Plant Circular RNA Database

Detail information of Os12g0538300_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os12g0538300_circ_g.4
					
						ID in PlantcircBase
						osa_circ_011873
					
						Alias
						Os_ciR7398
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr12: 21444328-21445864  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os12g0538300						
					
						Parent gene annotation
						
							Dor1-like protein family protein. (Os12t0538300-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os12g0538300_circ_g.1 Os12g0538300_circ_g.2 Os12g0538300_circ_g.3 Os12g0538300_circ_g.5 Os12g0538300_circ_g.6 Os12g0538300_circ_g.7 Os12g0538300_circ_g.8 Os12g0538300_circ_g.9 Os12g0538300_circ_g.10 						
					
						Support reads
						2/10
					
						Tissues
						root/shoot, seed
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							GT-AG							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						Os12t0538300-01:5

General Information
CircRNA Name	Os12g0538300_circ_g.4
ID in PlantcircBase	osa_circ_011873
Alias	Os_ciR7398
Organism	Oryza sativa
Position	chr12: 21444328-21445864 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ
Parent gene	Os12g0538300
Parent gene annotation	Dor1-like protein family protein. (Os12t0538300-01)
Parent gene strand	+
Alternative splicing	Os12g0538300_circ_g.1 Os12g0538300_circ_g.2 Os12g0538300_circ_g.3 Os12g0538300_circ_g.5 Os12g0538300_circ_g.6 Os12g0538300_circ_g.7 Os12g0538300_circ_g.8 Os12g0538300_circ_g.9 Os12g0538300_circ_g.10
Support reads	2/10
Tissues	root/shoot, seed
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	GT-AG The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	Os12t0538300-01:5

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							GGCAATGCACCAAATAAGTAATCATCTTACCACTCTTCAAGTTATGTTGCCAAATATAACGGAA
GGTGGCTCTCTCTCCAACATTCGTGAACAGTGCATGatagaggagataccgaatttaacatctg
gctgcaccgagtttgttgagtcagcacagcaaattttagaagagaggaagctcaatcagacatt
actagcca

									
								

					

						Assembled circRNA sequence  
						
							Yes
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							Transcript length: 693
Transcript exons: 21444328-21444476,21444676-21444753,21444831-21444924,21
445147-21445221,21445568-21445864
ATAGAGGAGATACCGAATTTAACATCTGGCTGCACCGAGTTTGTTGAGTCAGCACAGCAAATTT
TAGAAGAGAGGAAGCTCAATCAGACATTACTAGCCAATCACAGCACACTGCTTGATCTGCTTGA
AATCCCACAACTGATGGACACATGTATACGAAATGGGAACTATGATGAGGCACTTGACCTGGAA
GCCTTTGTTAGTAAAATATCAAAGTTGCACCCTGATTTACCTGTTATCCAAGGCTTAGCTGTTG
AAGTCAAGAAGACAATACAGTCATTAATTTCTCAGCTTCTCCAGAAGCTTCGATCAAATATTCA
GTTGCCTGAATGCCTCCGTATTGTTGCACATTTGCGCCGCATTGGAGTGTTCAGTGAATCAGAA
TTGCGTTTACAGTTCTTGAGATGCAGGGAAGCTTGGCTTTCTGGGATTCTTGATGACCTGGACC
AAAGGAATGTATATGGGTATCTAACAGGCATGGTGGGTTACCACAGAACACATCTATTTGATGT
TGTCAATCAATATCGAGCAATATTCAACAATGATAAGTCCGGAAGTGATGAGAACTACGATGGT
GGATTGCTTTTCAGCTGGGCAATGCACCAAATAAGTAATCATCTTACCACTCTTCAAGTTATGT
TGCCAAATATAACGGAAGGTGGCTCTCTCTCCAACATTCGTGAACAGTGCATG
						
					

						Genomic sequence
						
							ATAGAGGAGATACCGAATTTAACATCTGGCTGCACCGAGTTTGTTGAGTCAGCACAGCAAATTT
TAGAAGAGAGGAAGCTCAATCAGACATTACTAGCCAATCACAGCACACTGCTTGATCTGCTTGA
AATCCCACAACTGATGGACACGTATGTGCCATTTTTTTTTATAATTTCTTAAAGACCTTCAGTC
ATCTTGTGTTGTTTGATGTTGTTGATATGCTGTTTAGTTCTCGATTCTTCTCTAATTTCTGTAT
GCTACAGATCCATTTTGTTCAGTAAAACATGGTTTGATTTGTACAATTGACGAATCATGAAGAA
TTACATTTAACAATCTACATGCTCACAGATGTATACGAAATGGGAACTATGATGAGGCACTTGA
CCTGGAAGCCTTTGTTAGTAAAATATCAAAGTTGCACCCTGAGTAAGTCATTTGACATAATCTT
TATTATGGCCTTTGTAATTTGCAATTAATTTAACTGTATGCCTTTTCGATTGAAGTTTACCTGT
TATCCAAGGCTTAGCTGTTGAAGTCAAGAAGACAATACAGTCATTAATTTCTCAGCTTCTCCAG
AAGCTTCGATCAAATATTCAGGTGATTATGTTGGTGCACTAACAATCTGTCATTGGTTAAACCA
TTATCGTATTTTTCATTTGCTCCATCTGTTCTATGCAAGTTGAACATTGTAAAGATTGTATCCT
GTATATAACCGAGTTCTTTGTTGTGCAACTAATTTCATTTCTTTTCCAAATTTACTTGGTTTTG
TCTCCTCTTAGCACATCTATGTCTAACTCCTGGTCATTTGACTGTCTACAGTTGCCTGAATGCC
TCCGTATTGTTGCACATTTGCGCCGCATTGGAGTGTTCAGTGAATCAGAATTGCGTTTACAGGT
ATTCTGAACTTCTGATGTAATCTGGATTTTTTTTTTGCGGGGAATAATCTGAATAGAATTATAC
GTCAGTATAATGCTTTTACATTTAATTTTGAATTTATGAGTAATTCATTTGTTACCCTAAACCC
TTACTTCAAAGCGGTGGTCCAGAGTATATAAACTACTAATGGAGGAATTTTAATTGTAATAATG
ACATTTCATTTAGTTCAAAGTGTTGGTCCAGATTACTACAAACTACTATTGGAGGAATTTTAAT
TGATAATAATGATATTTCACTGAGTCAAATTCATTGGATGATACATATCGAGTATTTTTCTCTC
TCCTAATTCTGATATAGTTTCTAGTTCTTGAGATGCAGGGAAGCTTGGCTTTCTGGGATTCTTG
ATGACCTGGACCAAAGGAATGTATATGGGTATCTAACAGGCATGGTGGGTTACCACAGAACACA
TCTATTTGATGTTGTCAATCAATATCGAGCAATATTCAACAATGATAAGTCCGGAAGTGATGAG
AACTACGATGGTGGATTGCTTTTCAGCTGGGCAATGCACCAAATAAGTAATCATCTTACCACTC
TTCAAGTTATGTTGCCAAATATAACGGAAGGTGGCTCTCTCTCCAACATTCGTGAACAGTGCAT
G
						
					

			
		

Sequences
Splice junction sequence	GGCAATGCACCAAATAAGTAATCATCTTACCACTCTTCAAGTTATGTTGCCAAATATAACGGAA GGTGGCTCTCTCTCCAACATTCGTGAACAGTGCATGatagaggagataccgaatttaacatctg gctgcaccgagtttgttgagtcagcacagcaaattttagaagagaggaagctcaatcagacatt actagcca
Assembled circRNA sequence	Yes The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	Transcript length: 693 Transcript exons: 21444328-21444476,21444676-21444753,21444831-21444924,21 445147-21445221,21445568-21445864 ATAGAGGAGATACCGAATTTAACATCTGGCTGCACCGAGTTTGTTGAGTCAGCACAGCAAATTT TAGAAGAGAGGAAGCTCAATCAGACATTACTAGCCAATCACAGCACACTGCTTGATCTGCTTGA AATCCCACAACTGATGGACACATGTATACGAAATGGGAACTATGATGAGGCACTTGACCTGGAA GCCTTTGTTAGTAAAATATCAAAGTTGCACCCTGATTTACCTGTTATCCAAGGCTTAGCTGTTG AAGTCAAGAAGACAATACAGTCATTAATTTCTCAGCTTCTCCAGAAGCTTCGATCAAATATTCA GTTGCCTGAATGCCTCCGTATTGTTGCACATTTGCGCCGCATTGGAGTGTTCAGTGAATCAGAA TTGCGTTTACAGTTCTTGAGATGCAGGGAAGCTTGGCTTTCTGGGATTCTTGATGACCTGGACC AAAGGAATGTATATGGGTATCTAACAGGCATGGTGGGTTACCACAGAACACATCTATTTGATGT TGTCAATCAATATCGAGCAATATTCAACAATGATAAGTCCGGAAGTGATGAGAACTACGATGGT GGATTGCTTTTCAGCTGGGCAATGCACCAAATAAGTAATCATCTTACCACTCTTCAAGTTATGT TGCCAAATATAACGGAAGGTGGCTCTCTCTCCAACATTCGTGAACAGTGCATG
Genomic sequence	ATAGAGGAGATACCGAATTTAACATCTGGCTGCACCGAGTTTGTTGAGTCAGCACAGCAAATTT TAGAAGAGAGGAAGCTCAATCAGACATTACTAGCCAATCACAGCACACTGCTTGATCTGCTTGA AATCCCACAACTGATGGACACGTATGTGCCATTTTTTTTTATAATTTCTTAAAGACCTTCAGTC ATCTTGTGTTGTTTGATGTTGTTGATATGCTGTTTAGTTCTCGATTCTTCTCTAATTTCTGTAT GCTACAGATCCATTTTGTTCAGTAAAACATGGTTTGATTTGTACAATTGACGAATCATGAAGAA TTACATTTAACAATCTACATGCTCACAGATGTATACGAAATGGGAACTATGATGAGGCACTTGA CCTGGAAGCCTTTGTTAGTAAAATATCAAAGTTGCACCCTGAGTAAGTCATTTGACATAATCTT TATTATGGCCTTTGTAATTTGCAATTAATTTAACTGTATGCCTTTTCGATTGAAGTTTACCTGT TATCCAAGGCTTAGCTGTTGAAGTCAAGAAGACAATACAGTCATTAATTTCTCAGCTTCTCCAG AAGCTTCGATCAAATATTCAGGTGATTATGTTGGTGCACTAACAATCTGTCATTGGTTAAACCA TTATCGTATTTTTCATTTGCTCCATCTGTTCTATGCAAGTTGAACATTGTAAAGATTGTATCCT GTATATAACCGAGTTCTTTGTTGTGCAACTAATTTCATTTCTTTTCCAAATTTACTTGGTTTTG TCTCCTCTTAGCACATCTATGTCTAACTCCTGGTCATTTGACTGTCTACAGTTGCCTGAATGCC TCCGTATTGTTGCACATTTGCGCCGCATTGGAGTGTTCAGTGAATCAGAATTGCGTTTACAGGT ATTCTGAACTTCTGATGTAATCTGGATTTTTTTTTTGCGGGGAATAATCTGAATAGAATTATAC GTCAGTATAATGCTTTTACATTTAATTTTGAATTTATGAGTAATTCATTTGTTACCCTAAACCC TTACTTCAAAGCGGTGGTCCAGAGTATATAAACTACTAATGGAGGAATTTTAATTGTAATAATG ACATTTCATTTAGTTCAAAGTGTTGGTCCAGATTACTACAAACTACTATTGGAGGAATTTTAAT TGATAATAATGATATTTCACTGAGTCAAATTCATTGGATGATACATATCGAGTATTTTTCTCTC TCCTAATTCTGATATAGTTTCTAGTTCTTGAGATGCAGGGAAGCTTGGCTTTCTGGGATTCTTG ATGACCTGGACCAAAGGAATGTATATGGGTATCTAACAGGCATGGTGGGTTACCACAGAACACA TCTATTTGATGTTGTCAATCAATATCGAGCAATATTCAACAATGATAAGTCCGGAAGTGATGAG AACTACGATGGTGGATTGCTTTTCAGCTGGGCAATGCACCAAATAAGTAATCATCTTACCACTC TTCAAGTTATGTTGCCAAATATAACGGAAGGTGGCTCTCTCTCCAACATTCGTGAACAGTGCAT G

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.147497967

Conservation Information
Conserved circRNAs	NA
PMCS	0.147497967

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21444470-21445861(+)
21444354-21445808(-)
						
						Potential amino acid sequence
						
							MDTCIRNGNYDEALDLEAFVSKISKLHPDLPVIQGLAVEVKKTIQSLISQLLQKLRSNIQLPEC
LRIVAHLRRIGVFSESELRLQFLRCREAWLSGILDDLDQRNVYGYLTGMVGYHRTHLFDVVNQY
RAIFNNDKSGSDENYDGGLLFSWAMHQISNHLTTLQVMLPNITEGGSLSNIREQCMIEEIPNLT
SGCTEFVESAQQILEERKLNQTLLANHSTLLDLLEIPQLMDTCIRNGNYDEALDLEAFVSKISK
LHPDLPVIQGLAVEVKKTIQSLISQLLQKLRSNIQLPECLRIVAHLRRIGVFSESELRLQFLRC
REAWLSGILDDLDQRNVYGYLTGMVGYHRTHLFDVVNQYRAIFNNDKSGSDENYDGGLLFSWAM
HQISNHLTTLQVMLPNITEGGSLSNIREQCMIEEIPNLTSGCTEFVESAQQILEERKLNQTLLA
NHSTLLDLLEIPQLMDTCIRNGNYDEALDLEAFVSKISKLHPDLPVIQGLAVEVKKTIQSLISQ
LLQKLRSNIQLPECLRIVAHLRRIGVFSESELRLQFLRCREAWLSGILDDLDQRNVYGYLTGMV
GYHRTHLFDVVNQYRAIFNNDKSGSDENYDGGLLFSWAMHQISNHLTTLQVMLPNITEGGSLSN
IREQCMIEEIPNLTSGCTEFVESAQQILEERKLNQTLLANHSTLLDLLEIPQLMDTCIRNGNYD
EALDLEAFVSKISKLHPDLPVIQGLAVEVKKTIQSLISQLLQKLRSNIQLPECLRIVAHLRRIG
VFSESELRLQFLRCREAWLSGILDDLDQRNVYGYLTGMVGYHRTHLFDVVNQYRAIFNNDKSGS
DENYDGGLLFSWAMHQISNHLTTLQVMLPNITEGGSLSNIREQCM(+)
MLNSVSPLSCTVHECWRESHLPLYLAT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21444470-21445861(+) 21444354-21445808(-)
Potential amino acid sequence	MDTCIRNGNYDEALDLEAFVSKISKLHPDLPVIQGLAVEVKKTIQSLISQLLQKLRSNIQLPEC LRIVAHLRRIGVFSESELRLQFLRCREAWLSGILDDLDQRNVYGYLTGMVGYHRTHLFDVVNQY RAIFNNDKSGSDENYDGGLLFSWAMHQISNHLTTLQVMLPNITEGGSLSNIREQCMIEEIPNLT SGCTEFVESAQQILEERKLNQTLLANHSTLLDLLEIPQLMDTCIRNGNYDEALDLEAFVSKISK LHPDLPVIQGLAVEVKKTIQSLISQLLQKLRSNIQLPECLRIVAHLRRIGVFSESELRLQFLRC REAWLSGILDDLDQRNVYGYLTGMVGYHRTHLFDVVNQYRAIFNNDKSGSDENYDGGLLFSWAM HQISNHLTTLQVMLPNITEGGSLSNIREQCMIEEIPNLTSGCTEFVESAQQILEERKLNQTLLA NHSTLLDLLEIPQLMDTCIRNGNYDEALDLEAFVSKISKLHPDLPVIQGLAVEVKKTIQSLISQ LLQKLRSNIQLPECLRIVAHLRRIGVFSESELRLQFLRCREAWLSGILDDLDQRNVYGYLTGMV GYHRTHLFDVVNQYRAIFNNDKSGSDENYDGGLLFSWAMHQISNHLTTLQVMLPNITEGGSLSN IREQCMIEEIPNLTSGCTEFVESAQQILEERKLNQTLLANHSTLLDLLEIPQLMDTCIRNGNYD EALDLEAFVSKISKLHPDLPVIQGLAVEVKKTIQSLISQLLQKLRSNIQLPECLRIVAHLRRIG VFSESELRLQFLRCREAWLSGILDDLDQRNVYGYLTGMVGYHRTHLFDVVNQYRAIFNNDKSGS DENYDGGLLFSWAMHQISNHLTTLQVMLPNITEGGSLSNIREQCM(+) MLNSVSPLSCTVHECWRESHLPLYLAT*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os12g0538300_circ_g.4

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