Sequence
atgc intronic sequence ATGC exonic sequencegtattttttcccttcttgatgactaaacccaatattaatcatttttgtacctattttcttctctatgatatggataaagggtggtgatgtgtgcatgtacttgattttaattttttttcagGAAGCTTTGGATATTGTTCATGTCAGCAAAGAGGACCAAGAGAGTGTATTTGCCATGCTTGCTGCAGTTTTGTGGATGGGAAATGTCTCGTTTACTGTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 10
--gtattttttcccttcttgatgactaaaccca-atattaatcatttttgtacctattttcttctctatgatatggataaagggtggtgatgtgtgcatgtact-tgattttaattttttttcagGAAGCTTTGGATATTGTTCATGTCAGCAAAGAGGACCAAGAGAGTGTATTTGCCATGCTTGCTGCAGTTTTGTGGATGGGAAATGTCTCGTTTACTGTGA
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gtacactgtttttataatttatacatcattctacagaacaagctctttcgtagtttcatgtgtttttctgttctt---------tgcttatgt---catgttttctgatttc--ttctatttcagCAAGCTATGAACATTGTTCATATCAGCAAAGAGGACCAAGAGAGTGTTTTTGCAATGGTCTCTGCTGTTCTTTGGCTGGGGGATGTCTCGTTCACAGTAA
upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 10
gtattttttcccttcttgatgactaaacccaatattaatcatttttgtacctattttcttctctatgatatggataaagggtggtgatgtgtgcatgtacttgattttaattttttttcagGAAGCTTTGGATATTGTTCATGTCAGCAAAGAGGACCAAGAGAGTGTATTTGCCATGCTTGCTGCAGTTTTGTGGATGGGAAATGTCTCGTTTACTGTGA
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gtactgtttttatacctcattctacagaacaagctcttccgtgtgtgtgtgtgtgtgttttttttctgt-----tctttgctcctatcatgt-----tttctgatttc--ttctattttagGAAGCTATGGACATCGTTCATATCAGCAAAGAGGACCAAGAGAATGTTTTTGCAATGGTCTCTGCTGTTCTATGGCTGGGGGATGTCTCGTTCACAGTAA
upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 9
--------------------------------gtattttttcccttcttg-atgactaaacccaatattaatcatttttgtacctattttcttctctatgatatggataaagggtggtgatgtgtgcatgtacttgattttaatttt--ttttcagGAAGCTTTGGATATTGTTCATGTCAGCAAAGAGGACCAAGAGAGTGTATTTGCCATGCTTGCTGCAGTTTTGTGGATGGGAAATGTCTCGTTTACTGTGA
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gtacacattatttttcatcactttttgcttatgaatgatctgcattcacataggtttatatatgattttttacaatttccattttgtcttatggtttgagtctgaaataatagcttgacatacatgagtttttttcatgctatttttaatttccagGAAGCTCTGGATGTTGTCCACATTAGCAAAGGAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGG
upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 9
-----gtattttt-tcccttcttgatgactaaacccaata------ttaatcattt-ttgtacctattttcttctcta--tgatatggataaagggtggtgatgtgtgcatgtacttgattttaattttttttcagGAAGCTTTGGATATTGTTCATGTCAGCAAAGAGGACCAAGAGAGTGTATTTGCCATGCTTGCTGCAGTTTTGTGGATGGGAAATGTCTCGTTTACTGTGA
||| ||| | || ||||| ||| | ||| |||| || || || || || |||| | || | |||| ||| | | | || || ||||||||| | ||| |||| || |||| ||||| ||||| |||| ||||||||| |||||||||||||| || ||| | ||||| | || ||||||||||
gtacactatctttgtagtttaaagatgatctgctttcatagactcttaaatgatttcttacttctgcttgattgactgattgattttgaaatgatagtttgatacaaaaatgaatatactattg-ccaacttccagGAAGCTCTAGATGTTGTCCACATCAGAAAAGAAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGA
upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 11
----------------gtattttttcccttcttgatga-ctaaaccca-ata---ttaatcat--ttttgtacctattttcttct---ctatgatatggat---aaagggtggtgatgtgtgcatg---tacttgattttaatttt--ttttcagGAAGCTTTGGATATTGTTCATGTCAGCAAAGAGGACCAAGAGAGTGTATTTGCCATGCTTGCTGCAGTTTTGTGGATGGGAAATGTCTCGTTTACTGTGA
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gtatacattatttttcatcgcttgttgcttatgaatgatctgcattcacataagtttatatatgatttcttacaatttccattttgacttgtggtttgagtctgaaataatagcttgacatacatgagttttttcatgctatttttaatttccagGAAGCTCTGGATGTTGTCCACATTAGCAAAGGAGACCAGGAGAATGTATTTGCAATGCTTGCTGCAGTATTATGGTTAGGAAACATATCATTTACTGTGG
upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 12
gtattttttcccttcttgatgactaaacccaatattaatcatttttgtacctattttcttctctatgatatggataaagggtggtgatgtgtgcatgtacttgattttaattttt------tttcagGAAGCTTTGGATATTGTTCATGTCAGCAAAGAGGACCAAGAGAGTGTATTTGCCATGCTTGCTGCAGTTTTGTGGATGGGAAATGTCTCGTTTACTGTGA
|| | | || ||| || ||| | || || |||| || || | | || | | | || ||||||| || ||| || ||||||||| |||| ||||| ||||| || ||||| || ||||| ||||||||||| ||||||||||||||||| ||| ||||||| || || || || || |
-----------------------gtaattctctctt--tcagttagatactttcttcctcctcttctctactcatttcagacctttatttttctgttta-ttgatttaaaagtttctgttgttgcagGAAGCTCTGGACATTGTGCATGTTAGTAAAGAAGATCAAGAAAGTGTATTTGCAATGCTTGCTGCAGTTTTATGGCTGGGAAACGTTTCCTTCACCGTTA
upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 11
gtattttttcccttcttgatgactaaacccaatattaatc--atttttgtacctattttcttctctatgatatggataaagggtggtgatgtgtgcatgtacttgattttaattttttttcagGAAGCTTTGGATATTGTTCATGTCAGCAAAGAGGACCAAGAGAGTGTATTTGCCATGCTTGCTGCAGTTTTGTGGATGGGAAATGTCTCGTTTACTGTGA
||| || ||||| | || | || ||| |||||| | | || || | | | || | || | |||||||||||||| |||||||| ||||| || ||||| || ||||| | ||||||||| |||||||||||||| || ||| | || ||||| || ||||| | |
----------------------gtaactccctcattaagtcaaaccttttctctttttctttctctgcaacttcga-----------gacatttatttcgacctt-ttacgttgccgtttcagGAAGCTTTAGATATTGTGCATGTTAGTAAAGAAGATCAAGAAAATGTATTTGCAATGCTTGCTGCAGTATTATGGCTAGGGAATGTTTCTTTTACCATTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatggataaagggtggtgatgtgtgcatgtacttgattttaattttttttcagGAAGCTTTGGATATTGTTCATGTCAGCAAAGAGGACCAAGAGAGTGTATTTGCCATGCTTGCTGCAGTTTTGTGGATGGGAAATGTCTCGTTTACTGTGA
ttttaat putative branch site (score: 3)
ttttaattttttttc CT-rich tract
atgtacttgattttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttttcccttcttgatgactaaacccaatattaatcatttttgtacctattttcttctctatgatatggataaagggtggtgatgtgtgcatgtacttgattttaattttttttcagGAAGCTTTGGATATTGTTCATGTCAGCAAAGAGGACCAAGAGAGTGTATTTGCCATGCTTGCTGCAGTTTTGTGGATGGGAAATGTCTCGTTTACTGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG