Sequence
atgc intronic sequence ATGC exonic sequencegtgtgcaattcataaagggaacagtagtttgcctacaattctgttgccacatatgcttatttctgaaatctggtctgcagGATTCTTGTAATAGAAAAAGTAACCAACAAAACCTGGGGACAATTAAGTCTTCAAACTTGTGCACGGAGATTATTGAGTTCACAAGTCCCACTGAAACTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g56100.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA06G15350.1 (Glycine max), 3'ss of exon 8
-----------gtgtgcaattcataaagggaacagtagtttgcctacaattctgttgccacatatgcttatttctgaaatctggtctgca------gGATTCTTGTAATAGAAAAAGTAACCAACAAAACCTGGGGACAATTAAGTCTTCAAACTTGTGCACGGAGATTATTGAGTTCACAAGTCCCACTGAAACTG
|| || | | | |||| | | | | | || | | | ||| | | | | | || | || |||| |||| ||||| ||||| || ||||| || |||| |||||||| || ||||||||||| || ||||| ||||| | ||||||| ||||||||||
gtggtgttcttagatgtctttgactttcctcatgagattttgtatttattgttttcacc-cgttgagtaattccagcatttttgtttacactactagGATACTTGCAATAGGAAAAGCAATCAACAGAATTTGGGTACAATTAAATCGTCAAACTTGTGTACTGAGATAATTGAATATTCAAGTCCAACTGAAACTG
upper sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 8
---------------gtgtgcaattcataaagggaacagtagtttgcctacaattctgttgccacatatgcttatttctgaaatctggtctgc-agGATTCTTGTAATAGAAAAAGTAACCAACAAAACCTGGGGACAATTAAGTCTTCAAACTTGTGCACGGAGATTATTGAGTTCACAAGTCCCACTGAAACTG
|| | | | || | || | | ||| || ||| | | || | || | ||||| |||| ||||| ||||| |||||||| || |||| |||||||| || ||||||||||| || ||||| ||||||| ||||||| ||||||||||
gtggaacacttagatgtcttttactttccccatgagattttgtatttattgttttcacctgttgaataaatccaacatttttatttacactactagGATACTTGCAATAGGAAAAGCAACCAACAGAATTTGGGTACAATTAAATCATCAAACTTGTGTACTGAGATAATTGAGTATTCAAGTCCAACTGAAACTG
upper sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 8
---gtgtgcaattcataaagggaacagtagtttgcctacaattctgttgccacatatgcttatttct----gaaatctggtctgc------------agGATTCTTGTAATAGAAAAAGTAACCAACAAAACCTGGGGACAATTAAGTCTTCAAACTTGTGCACGGAGATTATTGAGTTCACAAGTCCCACTGAAACTG
|| | ||| | | ||| | | | | | | ||| ||| | | |||||| | |||| || || |||| |||| |||| |||||| |||||||| || |||| ||||| ||||| |||||||||||||| ||||| ||||||| |||||||| || ||||| |
gtggtttacaaat-gcatgtttaacttttgctaggtttctatttcagtgcattttgtatttatttttcattgaaacctcttcctttttctatatcctagGACACTTGCAATAAAAAAAGCAACCAACAGAATTTGGGCACAATCAAGTCATCAAACTTGTGCACTGAGATAATTGAGTATACAAGTCCAACAGAAACGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtttgcctacaattctgttgccacatatgcttatttctgaaatctggtctgcagGATTCTTGTAATAGAAAAAGTAACCAACAAAACCTGGGGACAATTAAGTCTTCAAACTTGTGCACGGAGATTATTGAGTTCACAAGTCCCACTGAAACTG
ttatttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgcaattcataaagggaacagtagtttgcctacaattctgttgccacatatgcttatttctgaaatctggtctgcagGATTCTTGTAATAGAAAAAGTAACCAACAAAACCTGGGGACAATTAAGTCTTCAAACTTGTGCACGGAGATTATTGAGTTCACAAGTCCCACTGAAACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT