGGGGAGTGCTACCATCTTTATCCACGATGTGTATATGATGCATTTGCTGACTACCAGTTACCAGAACTTC
upper sequence: Vv01s0011g04360.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 6
ctgattccttccaaattacattgacttagaaaataggaatcaagggtttattgcatatgtttgatatattttcctttcctatgctttgtctaata-tgtagAGAAGAGGAAGAGCTGGCCGTGTTCAACCAGGAAAATGTTACCATCTCTATCCTCGATGTGTATATGATGCTTTTGCAGATTATCAATTGCCTGAAATTT
||| | | || | | | || || || || | || | ||| | ||| ||| || |||| | | | | |||||||||||||||||||| ||||||||||||||| ||||||| |||||||||||| |||||||||||||| |||||||||| ||||||| ||||||||||
gcaattacctgtgaaccatgatcctacattaactaa-aaccatttgaccttttaacgactttattctatcctcccactaaattctttttttttttctctagAGAAGAGGAAGAGCTGGTCGTGTTCAACCAGGAGAATGTTATCATCTCTATCCTAGATGTGTATATGATTCTTTTGCAGAGCATCAATTACCTGAAATTT
upper sequence: Vv01s0011g04360.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G25800.1 (Glycine max), 3'ss of exon 14
-ctgattccttccaaatt---acattgacttagaaaataggaatcaagggtttattgcatatgtttgatatattttcctttcctatgctttgtctaatatgtagAGAAGAGGAAGAGCTGGCCGTGTTCAACCAGGAAAATGTTACCATCTCTATCCTCGATGTGTATATGATGCTTTTGCAGATTATCAATTGCCTGAAATTT
| | || || | ||| | ||| | || || | ||| || || | ||| | || || ||| | | |||||||||||||||||||| || |||||||||||| | |||||||||||||||||| ||||||| ||||||||||||||||| ||||| ||||| |||||||
accagtgaattttgaacttaattattaatcatgaatgaaattattggaccttaaatgctgatatt-gttatctgaattttcccctgatcctgtttt---tctagAGAAGAGGAAGAGCTGGTCGGGTTCAACCAGGAGAGTGTTACCATCTCTATCCTAGATGTGTGTATGATGCTTTTGCAGAGTATCAGTTGCCAGAAATTT
upper sequence: Vv01s0011g04360.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT2G01130.1 (Arabidopsis thaliana), 3'ss of exon 11
---ctgattccttccaaattacattgacttagaaaataggaatcaagggtttattgcatatgtttgatatattttcctttcctatgctttgtctaatat-gtagAGAAGAGGAAGAGCTGGCCGTGTTCAACCAGGAAAATGTTACCATCTCTATCCTCGATGTGTATATGATGCTTTTGCAGATTATCAATTGCCTGAAATTT
|||| | | || | || ||| | | | | ||| ||| || | || |||| | ||| ||||| ||| | || | |||||||||||||||| || ||||||| ||| ||| | ||||||||||| || || || |||||||||||||||||||| ||||| |||||||||||||
ataagtattcactgccaacaatcttaactatctgactggt--ccgtgggcttacatttagtgat--atttattgttgattctcatgctctgtttgtgattgcagAGAAGAGGAAGAGCCGGTCGTGTTCGACCTGGACAGTGTTACCATCTTTACCCAAAGTGCGTATATGATGCTTTTGCAGAATATCAGTTGCCTGAAATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttattgcatatgtttgatatattttcctttcctatgctttgtctaatatgtagAGAAGAGGAAGAGCTGGCCGTGTTCAACCAGGAAAATGTTACCATCTCTATCCTCGATGTGTATATGATGCTTTTGCAGATTATCAATTGCCTGAAATTT
gtctaat putative branch site (score: 3)
ttttcctttcctatgc CT-rich tract
atatgtttgatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgattccttccaaattacattgacttagaaaataggaatcaagggtttattgcatatgtttgatatattttcctttcctatgctttgtctaatatgtagAGAAGAGGAAGAGCTGGCCGTGTTCAACCAGGAAAATGTTACCATCTCTATCCTCGATGTGTATATGATGCTTTTGCAGATTATCAATTGCCTGAAATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - ccttcca
- - - - - - - - - cattgac
- - - - - - - - - - - - - -agaaaat
- - - - - - - - - - - - - - - - - - gaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - gcatatg
