Sequence
atgc intronic sequence ATGC exonic sequence...atattataatatgtattggttccttatacataagcttcataatgtctgggctgtttgcaagcatttgcctgtcaataactcatttttttgtcactttcagGAAGAAAGAGATGCGGTTTTGGCCAAGATAGAAGTTTCGCAGGTTCATCTAGAATTGTTAAAGCGTACAAATGTTCTCAATGATGCATTCTATATTTCAC
Basic information
species | Oryza sativa |
transcript | LOC_Os03g44200.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g44200.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G092112_T01 (Zea mays), 3'ss of exon 5
atattataatatgtattggttccttatacataagcttcataatgtctgggctgtttgcaagcatttgcctgtcaataactcatttttttgtcacttt-cagGAAGAAAGAGATGCGGTTTTGGCCAAGATAGAAGTTTCGCAGGTTCATCTAGAATTGTTAAAGCGTACAAATGTTCTCAATGATGCATTCTATATTTCAC
|| ||| ||| ||| | | | | || ||| | | | || ||| | | | | | | || | | | | |||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||||||| | ||| |||| |||||||| |||||||||||||||||||||||||| ||||
atttta-gttatctatatgcaatattttcttacactttaatagtttgccactattttctgtgctattcattttggtatattaaaaatatcacacttttcagGAAGAAAGAGATGCAGTTTTTGCCAAGATAGAAGTTTCTCAGGTTCATTTGGAACTGTTGAAGCGTACTAATGTTCTCAATGATGCATTCTATATATCAC
upper sequence: LOC_Os03g44200.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G027857_T01 (Zea mays), 3'ss of exon 5
atattataatatgtattggttccttatacataa-gcttcataatgtctgggctgtttgcaagcatttgcc-tgtcaataactcattttt----------ttgtcactttcagGAAGAAAGAGATGCGGTTTTGGCCAAGATAGAAGTTTCGCAGGTTCATCTAGAATTGTTAAAGCGTACAAATGTTCTCAATGATGCATTCTATATTTCAC
||| || |||| || || || ||| ||| |||||| | ||||| | ||||| | | | || | | | ||||||||||||||||| || ||||| |||||||||| |||||| ||||||||| | ||| |||| |||| ||| ||||||||||||||||||||||||||||||
------------taattacttatctatatgcaatattttatgatgcttggatagtttgccaccattttctgtgtcattcattttgttatatgaaaaatatcgctgttttcagGAAGAAAGAGACGCAGTTTTTGCCAAGATAGGAGTTTCTCAGGTTCATTTGGAAATGTTGAAGCATACTAATGTTCTCAATGATGCATTCTATATTTCAT
upper sequence: LOC_Os03g44200.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G21490.1 (Glycine max), 3'ss of exon 5
atattataatatgtattggttccttatacataagcttcataatgtctgggctgtttgcaagcatttgcctgtcaa--taactcattt--------ttttgtcactttcagGAAGAAAGAGATGCGGTTTTGGCCAAGATAGAAGTTTCGCAGGTTCATCTAGAATTGTTAAAGCGTACAAATGTTCTCAATGATGCATTCTATATTTCAC
| || | | | | |||| | ||| | | || || || | || ||| | ||||| | | | | | ||||| || |||||||| ||||||||||||| |||||||| || | ||| ||||||| || |||||||||||||| ||||||||||| ||| ||||| |
---------tgtg-gctagaagttcaaacatgtagccgaaaattttctcctttttctgaaaaatataacttccaagtctaagcatttagcaaaaatactttaattaacagGAGGAGAGAGATGCAATTTTGGCCAAGATTGAAGTTTCACAAGCACATTTAGAATTATTGAAGCGTACAAATGTGCTCAATGATGCCTTCCCCATTTCTC
upper sequence: LOC_Os03g44200.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G26840.1 (Glycine max), 3'ss of exon 5
atattataatatgtattggttccttatacataagcttcataatgtctgggctgtttgcaagcatttgcctgtcaataactcatttttttgtcactttcagGAAGAAAGAGATGCGGTTTTGGCCAAGATAGAAGTTTCGCAGGTTCATCTAGAATTGTTAAAGCGTACAAATGTTCTCAATGATGCATTCTATATTTCAC
||| || ||| | | | | | | || | || | ||| || | | | | | ||||| || |||||||| ||||||||||||| |||||||| |||| ||| ||||||| || |||||||||||||| |||||||| || ||| ||||| |
-----------------------gtattagaaaactttctcctttttctgaaaaatataataactt--ccagcaaaaa-------tactttaattaacagGAGGAGAGAGATGCAATTTTGGCCAAGATTGAAGTTTCACAGGCACATTTAGAATTATTGAAGCGTACAAATGTGCTCAATGACGCCTTCCCCATTTCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgggctgtttgcaagcatttgcctgtcaataactcatttttttgtcactttcagGAAGAAAGAGATGCGGTTTTGGCCAAGATAGAAGTTTCGCAGGTTCATCTAGAATTGTTAAAGCGTACAAATGTTCTCAATGATGCATTCTATATTTCAC
caataac putative branch site (score: 2)
tttttttgtcactttc putative PPT
aataactcattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atattataatatgtattggttccttatacataagcttcataatgtctgggctgtttgcaagcatttgcctgtcaataactcatttttttgtcactttcagGAAGAAAGAGATGCGGTTTTGGCCAAGATAGAAGTTTCGCAGGTTCATCTAGAATTGTTAAAGCGTACAAATGTTCTCAATGATGCATTCTATATTTCAC
- - - - -tatgtat
- - - - - - - - - - - - - - - - -gcttcat
- - - - - - - - - - - - - - - - - - - - - tgtctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcctg