Plant Circular RNA Database

Detail information of Os07g0139400_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os07g0139400_circ_g.6
					
						ID in PlantcircBase
						osa_circ_032728
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr7: 2081080-2082467  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os07g0139400						
					
						Parent gene annotation
						
							NAD(P)-binding domain containing protein. (Os07t0139400-01);NAD(
P)-binding domain containing protein. (Os07t0139400-02);Similar 
to UDP-D-xylose epimerase 1. (Os07t0139400-03)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os07g0139400_circ_g.3 Os07g0139400_circ_g.4 Os07g0139400_circ_g.5 						
					
						Support reads
						1
					
						Tissues
						root
					
						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
						Os07t0139400-03:5
Os07t0139400-01:7
Os07t0139400-02:7

General Information
CircRNA Name	Os07g0139400_circ_g.6
ID in PlantcircBase	osa_circ_032728
Alias	NA
Organism	Oryza sativa
Position	chr7: 2081080-2082467 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os07g0139400
Parent gene annotation	NAD(P)-binding domain containing protein. (Os07t0139400-01);NAD( P)-binding domain containing protein. (Os07t0139400-02);Similar to UDP-D-xylose epimerase 1. (Os07t0139400-03)
Parent gene strand	+
Alternative splicing	Os07g0139400_circ_g.3 Os07g0139400_circ_g.4 Os07g0139400_circ_g.5
Support reads	1
Tissues	root
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	Os07t0139400-03:5 Os07t0139400-01:7 Os07t0139400-02:7

			
						 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  
						
							AGGAAGGCTTGGCGAGGCTCCAAAACCTGAATTACGGGAGCATGGCCGTATATCTGGTGCATGC
TTTGATGCTGCACTGGGGATAATTCCTGGTTTGAAGacatggacttctccgatccgaagcgcaa
gccgcggtacctcagtaagatcctcatggtggcgctcctcaccgccatgtgcgtcgtcatgctc
acacagcc

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							ACATGGACTTCTCCGATCCGAAGCGCAAGCCGCGGTACCTCAGTAAGATCCTCATGGTGGCGCT
CCTCACCGCCATGTGCGTCGTCATGCTCACACAGCCGCCCTGCCATAGGAGGACTCCCAGTGTG
GTAACTCAATTTCAGATGTTTTTCAGCAGCTCTGTATGTTGCCATGAACAATTCATGGTCAGGC
AGCTAACATTTGTCTTCACTCTTCACTTGTGTGATGTGTCCAGTTCTCCATCCATGAACCCGGA
GTCACGCATGTTCTAGTGACGGGCGGCGCTGGATATATCGGTTCGCACGCTGCGCTTCGGCTGC
TGAAAGATTCCTTCAGAGTCACCATAGTGGTACTTCTTCGCGACTTTGTGTTGCCATTTCTTCC
TCGAATTTGGTGTTGTTGTAGTGCAATTTATGGAATGCTTGTGCCTATATGGTTTCTGCAGGAT
AATCTTTCAAGAGGAAATATGGGGGCAATCAAGGTTCTTCAGAACTTGTTTTCAGAGCCTGGGC
GGTTGCAGTTCATCTATGCTGATTTAGGCGATCCAAAAGCTGTATCCTGATTTATTTCTCTGAA
TAACTCAAATCGAATTTTTCTGTAGAGATATATCTTTCATTCAAAATGCGGCAAAATATGATGA
AGGAATTTTTTGAAAGATCTTTTTTCCTTAGCACATGCTTAGGTTAATAGAATATTTGCAGAAA
ATGCTTTTGATGCTGTCATGCACTTTGCTGCTGTCGCTTATGTTGGTGAGAGCACACTTGAGCC
TTTGAGGTACTAAAGTCTCTATTGTCCATCAAATTACCTCTCCACAAGACACACGAGATACTGA
AAACATTTTAAACAGGTACTATCATAACATCACCTCAAACACTTTAGTTGTGCTAGAGGCTATG
GCAGCACACAATGTGAGAACCCTGATCTACTCTAGCACATGTGCCACCTATGGAGAACCCGAGA
AGATGCCTATCACCGAAGGAACTCCCCAGGTCAGCTGTTGCTTCTGCATCCTCTTTACTTTCAG
ATAATGCTGAAGGCTTTTGCTCACCAAATCCTACTGTACAGTTTCCGATCAACCCATATGGTAA
AGCCAAGAAGATGGCAGAGGACATCATCTTGGATTTTTCCAAATCCAAGAAGGCAGACATGGCT
GTGATGATTCTAAGGTATGTACCGTTTACAAAACAAAAGCATGAAACCCACTATTTAAACCACC
ATTTGATTCCTGACTTACGAATATGTAACCTAATACTTCTAGATACTTCAACGTCATTGGTTCT
GACCCTGAAGGAAGGCTTGGCGAGGCTCCAAAACCTGAATTACGGGAGCATGGCCGTATATCTG
GTGCATGCTTTGATGCTGCACTGGGGATAATTCCTGGTTTGAAG

Sequences
Splice junction sequence	AGGAAGGCTTGGCGAGGCTCCAAAACCTGAATTACGGGAGCATGGCCGTATATCTGGTGCATGC TTTGATGCTGCACTGGGGATAATTCCTGGTTTGAAGacatggacttctccgatccgaagcgcaa gccgcggtacctcagtaagatcctcatggtggcgctcctcaccgccatgtgcgtcgtcatgctc acacagcc
Assembled circRNA sequence	NA 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	NA
Genomic sequence	ACATGGACTTCTCCGATCCGAAGCGCAAGCCGCGGTACCTCAGTAAGATCCTCATGGTGGCGCT CCTCACCGCCATGTGCGTCGTCATGCTCACACAGCCGCCCTGCCATAGGAGGACTCCCAGTGTG GTAACTCAATTTCAGATGTTTTTCAGCAGCTCTGTATGTTGCCATGAACAATTCATGGTCAGGC AGCTAACATTTGTCTTCACTCTTCACTTGTGTGATGTGTCCAGTTCTCCATCCATGAACCCGGA GTCACGCATGTTCTAGTGACGGGCGGCGCTGGATATATCGGTTCGCACGCTGCGCTTCGGCTGC TGAAAGATTCCTTCAGAGTCACCATAGTGGTACTTCTTCGCGACTTTGTGTTGCCATTTCTTCC TCGAATTTGGTGTTGTTGTAGTGCAATTTATGGAATGCTTGTGCCTATATGGTTTCTGCAGGAT AATCTTTCAAGAGGAAATATGGGGGCAATCAAGGTTCTTCAGAACTTGTTTTCAGAGCCTGGGC GGTTGCAGTTCATCTATGCTGATTTAGGCGATCCAAAAGCTGTATCCTGATTTATTTCTCTGAA TAACTCAAATCGAATTTTTCTGTAGAGATATATCTTTCATTCAAAATGCGGCAAAATATGATGA AGGAATTTTTTGAAAGATCTTTTTTCCTTAGCACATGCTTAGGTTAATAGAATATTTGCAGAAA ATGCTTTTGATGCTGTCATGCACTTTGCTGCTGTCGCTTATGTTGGTGAGAGCACACTTGAGCC TTTGAGGTACTAAAGTCTCTATTGTCCATCAAATTACCTCTCCACAAGACACACGAGATACTGA AAACATTTTAAACAGGTACTATCATAACATCACCTCAAACACTTTAGTTGTGCTAGAGGCTATG GCAGCACACAATGTGAGAACCCTGATCTACTCTAGCACATGTGCCACCTATGGAGAACCCGAGA AGATGCCTATCACCGAAGGAACTCCCCAGGTCAGCTGTTGCTTCTGCATCCTCTTTACTTTCAG ATAATGCTGAAGGCTTTTGCTCACCAAATCCTACTGTACAGTTTCCGATCAACCCATATGGTAA AGCCAAGAAGATGGCAGAGGACATCATCTTGGATTTTTCCAAATCCAAGAAGGCAGACATGGCT GTGATGATTCTAAGGTATGTACCGTTTACAAAACAAAAGCATGAAACCCACTATTTAAACCACC ATTTGATTCCTGACTTACGAATATGTAACCTAATACTTCTAGATACTTCAACGTCATTGGTTCT GACCCTGAAGGAAGGCTTGGCGAGGCTCCAAAACCTGAATTACGGGAGCATGGCCGTATATCTG GTGCATGCTTTGATGCTGCACTGGGGATAATTCCTGGTTTGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_017222 						
					
						PMCS
						0.173701717

Conservation Information
Conserved circRNAs	osi_circ_017222
PMCS	0.173701717

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2081083-2081348(+)
2081346-2082025(-)
2081426-2082351(-)
						
						Potential amino acid sequence
						
							MDFSDPKRKPRYLSKILMVALLTAMCVVMLTQPPCHRRTPSVFSIHEPGVTHVLVTGGAGYIGS
HAALRLLKDSFRVTIVDNLSRGNMGAIKVLQNLFSEPGRLQFIYADLGDPKAVNRIFAENAFDA
VMHFAAVAYVGESTLEPLRYYHNITSNTLVVLEAMAAHNVRTLIYSSTCATYGEPEKMPITEGT
PQFPINPYGKAKKMAEDIILDFSKSKKADMAVMILRYFNVIGSDPEGRLGEAPKPELREHGRIS
GACFDAALGIIPGLKTWTSPIRSASRGTSVRSSWWRSSPPCASSCSHSRPAIGGLPVCSPSMNP
ESRMF*(+)
MRDSGFMDGEHTGSPPMAGRLCEHDDAHGGEERHHEDLTEVPRLALRIGEVHVFKPGIIPSAAS
KHAPDIRPCSRNSGFGASPSLPSGSEPMTLKYLRIITAMSAFLDLEKSKMMSSAIFLALPYGLI
GNWGVPSVIGIFSGSP*(-)
MVTLKESFSSRSAACEPIYPAPPVTRTCVTPGSWMENTLGVLLWQGGCVSMTTHMAVRSATMRI
LLRYRGLRFGSEKSMSSNQELSPVQHQSMHQIYGHAPVIQVLEPRQAFLQGQNQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2081083-2081348(+) 2081346-2082025(-) 2081426-2082351(-)
Potential amino acid sequence	MDFSDPKRKPRYLSKILMVALLTAMCVVMLTQPPCHRRTPSVFSIHEPGVTHVLVTGGAGYIGS HAALRLLKDSFRVTIVDNLSRGNMGAIKVLQNLFSEPGRLQFIYADLGDPKAVNRIFAENAFDA VMHFAAVAYVGESTLEPLRYYHNITSNTLVVLEAMAAHNVRTLIYSSTCATYGEPEKMPITEGT PQFPINPYGKAKKMAEDIILDFSKSKKADMAVMILRYFNVIGSDPEGRLGEAPKPELREHGRIS GACFDAALGIIPGLKTWTSPIRSASRGTSVRSSWWRSSPPCASSCSHSRPAIGGLPVCSPSMNP ESRMF(+) MRDSGFMDGEHTGSPPMAGRLCEHDDAHGGEERHHEDLTEVPRLALRIGEVHVFKPGIIPSAAS KHAPDIRPCSRNSGFGASPSLPSGSEPMTLKYLRIITAMSAFLDLEKSKMMSSAIFLALPYGLI GNWGVPSVIGIFSGSP(-) MVTLKESFSSRSAACEPIYPAPPVTRTCVTPGSWMENTLGVLLWQGGCVSMTTHMAVRSATMRI LLRYRGLRFGSEKSMSSNQELSPVQHQSMHQIYGHAPVIQVLEPRQAFLQGQNQ*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os07g0139400_circ_g.6

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