Sequence
atgc intronic sequence ATGC exonic sequence...tttctcaatcctgcgattcaaaggggcctagtttactgcacctactctgacacctattttaatttattttctgttattgttatcttggtgtaaattgcagGGTCTAGTGCAACATCATGAAGAGGTAGTTGAATACTTCAACCGAAGAGGCGTGTCTGCAATCTTCCTTTTAAGAAGAAATACTCTCCAGCGTTATGTCT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g57550.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g57550.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G142507_T02 (Zea mays), 3'ss of exon 4
---------tttctcaatcctgcgatt--caaaggggcctagtttactgcacctactctgacacct-attttaatttattttctgttattgttatcttggtgtaaattgcagGGTCTAGTGCAACATCATGAAGAGGTAGTTGAATACTTCAACCGAAGAGGCGTGTCTGCAATCTTCCTTTTAAGAAGAAATACTCTCCAGCGTTATGTCT
|||| | ||||| | ||| | || | || || | ||| | | ||||| | || ||| |||| | ||| ||||| |||||||| || | || ||| ||||| |||||||||||||||||||||| || || || ||||| || || ||||||||||| ||| |
catagaactattctttgtatcacgattgtttgtgcggctaatttccaaagatatattcagcttccttgatctgttttatctagtgatatgcttattctagTGAAAATTATAGGGTCTAATGAAGCACCATCAAGAGATAGTTGAATACTTCAACCGAAGGGGTGTTTCCGCAATTTTTCTACTAAGAAGAAATCTTCTTC------------
upper sequence: LOC_Os01g57550.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G142507_T01 (Zea mays), 3'ss of exon 3
tttctcaatcctgcgattcaaaggggcctagtttactgcacctactctgacacct-attttaatttattttctgttattgttatcttggtgtaaattgcagGGTCTAGTGCAACATCATGAAGAGGTAGTTGAATACTTCAACCGAAGAGGCGTGTCTGCAATCTTCCTTTTAAGAAGAAATACTCTCCAGCGTTATGTCT
| | ||| | | | ||| | || | || || | ||| | | ||||| | || ||| |||| | ||| ||||| |||||||| || | || ||| ||||| |||||||||||||||||||||| || || || ||||| || || ||||||||||| ||| | |||||| ||||
-ctttgtatcacgattgtttgtgcggctaatttccaaagatatattcagcttccttgatctgttttatctagtgatatgcttattctagtgaaaattatagGGTCTAATGAAGCACCATCAAGAGATAGTTGAATACTTCAACCGAAGGGGTGTTTCCGCAATTTTTCTACTAAGAAGAAATCTTCTTCGGCGTTACGTCT
upper sequence: LOC_Os01g57550.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G877077_T01 (Zea mays), 3'ss of exon 3
tttctcaatcctgcgattcaaaggggcctagtttactgcacctactctgacacct-attttaatttattttctgttattgttatcttggtgtaaattgcagGGTCTAGTGCAACATCATGAAGAGGTAGTTGAATACTTCAACCGAAGAGGCGTGTCTGCAATCTTCCTTTTAAGAAGAAATACTCTCCAGCGTTATGTCT
| | ||| | | | ||| | || | || || | ||| | | |||| | || ||| |||| | ||| ||||| |||| || || | || ||| ||||| |||||||||||||||||||||| ||||| |||||||| || || ||||||||||| |||| |||||||||||
-ctttgtatcaagattgtttgtgtggcaaatttccaaagatatattcagcttccttgatctgtcttatctagtgatatgcttattctagtgaaaattatagGGCTTAATGAAGCACCATCAAGAGATAGTTGAATACTTCAACCGAAGGGGCGTTTCTGCAATTTTTCTACTAAGAAGAAATCTTCTCAGGCGTTATGTCT
upper sequence: LOC_Os01g57550.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G15730.1 (Arabidopsis thaliana), 3'ss of exon 3
-tttctcaatcctgcgattcaaaggggcctagtttactgcacctactctgacacctattttaatttattttctgttattgttatcttggtgtaaatt--gcagGGTCTAGTGCAACATCATGAAGAGGTAGTTGAATACTTCAACCGAAGAGGCGTGTCTGCAATCTTCCTTTTAAGAAGAAATACTCTCCAGCGTTATGTCT-
| | | | || | || | | | || | | | || | | || |||| || | ||| |||| | | | || || || |||||||||| || || | ||||||||| |||| ||||||||||| ||||||||||||| || ||||| || |||||||| |||| || ||| |
ctctgttagatctcctat-cttggtttattggtggattcttcatatttcattatcttgtttacgttgtaa--tgtgattggtttggggatgaaacttatgcagGGTCTAATGAAAAACCATGAAGAGATAGTAGAATACTTCAAAACCCGAGGCGTGTCTGCTATTTTCCTCTTTAGAAGAAAC-CTCTTGCGCCGGATGATTT
upper sequence: LOC_Os01g57550.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G34420.1 (Arabidopsis thaliana), 3'ss of exon 3
-tttctcaatcctgcgattcaaaggggcctagttta-ctgcacctactctgacacctattttaatttattttctgttattgttatcttggtgtaaattgcagGGTCTAGTGCAACATCATGAAGAGGTAGTTGAATACTTCAACCGAAGAGGCGTGTCTGCAATCTTCCTTTTAAGAAGAAA--TACTCTCCAGCGTTATGTCT
|||| | | | || | || | || | | | | |||| | | | | ||||||| | | || | | | | | ||||||||||||| || ||||||||||||| |||| ||||||||||| ||||||| ||||| || ||||| || |||| ||| || | | || | || |
ccttcttatttgatccataaacctcggttctatgtagcagtaattgaactgataaatgatcacagttattttatctgatgatgaatt--attaacattgcagGGTCTAATGAAACATCATGAAGAAATAGTAGAATACTTCAAAACCCGAGGCGTCTCTGCGATTTTCCTATTCAGAAAAAACCTATTGCGCCGCATGATAT-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgacacctattttaatttattttctgttattgttatcttggtgtaaattgcagGGTCTAGTGCAACATCATGAAGAGGTAGTTGAATACTTCAACCGAAGAGGCGTGTCTGCAATCTTCCTTTTAAGAAGAAATACTCTCCAGCGTTATGTCT
ttttaat putative branch site (score: 3)
tattttaatttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctcaatcctgcgattcaaaggggcctagtttactgcacctactctgacacctattttaatttattttctgttattgttatcttggtgtaaattgcagGGTCTAGTGCAACATCATGAAGAGGTAGTTGAATACTTCAACCGAAGAGGCGTGTCTGCAATCTTCCTTTTAAGAAGAAATACTCTCCAGCGTTATGTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA