Sequence
atgc intronic sequence ATGC exonic sequencegtaagagcacattccttttgcttttcttttctgtcattattgctcataacgttctttttcatggcatagGAAGACTCTAATGCAACTCCTGCTTCATCTCGTCATAAAAGAGGTTGCAATTGCAAGAGATCATATTGTGTGAAGAAATACTGTGAATGCTTTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g43730.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g43730.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G366584_T01 (Zea mays), 3'ss of exon 5
----------gtaagagcacattccttttgct----tttcttttctgtcattattgctcataacgttctttttcatggcatagGAAGACTCTAATGCAACTCCTGCTTCATCTCGTCATAAAAGAGGTTGCAATTGCAAGAGATCATATTGTGTGAAGAAATACTGTGAATGCTTTCAG
|||| || || | || | | ||| ||| | ||| |||||||||| | | | | ||| |||||| || ||||| |||||||||||| |||| ||||||||||| |||||||||| || || | |||| | || |||||||| || |||||||||
gtaagaactaagaagaacagatcctattagttgcatttttatttttttcactattgctcatggcatcccgct-cat--tatagGATGATTCTAACAAAACTCCTGCTTCTGCTCGACATAAAAGAGGATGCAATTGCAGGAAGTCTTCTTGTCTTAAAAAATACTGCGAGTGCTTTCAG
upper sequence: LOC_Os03g43730.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT4G14770.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagagcacattccttttgcttt---tcttttctgtcat-----tattgctcataacgttct-------ttttcatggcata--gGAAGACTCTAATGCAACTCCTGCTTCATCTCGTCATAAAAGAGGTTGCAATTGCAAGAGATCATATTGTGTGAAGAAATACTGTGAATGCTTTCAG
||| || |||| | |||| || | | |||| ||| | | | ||| | || | ||| || | ||| || | | |||||| ||||| | || |||||| | || ||||| ||||||| |||| | ||| ||||||||||||||||||||| ||||
gtaggattcttttccccgtcctttgattcctctgcatcatccatctatcttgcttgaagttataataatattgtaatgacacacagGATGATGCAAGCAAAACTCCAGCTTCTGCGCGCCATAAACGTGGCTGCAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
upper sequence: LOC_Os03g43730.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G22760.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagagcaca------ttccttttgcttttctt-----------ttctgtcatt--attgctcataacgttctttttcatggcatagGAAGACTCTAATGCAACTCCTGCTTCATCTCGTCATAAAAGAGGTTGCAATTGCAAGAGATCATATTGTGTGAAGAAATACTGTGAATGCTTTCAG
||||| | | |||||||| ||| || | || | ||||| | | |||| |||| | || |||| || | | | |||||| |||||| | || || ||| |||| || || ||||||| |||| | ||| ||||||||||||||||||||| ||||
gtaagtgttctcaatatttccttttacttatcatcctcaatacatttatctcattgaaaaggctataaaattctgcattggttcacagGAGGATGCAAGTAAAACTCCAGCTTCAGCGCGACACAAACGAGGCTGTAACTGCAAGAAATCAAACTGTCTGAAGAAATACTGTGAATGCTATCAG
upper sequence: LOC_Os03g43730.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------------gtaagagcacattccttttgcttttcttttctgtcattattgctcataacgttcttttt-catggcatagGAAGACTCTAATGCAACTCCTGCTTCATCTCGTCATAAAAGAGGTTGCAATTGCAAGAGATCATATTGTGTGAAGAAATACTGTGAATGCTTTCAG
| | || | || | | || ||||| | | | | || | ||| |||| || | | | ||| || ||||| | || || ||| | || ||||| ||||||| |||| | ||| ||||||||||||||||||||| ||||
gtaagagctctctattccatctttttattccccccccccccccccctctctcactctctctgtcctccattaatctaagggatgacatcgttatcttgcacagGATGATGCCAGTAAAACCCCGGCTTCTGCACGACACAAACGTGGCTGCAACTGCAAGAAATCAAACTGTATGAAGAAATACTGTGAATGCTATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttgcttttcttttctgtcattattgctcataacgttctttttcatggcatagGAAGACTCTAATGCAACTCCTGCTTCATCTCGTCATAAAAGAGGTTGCAATTGCAAGAGATCATATTGTGTGAAGAAATACTGTGAATGCTTTCAG
tcataac putative branch site (score: 2)
cgttctttttc CT-rich tract
ttttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagcacattccttttgcttttcttttctgtcattattgctcataacgttctttttcatggcatagGAAGACTCTAATGCAACTCCTGCTTCATCTCGTCATAAAAGAGGTTGCAATTGCAAGAGATCATATTGTGTGAAGAAATACTGTGAATGCTTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA