Sequence
atgc intronic sequence ATGC exonic sequencegtaaatttccatattttttttttcaattgttttcatctgccttgcctgcctttagaaactttcaatgagttctaacctgtttgctcttgctcctggcattttctgttgctttcgtagAATACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGGAGCAATCGTGGAGATTTCAAAGAAAGTACAATACTTGGTTCCAACGGCATGTGGAGCCAC
Basic information
species | Oryza sativa |
transcript | LOC_Os03g44944.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g44944.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G340749_T01 (Zea mays), 3'ss of exon 12
gtaaatttccatattttttttttcaattgttttcatctgccttgcctgcctttagaaactttcaatgagttctaacctgtttgctcttgctcctggcattttctgttgctttcgtagAATACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGGAGCAATCGTGGAGATTTCAAAGAAAGTACAATACTTGGTTCCAACGGCATGTGGAGCCAC
||||||| ||| || || | || | ||| | || | | || || | ||| || || | || | | |||| || | | |||| ||||| || |||| | ||| |||||| | ||| ||||||||||||||||||| | | ||||||||| |||||||| ||||||||||||||||
-----------gtcaattttttttaatctttccaatttatatttgtttcctcca----ctacccacgaattttcaccagtccttagtttttactcataataa-tgtt-ctgttgcagAACACATATCAACAATACATGGCTGCTAGAGAATTGAAGAAGCAATCGTGGAGATTTCACCGGAGGTACAATACCTGGTTCCAGCGGCATGTGGAGCCAC
upper sequence: LOC_Os03g44944.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G100246_T01 (Zea mays), 3'ss of exon 4
gtaaatttccatattttttttttcaattgttttcatctgccttgcctgcctttagaaactttcaatgagttctaacctgtttgctcttgctcctggcattttctgttgctttcgtagAATACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGGAGCAATCGTGGAGATTTCAAAGAAAGTACAATACTTGGTTCCAACGGCATGTGGAGCCAC
|| ||||| | || | ||| |||| | || | || |||||| || | ||| || | | | ||| | | || ||| | || | | | |||| | |||| ||||| || |||| || ||| |||||||| ||| ||||||| ||||||||||| | | ||||||||| |||||||| ||||||||||||||||
gtcaattttcc--ttgctctttccaat-----ttatatttatttcctgcc-------accaccggtgaattttcatcagttagtttttactcgtaacaatgttctt--cttttgcagAACACATATCAACAATACTTGGCTGCTAGAGAACTGAAGAAGCAATCATGGAGATTTCACCGGAGGTACAATACCTGGTTCCAGCGGCATGTGGAGCCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatgagttctaacctgtttgctcttgctcctggcattttctgttgctttcgtagAATACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGGAGCAATCGTGGAGATTTCAAAGAAAGTACAATACTTGGTTCCAACGGCATGTGGAGCCAC
ttctaac putative branch site (score: 1)
ttttctgttgctttc putative PPT
attttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatttccatattttttttttcaattgttttcatctgccttgcctgcctttagaaactttcaatgagttctaacctgtttgctcttgctcctggcattttctgttgctttcgtagAATACATACCAGCAATTTTTAAGTGCCAGAGAACTAAAGGAGCAATCGTGGAGATTTCAAAGAAAGTACAATACTTGGTTCCAACGGCATGTGGAGCCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG