Sequence
atgc intronic sequence ATGC exonic sequence...cgttgtttaagagataagagagacataaactgtataaatcgttatgtttcttgatcagtattcctcttattaacgaactctgacacaatccgtttgccagGGAATACTTGTTTTTGCTTCTGTTATGGCAACGCTTGGCCTTCAAATTATCCTAGAATCTACACGCTCATTGTTTTATGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os05g38670.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g38670.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G52280.1 (Glycine max), 3'ss of exon 3
cgttgtttaagagataagagagacataaactgtataaatcgttatgtttcttgatcagtattcctcttattaacgaactctgacacaatccgtttgccagGGAATACTTGTTTTTGCTTCTGTTATGGCAACGCTTGGCCTTCAAATTATCCTAGAATCTACACGCTCATTGTTTTATGAT
| ||| || | | |||| ||| | | | | | | | || | | | ||| || | | ||| | |||||||| ||||||||||| ||||||||||| || ||||| || || || ||| | || ||||| ||| |||| | | | |
aaactataaagtgaaagttcattattaaattgttaatggcttaacgagttattatgactgtgccttggtgctgagattttgaattcaaaatttggtacagGGAATTCTTGTTTTTGCCTCTGTTATGGCGACACTTGGACTGCAGATAATCTTGGAGTCTACCCGCACATTAATATCTTCT
upper sequence: LOC_Os05g38670.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G10580.1 (Glycine max), 3'ss of exon 3
cgttgtttaagagataagagagacataaactgtataaatcgttatgtttcttgatcagtattcctcttattaacgaactctgacacaatccgtttgccagGGAATACTTGTTTTTGCTTCTGTTATGGCAACGCTTGGCCTTCAAATTATCCTAGAATCTACACGCTCATTGTTTTATGAT
| || || | |||| | | | | | | | || | | | ||| || | | ||| | |||||||| ||||||||||| ||||||||||| || ||||| || || || ||| | || ||||| ||| |||| | | | |
aacttcgtaccccattgcccattattaaatagctaatggcctaacaagttattatgactgtgccttggtgctgagattttgaattcaaaatttggtacagGGAATTCTTGTTTTTGCCTCTGTTATGGCGACACTTGGACTGCAGATAATCTTGGAGTCTACCCGCACATTAATATCTTCT
upper sequence: LOC_Os05g38670.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0019g00020.t01 (Vitis vinifera), 3'ss of exon 3
cgttgtttaag-agataagagagacataaactgtataaatcgttatgtttcttgatcagtattcctcttattaacgaactctgacacaatccgtttgccagGGAATACTTGTTTTTGCTTCTGTTATGGCAACGCTTGGCCTTCAAATTATCCTAGAATCTACACGCTCATTGTTTTATGAT
| || || ||| | | | | | || ||| || || | | ||| | | | | ||| || | ||| ||||||| |||||||||||||||||||||||||| || || || || || ||| | || || |||| || | | | |||
tgctgcaaaaatagagcatttggtttctagaatcctggaaagtgtctttttctgggttgtgatattgttactgaagccttgaatcaccattgatgtgc-agGGAATCCTTGTTTTTGCTTCTGTTATGGCAACTCTGGGACTGCAGATAATCTTGGAGTCAGTACGCACACTATCATCTGAC
upper sequence: LOC_Os05g38670.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S119_25V6.1 (Physcomitrella patens), 3'ss of exon 2
cgttgtttaagagataagagagacataaactgtataaatcgttat--gtttcttgatcagtattcctcttattaacgaactctgacacaatccgtttgccagGGAATACTTGTTTTTGCTTCTGTTATGGCAACGCTTGGCCTTCAAATTATCCTAGAATCTACACGCTCATTGTTTTATGAT------------------
| ||| | | |||| | | || | |||| | || || | | ||| | | | | | | |||| || || |||||||| || || |||||||| ||||||||||||||||| | || || | || | |||| | |
taccagcatgttggtaacacttgtttgcactg-acgtgtgattgtcaatttcaaggagggtctttgtgtaatttcttatcggcttttggctatggctac-agGGCATTCTAGTTTTTGCGTCAGTAATGGCAACACTTGGCCTTCAAATTATTTTGGAGTCCGCTCGGACGCTGTTCTCACAGGCAGGACGAACAACCTTG
upper sequence: LOC_Os05g38670.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S11_299V6.2 (Physcomitrella patens), 3'ss of exon 4
cgttgtttaagagataagagagacataaactgtataaatcgtt-atgtttcttgatcagtattcctc-ttattaacgaact--ctgacacaatccgtttgcc---agGGAATACTTGTTTTTGCTTCTGTTATGGCAACGCTTGGCCTTCAAATTATCCTAGAATCTACACGCTCATTGTTTTATGAT
||| | | | || | | | ||| || | | |||| || ||| ||| | | || || | ||| | |||| || || ||||||||||| || |||||||| ||||| |||||||| || |||||||| ||| | | | | |
-------taaagttttttctacccttataacatgtctgcagttgatacatgtctgcagaaattcatcgttactaaaaagataccttttgttttctgcttggcgacagGGTATTCTGGTTTTTGCTTCAGTAATGGCAACACTTGGTCTTCAAATCATTCTAGAATCCGTACGGACTCTAATCACTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttcttgatcagtattcctcttattaacgaactctgacacaatccgtttgccagGGAATACTTGTTTTTGCTTCTGTTATGGCAACGCTTGGCCTTCAAATTATCCTAGAATCTACACGCTCATTGTTTTATGAT
tccgttt CT-rich tract
tcttattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgttgtttaagagataagagagacataaactgtataaatcgttatgtttcttgatcagtattcctcttattaacgaactctgacacaatccgtttgccagGGAATACTTGTTTTTGCTTCTGTTATGGCAACGCTTGGCCTTCAAATTATCCTAGAATCTACACGCTCATTGTTTTATGAT
-gttgttt
- - - - aagagata
- - - - - - - - - - - acataaa
- - - - - - - - - - - - - - - - - - - - - - tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacaat