Sequence
atgc intronic sequence ATGC exonic sequence...aaaaaatattgccatattattttctcaaatctgttattttattggttttttcttcttgttggtttaaaattttgactcttttaattgttttcaattttagGCAGTGATCATGGAGTCAAAGCACAAGGAGATGGGTGGCTGCTAACTGTTGCCTTGATTGAAGGCAGTAATTTAGCAGCTGTTGACTCAAGTGGATTCTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g19400.1 (Oryza sativa), 3'ss of exon 2
---aaaaaatattgccatattattttctcaaatctgt-tattttattggttttttcttcttgttggtttaaaattttgactcttttaattgttttcaattt-tagGCAGTGATCATGGAGTCAAAGCACAAGGAGATGGGTGGCTGCTAACTGTTGCCTTGATTGAAGGCAGTAATTTAGCAGCTGTTGACTCAAGTGGATTCTC
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ctttagaaaaaccttc-tattcttgttctggacatatatactcccgtgatttatgcacata--tgaactaaacttt--gcttacatggtatttgggagtatatagGAAGTGATCATGGAGTCAAAGCACAAGGGAATGGTTGGTTGCTGACTGTCGCTCTGATTGATGGTACCAATTTAGCAGCAACCAAATCATCTGGTTACTC
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G005195_T03 (Zea mays), 3'ss of exon 2
aaaaaatattgccatattattttctcaaatctgtta-ttttattggttttttcttcttgttggt-ttaaaattttgactcttttaattgttttcaattttagGC--AGTGATCATGGAGTCAAAGCACAAGGAGATGGGTGGCTGCTAACTGTTGCCTTGATTGAAGGCAGTAATTTAGCAGCTGTTGACTCAAGTGGATTCTC---
|||| | | ||| ||| | ||| | | || | || | ||| ||| || | | || || |||| ||| || ||||||||||||||||||||||||| ||||| ||| |||| |||||||| |||| || || | || || ||||| | ||| ||| | |||
----tttatttttctttgattcaacaaaacttccaggtttcagatactgttctggataattactcttacaatctt--ccttattgatc-ttttggattgtatattagGTGATCATGGAGTCAAAGCACAAGGGGATGGCTGGTTGCTGACTGTTGCTCTGATGGAGGGAACCAACTTGGCAGCAACCAAATCATCTGGTTACTCTGA
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G12790.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------------------------------------------aaaaaatattgccatattattttctcaaatctgttat-tttattggttttttct--tcttgttggtttaaa--attttgactcttttaattgttttcaattttagGCAGTGATCATGGAGTCAAAGCACAAGGAGATGGGTGGCTGCTAACTGTTGCCTTGATTGAAGGCAGTAATTTAGCAGCTGTTGACTCAAGTGGATTCTC
| | ||| || | | | | | | | | | ||| || || | | || ||| || || ||||| |||| | || ||| ||||| |||||||||||| ||||||||||||||||||||||| |||||||||||||||| |||||||| || | |||||| ||||||| || ||||| || ||
gtaatctcaagagtgttcagttacttcacacttattgaatttggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcactcttgtcttttgactgtttagtgcccattaacttattttaatgcccatgtttttaattatattgacctttttggta--ttctaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------------------------------aaaaaatattgccatattattttctcaaatctgttat-tttattggttttttctt---cttgttggtttaaaatt---ttgactcttttaattgttttcaattttagGCAGTGATCATGGAGTCAAAGCACAAGGAGATGGGTGGCTGCTAACTGTTGCCTTGATTGAAGGCAGTAATTTAGCAGCTGTTGACTCAAGTGGATTCTC
| | ||| | | | | | ||| | | | |||| || || | | || || | |||| ||||| |||| | || |||| ||||| |||||||||||| ||||||||||||||||||||||| |||||||||||||||| |||||||| || | |||||| ||||||| || ||||| || ||
gtaatctcagaatgttcagttacttcacacttcatgaatctggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcgctcttgtcttttgaatgtttagtgcctattaacttattttaatgcctgcgtgtctgtaattatattgaccatttttggtattc-caatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G00850.1 (Glycine max), 3'ss of exon 4
----aaaaaatattgccatattattttctcaaatctgttattttattggttttttcttcttgttggtttaaaattttgactcttttaattgttttcaattttagGCAGTGATCATGGAGTCAAAGCACAAGGAGATGGGTGGCTGCTAACTGTTGCCTTGATTGAAGGCAGTAATTTAGCAGCTGTTGACTCAAGTGGATTCTC
| || | ||||||| | | ||| |||||| | | | | || ||| | | ||| |||| | |||| ||||| |||||||||||| | || ||||||||||| || ||| |||||||||| ||||| |||||||| || |||||||| ||||||| || |||| |||||
ttttctgttgtgtttcttaattatttggccc--ttgtttactttatttagtatctatatatgcc--tttgctgatataacttttttggggtactccaatattagGTAGTGATCATGGAATTAAGGCACAAGGAGAAGGATGGATGCTAACTGTGGCCTTAATTGAAGGAAGCAATTTAGCTACTGTTGATTCTAGTGCATTCTG
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G39920.1 (Glycine max), 3'ss of exon 3
aaaaaatattgccatattattttctcaaatctgtt-attttattggttttttcttcttgttggtttaaaattttgactcttttaattgt-tttcaattttagGCAGTGATCATGGAGTCAAAGCACAAGGAGATGGGTGGCTGCTAACTGTTGCCTTGATTGAAGGCAGTAATTTAGCAGCTGTTGACTCAAGTGGATTCTC
| ||| | ||| | | |||| | |||||| | | | | || ||| | | || |||| || | | || ||||| |||||||||||| | || ||||||||||| || ||| |||||||||| ||||| |||||||| || ||| |||| ||||||| || ||| |||||
tttctctcttgtttcttaattatttggcccttgtttactttatttagtgtctatatatgcc--tttgctgatataacattttttggggtactccgatgttagGTAGTGATCATGGAATTAAGGCACAAGGAGAAGGATGGATGCTAACTGTGGCCTTAATTGAAGGAAGCAATCTAGCTACTGTTGATTCTGGTGCATTCTG
upper sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 2
--aaaaaatattgccatattattttctcaaatctgttattttattggttttttcttcttgttggtttaaaattttgactcttttaattgtt----------ttcaattttagGCAGTGATCATGGAGTCAAAGCACAAGGAGATGGGTGGCTGCTAACTGTTGCCTTGATTGAAGGCAGTAATTTAGCAGCTGTTGACTCAAGTGGATTCTC
|| | || ||| | | | | | | || | | | ||| ||||| | | | || | | | || || | ||||| |||||||||||||||| ||||||| || |||||||| ||| ||||||||||||| | ||||| || || |||||||||| || |||| || |
gtaacatccatgaagatacagcatcgaccatttcatattctttcttgcggtctctcattgttagcgtggtgtgtttatccgactgatcattacatgtcaaatccaattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCTAGCAGCTGTAGATCCAAGCGGGCATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttcttcttgttggtttaaaattttgactcttttaattgttttcaattttagGCAGTGATCATGGAGTCAAAGCACAAGGAGATGGGTGGCTGCTAACTGTTGCCTTGATTGAAGGCAGTAATTTAGCAGCTGTTGACTCAAGTGGATTCTC
ttttaat putative branch site (score: 3)
ttgttttc CT-rich tract
tttaaaattttgactc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaaatattgccatattattttctcaaatctgttattttattggttttttcttcttgttggtttaaaattttgactcttttaattgttttcaattttagGCAGTGATCATGGAGTCAAAGCACAAGGAGATGGGTGGCTGCTAACTGTTGCCTTGATTGAAGGCAGTAATTTAGCAGCTGTTGACTCAAGTGGATTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
aaaaaat
- - - - ttgccat
