Sequence
atgc intronic sequence ATGC exonic sequence...tgggcgcattcgtgcccaattttgtcatcgtttttcttgacatcttgatgaagaaaatgaagtgattgaatggagttctttgatttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
Basic information
| species | Oryza sativa |
| transcript | LOC_Os06g08500.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G067654_T01 (Zea mays), 3'ss of exon 4
--------------------tgggcgcattcgtgcccaattttgtcatcgtttttcttgacatcttgatgaagaaaatgaagtgattgaatggagttctttgat-----ttgattttg--cttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
| | | | | | | | | || | | ||| || | | |||| || ||| || | | | ||| || || ||||||||||||||||||||||||||||||||||||||||||||||||| |||| |||||||||||||||||
gtcggcatcccccctctagctagctagctcctttctcttctctctcgctcgcgtcgtcaacaatcaacagacaacactgaaatggcgacgtggtgtgggtcggtcgtcgttgtttgtggttttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAGGTTCTTGCAGCTCCAAGTCAAG
upper sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
-----tgggcgcattcgtgcccaattttgtcatcgtttt-tcttgacatcttgatgaagaaaatgaagtgattgaatggagttctttgatttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
| ||| | | | ||||||| || | | || |||| | ||| || | | |||||| | | |||| |||| | | ||||| |||||||| || ||||| || ||||||||||| ||||| ||||||||||||||||||||||||
attataatgtttatttgcaaatattattgtcattattatatgttaacattat-atgggtcaatcgc--taattgaa-atattcgtttggtttg--tggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
upper sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G33020.1 (Glycine max), 3'ss of exon 4
tgggcgcattcgtgcccaattttgtcatcgtttttcttgacatcttgatgaagaaaatgaagtgattgaatggagttctttgatttgattttgc--ttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
| | || | || ||| || || || | || | | || | ||| || | || | || | || || | ||||| |||||||| || ||||| || ||||||||||| ||||| ||||||||||||||||||||||||
tcactattataatgttta-ttatgtaattattattatcc-tatgctaacattaaatgggtcaatccctaattgaaatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG
upper sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
tgggcgcattcgtgcccaattttgtcatcgtttttcttgacatcttgatgaagaaaatga-----agtgattgaatg-gagttctttgatttgatt--ttgcttg-cagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
|| | || | | | || | | | || | ||| | || | ||| | |||| ||| ||| | | | ||| ||||| |||||||| || |||||||| ||||||||||| || || |||||||| |||||||||||||||
---------tcaacatctatctctcttttagtattaaaaatacacaaacaaatacaatttcttccattgttaaaatatgtgttcattgggttggctcgtggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
upper sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G14380.2 (Glycine max), 3'ss of exon 4
-----tgggcgcattcgtgcccaattttgtcatcgtttt-tcttgacatcttgatgaagaaaatgaagtgattgaatggagttctttgatttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG----------------------------------
| ||| | | | ||||||| || | | || |||| | ||| || | | |||||| | | |||| |||| | | ||||| |||||||| || ||||| || ||||||||||| ||||| ||||||||||||||||||||||||
attataatgtttatttgcaaatattattgtcattattatatgttaacattat-atgggtcaatcgc--taattgaa-atattcgtttggtttg--tggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAGGTGCGCATCCCGCGTTTTTCTCTTGTACTAGCAT
upper sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
-------tgggcgcattcgtgcccaattttgtcatcgtttttcttgacatcttgatgaagaaaatgaagtgattgaatggagttctttgatttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
| | | ||| || || | || |||| | || | | || ||| || || || | | || || ||||| |||||||| |||||||| || |||||||| || || |||||||| | || ||||||||||||
taggctacaataataaagttaactaatgcagtaataaatgag-ttaggatctcagttctgacagttttgtttttgtat----tttatttgtataataatg--gacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
upper sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G30980.1 (Arabidopsis thaliana), 3'ss of exon 3
tgggcgcattcgtgcccaattttg--tcatcgtttttcttgacatcttgatgaagaa--aatgaagtgattgaatggagttctttgatttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
|| ||| | | || ||| | || | | ||| | | |||| |||| | | | || | | || || | | || | ||||| ||||| || || ||||| || ||||| ||||| || ||||||||| | |||||||||||||||
-tagctaattaattctaaaatttaattgataataatacttaataaacagatgcagaattgctaacaaggtttttttta-ttgttaaaaataata--attaacagACAGACAAAGCATCAATGCTCGATGAGATTATCGATTATGTCAAGTTCTTACAGCTCCAAGTCAAG
upper sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
---------------tgggcgcattcgtgcccaattttgtcatcgtttttcttgacatcttgatgaagaaaatgaagtgattgaatggagttctttgatttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
|| | | || ||| | || | |||| || | || || | |||| || ||| ||| || ||| |||||||||||||| || |||||||| |||||||| ||||| ||||| ||||||||||||||||| |||
cccggtctcgagcagtgcggcgagtcatgcgtagcgaaaccacctattttatttttactttaat-acgaaatcgataatgttgggtggggtggaatga--------------cagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
upper sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S209_22V6.2 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------------------------tgggcgcattcgtgcccaattttgtcatcgtttttcttgacatcttgatgaagaaaatgaagtgattgaa---tggagttctttgatttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
| || ||||| ||| | ||| || | | || | ||| | ||| | | ||||||| ||| | || | | | | ||| | ||||| || |||||||| |||||||| || ||||||||||| |||||||||||||| || ||||| |||
gtgcggcatcgttcgaacctgcctttcacttttttgtgctctgaatcagttgtatatgtatggtttagccacgtggtgaaaacataggtgcattagtgt--atctttctctacctacttatgtacagcatga-aagacagatgaagtctttgctatttaatcttatctcactgctgtttattaacagACTGATAAGGCGTCTATGCTGGATGAAATCATCGACTATGTCAAGTTCCTGCAACTTCAAGTGAAG
upper sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S173_83V6.1 (Physcomitrella patens), 3'ss of exon 3
tgggcgcattcgtgcccaattttgtcatcgtttttcttgacatcttgatgaagaaaatgaagtgattgaatgg---agttctttgatt--tgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
| |||||| | |||| ||||| |||| ||| | | || | | || |||| | | || | | | || | || | |||||||| ||||||||||||||||| || |||||||| ||||||||||||||||| |||||||| |||
---gaaacttcgtgt--atttttttcatctactttcacttgggcttattttaaaatctaattagaagaaatgatccaatcctcttactgctgtctgtggatacagACGGATAAGGCGTCGATGCTGGATGAAATCATCGATTACGTCAAGTTCCTGCAACTCCAAGTAAAG
upper sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ12627 (Selaginella moellendorffii), 3'ss of exon 4
--------tgggcgcattcgtgcccaattttg--tcatcgtt------tttcttgacatcttgatgaagaaaatgaagtga-ttgaatggagttctttgat-ttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
| ||| | | ||| ||||| | | ||| ||| ||| |||| || | | ||| || | ||| ||| || | | ||||| || || || |||||||| ||||| |||||||||||||| ||||| |||||||||||||||||
gtaagatcatatcccatccatcaccagttttggtttttagttcttaaattttttgctttctttatatgatcatttggatgacttccactgagctctgatatactcgcgtgataaacagACTGATAAAGCCTCGATGCTCGACGAAATCATCGACTACGTAAAGTTTTTGCAGCTCCAAGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgaagaaaatgaagtgattgaatggagttctttgatttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
ttttgctt CT-rich tract
tttgatttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgggcgcattcgtgcccaattttgtcatcgtttttcttgacatcttgatgaagaaaatgaagtgattgaatggagttctttgatttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - cgtgccc
- - - - - - - - - - - - - - - - tttcttg
- - - - - - - - - - - - - - - - - - - - - -cttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaatgg
