Plant Circular RNA Database

Detail information of Zm00001d025111_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d025111_circ_g.2
					
						ID in PlantcircBase
						zma_circ_003194
					
						Alias
						circ346
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 104831196-104832393  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Zm00001d025111						
					
						Parent gene annotation
						
							Protein RAE1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d025111_circ_g.1 						
					
						Support reads
						2
					
						Tissues
						seedling leaves
					
						Exon boundary  
						
							No-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  
						
							CT-TA							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
						Zm00001d025111_T044:5
Zm00001d025111_T047:5
Zm00001d025111_T003:5
Zm00001d025111_T041:5
Zm00001d025111_T011:5
Zm00001d025111_T051:5
Zm00001d025111_T029:5
Zm00001d025111_T036:5
Zm00001d025111_T058:5
Zm00001d025111_T024:5
Zm00001d025111_T063:5
Zm00001d025111_T061:5
Zm00001d025111_T031:5
Zm00001d025111_T053:5
Zm00001d025111_T039:5
Zm00001d025111_T055:5
Zm00001d025111_T048:3
Zm00001d025111_T045:5
Zm00001d025111_T046:5
Zm00001d025111_T023:5
Zm00001d025111_T002:5
Zm00001d025111_T043:5
Zm00001d025111_T052:5
Zm00001d025111_T007:5
Zm00001d025111_T014:5
Zm00001d025111_T004:5
Zm00001d025111_T059:5
Zm00001d025111_T040:5
Zm00001d025111_T050:5
Zm00001d025111_T062:5
Zm00001d025111_T009:5
Zm00001d025111_T057:5
Zm00001d025111_T056:5
Zm00001d025111_T025:5
Zm00001d025111_T032:5
Zm00001d025111_T010:5
Zm00001d025111_T028:4
Zm00001d025111_T022:4
Zm00001d025111_T035:5
Zm00001d025111_T049:5
Zm00001d025111_T060:5
Zm00001d025111_T054:5
Zm00001d025111_T020:5

General Information
CircRNA Name	Zm00001d025111_circ_g.2
ID in PlantcircBase	zma_circ_003194
Alias	circ346
Organism	Zea mays
Position	chr10: 104831196-104832393 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI
Parent gene	Zm00001d025111
Parent gene annotation	Protein RAE1
Parent gene strand	-
Alternative splicing	Zm00001d025111_circ_g.1
Support reads	2
Tissues	seedling leaves
Exon boundary	No-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	CT-TA 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	Zm00001d025111_T044:5 Zm00001d025111_T047:5 Zm00001d025111_T003:5 Zm00001d025111_T041:5 Zm00001d025111_T011:5 Zm00001d025111_T051:5 Zm00001d025111_T029:5 Zm00001d025111_T036:5 Zm00001d025111_T058:5 Zm00001d025111_T024:5 Zm00001d025111_T063:5 Zm00001d025111_T061:5 Zm00001d025111_T031:5 Zm00001d025111_T053:5 Zm00001d025111_T039:5 Zm00001d025111_T055:5 Zm00001d025111_T048:3 Zm00001d025111_T045:5 Zm00001d025111_T046:5 Zm00001d025111_T023:5 Zm00001d025111_T002:5 Zm00001d025111_T043:5 Zm00001d025111_T052:5 Zm00001d025111_T007:5 Zm00001d025111_T014:5 Zm00001d025111_T004:5 Zm00001d025111_T059:5 Zm00001d025111_T040:5 Zm00001d025111_T050:5 Zm00001d025111_T062:5 Zm00001d025111_T009:5 Zm00001d025111_T057:5 Zm00001d025111_T056:5 Zm00001d025111_T025:5 Zm00001d025111_T032:5 Zm00001d025111_T010:5 Zm00001d025111_T028:4 Zm00001d025111_T022:4 Zm00001d025111_T035:5 Zm00001d025111_T049:5 Zm00001d025111_T060:5 Zm00001d025111_T054:5 Zm00001d025111_T020:5

			
						 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  
						
							AGGCAATTGGCTACCACGGTCGTCTTCTGTTTGTGGCAACAAACACGCAACACATGCTACCAGA
AATCGTCCACATGGGGAAAAATGGGCACCCATTTCAcctcaaccatattttcctcaatgaagca
acccacccccatgtttgtcatgtctgcgccattgtgctgaaggatcctgagcttcccttcctat
atagttca

						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
						
							CCTCAACCATATTTTCCTCAATGAAGCAACCCACCCCCATGTTTGTCATGTCTGCGCCATTGTG
CTGAAGGATCCTGAGCTTCCCTTCCTATATAGTTCACCAGAATGAAAGCCTTAGCAATCCGCCA
TACCTCTTTGTTTATTGAATAGTTTTCTACCGACCTTAGTGCCATAAACAAGGCCACCTCCTGG
TGAAGGATGAAAGCATGCAACATTAACTTCATCTTCAGCGCTAGGAAGCACTCTCACAAGCTCC
ATATCTGAAACTCTATATACCTAAAAGTAATAAATGAAGAAAATGATAATTTGACTTACATTGT
ACACAAAGTATGAGCAATATTAGTAGTTGAGGAGGATAATAAGTAAATTATTTTGAAACTCAAG
TATCAGATAGTAAGTATCATGAAACTGCAGAACCAGCACTGTCACCATCCCCATACAATAATTA
ATATGATATCAGTTACCAATCAAACTATGATTTGGAAATTGGAATATGATTGCCATAACTACCT
CCAAAATAGTATATACGGGAACCCCATTTTCGCCTTCCACAACTATGCTCCTAAGGAGCGAGCT
ATGACGACGACCATATGCCAAAAGTATGTGTTCGGATGTAGGTGAGAACTGCATCAAAAGAGAG
ACAAACAGGATCCAATTCAATGATGAAAACTGCAAAAATGTAAGATCCATCTGTCATCAGACTC
AGGTCCTAAATGCTTTTTTGCAACAAAAATGACTGTTACAGAGGGAATCCCAAAGAAGTGACAA
GATATAAAACATGATAAAAGATTGCTATCGACATATAAAAATGCAAAGAAACACGAATAAATGA
AGAAAACCTGAATGGATGTTAAGCAATGTGCTGCCCGTATTGCTCTGGAAGCAAGAATATCCCC
AAATCTGCAAAGGTATATAACCAGTTTTGAGATATGTGGGCCATTCACAAACAGTAACTTAGTA
TATAAAAAATATTAAAAAGACAACCAAGAAAAAAAAGTACGTCTCAGCCTCAAGGGAATAAACC
CGGAGCTCATAAATAACTCGATGAGAGGGAAGCGGGTGACGAGTTGGTGATGATCCAGCCCCTT
CGTAAGACACAGGCAATTGGCTACCACGGTCGTCTTCTGTTTGTGGCAACAAACACGCAACACA
TGCTACCAGAAATCGTCCACATGGGGAAAAATGGGCACCCATTTCA

Sequences
Splice junction sequence	AGGCAATTGGCTACCACGGTCGTCTTCTGTTTGTGGCAACAAACACGCAACACATGCTACCAGA AATCGTCCACATGGGGAAAAATGGGCACCCATTTCAcctcaaccatattttcctcaatgaagca acccacccccatgtttgtcatgtctgcgccattgtgctgaaggatcctgagcttcccttcctat atagttca
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	CCTCAACCATATTTTCCTCAATGAAGCAACCCACCCCCATGTTTGTCATGTCTGCGCCATTGTG CTGAAGGATCCTGAGCTTCCCTTCCTATATAGTTCACCAGAATGAAAGCCTTAGCAATCCGCCA TACCTCTTTGTTTATTGAATAGTTTTCTACCGACCTTAGTGCCATAAACAAGGCCACCTCCTGG TGAAGGATGAAAGCATGCAACATTAACTTCATCTTCAGCGCTAGGAAGCACTCTCACAAGCTCC ATATCTGAAACTCTATATACCTAAAAGTAATAAATGAAGAAAATGATAATTTGACTTACATTGT ACACAAAGTATGAGCAATATTAGTAGTTGAGGAGGATAATAAGTAAATTATTTTGAAACTCAAG TATCAGATAGTAAGTATCATGAAACTGCAGAACCAGCACTGTCACCATCCCCATACAATAATTA ATATGATATCAGTTACCAATCAAACTATGATTTGGAAATTGGAATATGATTGCCATAACTACCT CCAAAATAGTATATACGGGAACCCCATTTTCGCCTTCCACAACTATGCTCCTAAGGAGCGAGCT ATGACGACGACCATATGCCAAAAGTATGTGTTCGGATGTAGGTGAGAACTGCATCAAAAGAGAG ACAAACAGGATCCAATTCAATGATGAAAACTGCAAAAATGTAAGATCCATCTGTCATCAGACTC AGGTCCTAAATGCTTTTTTGCAACAAAAATGACTGTTACAGAGGGAATCCCAAAGAAGTGACAA GATATAAAACATGATAAAAGATTGCTATCGACATATAAAAATGCAAAGAAACACGAATAAATGA AGAAAACCTGAATGGATGTTAAGCAATGTGCTGCCCGTATTGCTCTGGAAGCAAGAATATCCCC AAATCTGCAAAGGTATATAACCAGTTTTGAGATATGTGGGCCATTCACAAACAGTAACTTAGTA TATAAAAAATATTAAAAAGACAACCAAGAAAAAAAAGTACGTCTCAGCCTCAAGGGAATAAACC CGGAGCTCATAAATAACTCGATGAGAGGGAAGCGGGTGACGAGTTGGTGATGATCCAGCCCCTT CGTAAGACACAGGCAATTGGCTACCACGGTCGTCTTCTGTTTGTGGCAACAAACACGCAACACA TGCTACCAGAAATCGTCCACATGGGGAAAAATGGGCACCCATTTCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_003832 						
					
						PMCS
						0.048482999

Conservation Information
Conserved circRNAs	osi_circ_003832
PMCS	0.048482999

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d025111_circ_g.2

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