Plant Circular RNA Database

Detail information of Zm00001d030340_circ_g.5

			
						 General Information
					
						CircRNA Name
						Zm00001d030340_circ_g.5
					
						ID in PlantcircBase
						zma_circ_006622
					
						Alias
						Zm01circ00100, zma_circ_0000264, ZmciR11
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 123422367-123424238  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d030340						
					
						Parent gene annotation
						
							protein_coding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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  
						
							CT-AC							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
						Zm00001d030340_T053:4
Zm00001d030340_T026:4
Zm00001d030340_T037:4
Zm00001d030340_T015:4
Zm00001d030340_T039:4
Zm00001d030340_T021:4
Zm00001d030340_T023:4
Zm00001d030340_T007:4
Zm00001d030340_T060:4
Zm00001d030340_T033:4
Zm00001d030340_T034:4
Zm00001d030340_T028:4
Zm00001d030340_T030:4
Zm00001d030340_T009:4
Zm00001d030340_T046:4
Zm00001d030340_T049:4
Zm00001d030340_T050:4
Zm00001d030340_T041:4
Zm00001d030340_T002:4
Zm00001d030340_T040:4
Zm00001d030340_T048:4
Zm00001d030340_T013:4
Zm00001d030340_T054:4
Zm00001d030340_T005:4
Zm00001d030340_T043:4
Zm00001d030340_T059:4
Zm00001d030340_T051:4
Zm00001d030340_T057:2
Zm00001d030340_T001:4
Zm00001d030340_T010:4
Zm00001d030340_T006:4

General Information
CircRNA Name	Zm00001d030340_circ_g.5
ID in PlantcircBase	zma_circ_006622
Alias	Zm01circ00100, zma_circ_0000264, ZmciR11
Organism	Zea mays
Position	chr1: 123422367-123424238 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d030340
Parent gene annotation	protein_coding
Parent gene strand	-
Alternative splicing	NA
Support reads	NA
Tissues	leaf, endosperm, 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	CT-AC 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	Zm00001d030340_T053:4 Zm00001d030340_T026:4 Zm00001d030340_T037:4 Zm00001d030340_T015:4 Zm00001d030340_T039:4 Zm00001d030340_T021:4 Zm00001d030340_T023:4 Zm00001d030340_T007:4 Zm00001d030340_T060:4 Zm00001d030340_T033:4 Zm00001d030340_T034:4 Zm00001d030340_T028:4 Zm00001d030340_T030:4 Zm00001d030340_T009:4 Zm00001d030340_T046:4 Zm00001d030340_T049:4 Zm00001d030340_T050:4 Zm00001d030340_T041:4 Zm00001d030340_T002:4 Zm00001d030340_T040:4 Zm00001d030340_T048:4 Zm00001d030340_T013:4 Zm00001d030340_T054:4 Zm00001d030340_T005:4 Zm00001d030340_T043:4 Zm00001d030340_T059:4 Zm00001d030340_T051:4 Zm00001d030340_T057:2 Zm00001d030340_T001:4 Zm00001d030340_T010:4 Zm00001d030340_T006:4

			
						 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  
						
							TAACCAATAGATTTGCATTTACCTGATAAGATACCTCATATGAAGCGATGAATGCTGAAATGAA
TGTCCGCAATATACCCCGATAACCAGAAACAGGACCctcccagcgaactaatgtggtatcctct
tgaagaactttcaaaatgtagccatgggttccttgtggaattgtaatgccttcaatactaggaa
tgctgact

									
								

					

						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: 498
Transcript exons: 123422367-123422568,123423174-123423331,123423414-123423
473,123424161-123424238
CTCCCAGCGAACTAATGTGGTATCCTCTTGAAGAACTTTCAAAATGTAGCCATGGGTTCCTTGT
GGAATTGTAATGCCTTCAATACTAGGAATGCTGACTGGATGATGACTTTCAATTTGATGGCCAT
AACCAACACCATCAGCAACACAAGGGATGGTATAGATTGTTGTAACTCCATTCATCCTCTCAAG
ATAATTATATACACAATTAGCAGGCCAGGTCCCATGGCAAACTGCTGATAAGAAACGTATCAGT
TCAGATATCTGAAAAGGATACTCCTCCTCCAGCATATGAAGAACAGATCTGATAGGACCATCAA
CAAAGCTATCTTTATCCCAAAATTGCATACAGAGAGATTCCTCTCCATCATAAACTTCACATAA
AATACTCGAAATCATGTCAAAGGAACTGTGTTCTTTCTGATAAGATACCTCATATGAAGCGATG
AATGCTGAAATGAATGTCCGCAATATACCCCGATAACCAGAAACAGGACC
						
					

						Genomic sequence
						
							CTCCCAGCGAACTAATGTGGTATCCTCTTGAAGAACTTTCAAAATGTAGCCATGGGTTCCTTGT
GGAATTGTAATGCCTTCAATACTAGGAATGCTGACTGGATGATGACTTTCAATTTGATGGCCAT
AACCAACACCATCAGCAACACAAGGGATGGTATAGATTGTTGTAACTCCATTCATCCTCTCAAG
ATAATTATATCTGTGACAAGCCCCAAAAATATTGAAATACATTACTATATCACGCGGCAAAGAA
TATCATGATCTTTTTTGTATTGCTTTTAAACAAAAATTTACACAACCACATCAGCACCTCTTGA
ATACCAAAAACAGTTAATTATATTTTGCTAAGATAAAATTCTTGGTAAGAGAATGAAATCATTG
GTAAGGATCATTTTGCATGTTGCAATTTGGAAACCAAGATGGCCTGTATACTGCTGCCTAAGTA
CTAATAATATCAATAATTCTGAATGTTTTTTATATTTCATCCACCGATAAAGAAATTACAAATT
CATGCTCATCATCACTATTCCAAAAACTGGAGACCAGAGAAAAAATAAAATAACAGTACTCGCT
CAAAAGCAATTTATGAATTTGAAATGAGATAATAAATGTTCTCTTGTCAAATATACCAAATTCA
TCATCCATATTTAAGTTATGTTTGTCTGAGTAAACCATATCACAGTAATAGCATAGAAGAAATC
AACGCAGCACAAGATGGGAAGCACACAAATTTTCTATTGGGGAAGGAACATCAATCCCGACACA
GTAGTGCCAAAAATAAAGAAAGAAAAAAGGAAAACATACACACAATTAGCAGGCCAGGTCCCAT
GGCAAACTGCTGATAAGAAACGTATCAGTTCAGATATCTGAAAAGGATACTCCTCCTCCAGCAT
ATGAAGAACAGATCTGATAGGACCATCAACAAAGCTATCTTTATCCCAAAATTGCATACAGAGA
GATTCCTGGACAATTAAAATATCATTATTCTGTAGTCTTCATGCATAAATTATTCCACATCAAT
AATCACAATAATCATATTAATACCTCTCCATCATAAACTTCACATAAAATACTCGAAATCATGT
CAAAGGAACTGTGTTCTTTCTGCACAGAAAATAATTCAACTAACCAGTTAAGCTCATAGTTGTT
AAAGCAGTAAGGCGAGTGACCCCCTTTTTAACTTTTAAGCAATAAAGCGTAAGGCGAGGCGACG
CCTTAAATATATTTAAAAATAGGAAAAATATTGATATTTGAGAAAGTATTTAGCACAATAATAA
TAATAAAGAGAAAAGGATAAAGATAAGGAAAAGACTAGCCCAATCAGCCCAAACCAGCCCAACT
AGCCCATTTCTTCACTCTCCCCCTCTCCCTCTATCTCCCAGTCCCAGCCGACTCCCTCCCGCTC
CCAGCCGCCTCTCTCACCCCTCTCTCCCTCTCTCACCGCTCTCTCCCTCTGTGCTCACTTCTCC
CTCTCTCACCGCTCTCTCCCTCTGTGCTCACTTCTCCCTCTCTCCTCTACTGGCCCTGCCACGT
CGCGCCGCTGGAGCCCGCCGCGCACGCCCGCGCCGCTGGGAGACGCCGTGCGTGCCCACGCCGC
CACGCTGCCAGCCTCCGGTAACCTCTCGTCCACACGCCTTAGGTCCGCGAATAAGGCGAGAAGG
ACGCCTTACGTCGCCGGCGCGCCTTACCGCCTAGGCGACGCCTTAACAACTATGGTTAAGCTCC
TTAGTATTACCTTCACCAAGAGTTAATTTAAACATGACTGTAACTAACCAATAGATTTGCATTT
ACCTGATAAGATACCTCATATGAAGCGATGAATGCTGAAATGAATGTCCGCAATATACCCCGAT
AACCAGAAACAGGACC
						
					

			
		

Sequences
Splice junction sequence	TAACCAATAGATTTGCATTTACCTGATAAGATACCTCATATGAAGCGATGAATGCTGAAATGAA TGTCCGCAATATACCCCGATAACCAGAAACAGGACCctcccagcgaactaatgtggtatcctct tgaagaactttcaaaatgtagccatgggttccttgtggaattgtaatgccttcaatactaggaa tgctgact
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: 498 Transcript exons: 123422367-123422568,123423174-123423331,123423414-123423 473,123424161-123424238 CTCCCAGCGAACTAATGTGGTATCCTCTTGAAGAACTTTCAAAATGTAGCCATGGGTTCCTTGT GGAATTGTAATGCCTTCAATACTAGGAATGCTGACTGGATGATGACTTTCAATTTGATGGCCAT AACCAACACCATCAGCAACACAAGGGATGGTATAGATTGTTGTAACTCCATTCATCCTCTCAAG ATAATTATATACACAATTAGCAGGCCAGGTCCCATGGCAAACTGCTGATAAGAAACGTATCAGT TCAGATATCTGAAAAGGATACTCCTCCTCCAGCATATGAAGAACAGATCTGATAGGACCATCAA CAAAGCTATCTTTATCCCAAAATTGCATACAGAGAGATTCCTCTCCATCATAAACTTCACATAA AATACTCGAAATCATGTCAAAGGAACTGTGTTCTTTCTGATAAGATACCTCATATGAAGCGATG AATGCTGAAATGAATGTCCGCAATATACCCCGATAACCAGAAACAGGACC
Genomic sequence	CTCCCAGCGAACTAATGTGGTATCCTCTTGAAGAACTTTCAAAATGTAGCCATGGGTTCCTTGT GGAATTGTAATGCCTTCAATACTAGGAATGCTGACTGGATGATGACTTTCAATTTGATGGCCAT AACCAACACCATCAGCAACACAAGGGATGGTATAGATTGTTGTAACTCCATTCATCCTCTCAAG ATAATTATATCTGTGACAAGCCCCAAAAATATTGAAATACATTACTATATCACGCGGCAAAGAA TATCATGATCTTTTTTGTATTGCTTTTAAACAAAAATTTACACAACCACATCAGCACCTCTTGA ATACCAAAAACAGTTAATTATATTTTGCTAAGATAAAATTCTTGGTAAGAGAATGAAATCATTG GTAAGGATCATTTTGCATGTTGCAATTTGGAAACCAAGATGGCCTGTATACTGCTGCCTAAGTA CTAATAATATCAATAATTCTGAATGTTTTTTATATTTCATCCACCGATAAAGAAATTACAAATT CATGCTCATCATCACTATTCCAAAAACTGGAGACCAGAGAAAAAATAAAATAACAGTACTCGCT CAAAAGCAATTTATGAATTTGAAATGAGATAATAAATGTTCTCTTGTCAAATATACCAAATTCA TCATCCATATTTAAGTTATGTTTGTCTGAGTAAACCATATCACAGTAATAGCATAGAAGAAATC AACGCAGCACAAGATGGGAAGCACACAAATTTTCTATTGGGGAAGGAACATCAATCCCGACACA GTAGTGCCAAAAATAAAGAAAGAAAAAAGGAAAACATACACACAATTAGCAGGCCAGGTCCCAT GGCAAACTGCTGATAAGAAACGTATCAGTTCAGATATCTGAAAAGGATACTCCTCCTCCAGCAT ATGAAGAACAGATCTGATAGGACCATCAACAAAGCTATCTTTATCCCAAAATTGCATACAGAGA GATTCCTGGACAATTAAAATATCATTATTCTGTAGTCTTCATGCATAAATTATTCCACATCAAT AATCACAATAATCATATTAATACCTCTCCATCATAAACTTCACATAAAATACTCGAAATCATGT CAAAGGAACTGTGTTCTTTCTGCACAGAAAATAATTCAACTAACCAGTTAAGCTCATAGTTGTT AAAGCAGTAAGGCGAGTGACCCCCTTTTTAACTTTTAAGCAATAAAGCGTAAGGCGAGGCGACG CCTTAAATATATTTAAAAATAGGAAAAATATTGATATTTGAGAAAGTATTTAGCACAATAATAA TAATAAAGAGAAAAGGATAAAGATAAGGAAAAGACTAGCCCAATCAGCCCAAACCAGCCCAACT AGCCCATTTCTTCACTCTCCCCCTCTCCCTCTATCTCCCAGTCCCAGCCGACTCCCTCCCGCTC CCAGCCGCCTCTCTCACCCCTCTCTCCCTCTCTCACCGCTCTCTCCCTCTGTGCTCACTTCTCC CTCTCTCACCGCTCTCTCCCTCTGTGCTCACTTCTCCCTCTCTCCTCTACTGGCCCTGCCACGT CGCGCCGCTGGAGCCCGCCGCGCACGCCCGCGCCGCTGGGAGACGCCGTGCGTGCCCACGCCGC CACGCTGCCAGCCTCCGGTAACCTCTCGTCCACACGCCTTAGGTCCGCGAATAAGGCGAGAAGG ACGCCTTACGTCGCCGGCGCGCCTTACCGCCTAGGCGACGCCTTAACAACTATGGTTAAGCTCC TTAGTATTACCTTCACCAAGAGTTAATTTAAACATGACTGTAACTAACCAATAGATTTGCATTT ACCTGATAAGATACCTCATATGAAGCGATGAATGCTGAAATGAATGTCCGCAATATACCCCGAT AACCAGAAACAGGACC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_006238 						
					
						PMCS
						0.06327948

Conservation Information
Conserved circRNAs	osa_circ_006238
PMCS	0.06327948

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							123424203-123422437(+)
123423454-123422369(-)
						
						Potential amino acid sequence
						
							MSAIYPDNQKQDPPSELMWYPLEELSKCSHGFLVEL*(+)
MISSILCEVYDGEESLCMQFWDKDSFVDGPIRSVLHMLEEEYPFQISELIRFLSAVCHGTWPAN
CVYNYLERMNGVTTIYTIPCVADGVGYGHQIESHHPVSIPSIEGITIPQGTHGYILKVLQEDTT
LVRWEGPVSGYRGILRTFISAFIASYEVSYQKEHSSFDMISSILCEVYDGEESLCMQFWDKDSF
VDGPIRSVLHMLEEEYPFQISELIRFLSAVCHGTWPANCVYNYLERMNGVTTIYTIPCVADGVG
YGHQIESHHPVSIPSIEGITIPQGTHGYILKVLQEDTTLVRWEGPVSGYRGILRTFISAFIASY
EVSYQKEHSSFDMISSILCEVYDGEESLCMQFWDKDSFVDGPIRSVLHMLEEEYPFQISELIRF
LSAVCHGTWPANCVYNYLERMNGVTTIYTIPCVADGVGYGHQIESHHPVSIPSIEGITIPQGTH
GYILKVLQEDTTLVRWEGPVSGYRGILRTFISAFIASYEVSYQKEHSSFDMISSILCEVYDGEE
SLCMQFWDKDSFVDGPIRSVLHMLEEEYPFQISELIRFLSAVCHGTWPANCVYNYLERMNGVTT
IYTIPCVADGVGYGHQIESHHPVSIPSIEGITIPQGTHGYILKVLQEDTTLVRWE(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	123424203-123422437(+) 123423454-123422369(-)
Potential amino acid sequence	MSAIYPDNQKQDPPSELMWYPLEELSKCSHGFLVEL*(+) MISSILCEVYDGEESLCMQFWDKDSFVDGPIRSVLHMLEEEYPFQISELIRFLSAVCHGTWPAN CVYNYLERMNGVTTIYTIPCVADGVGYGHQIESHHPVSIPSIEGITIPQGTHGYILKVLQEDTT LVRWEGPVSGYRGILRTFISAFIASYEVSYQKEHSSFDMISSILCEVYDGEESLCMQFWDKDSF VDGPIRSVLHMLEEEYPFQISELIRFLSAVCHGTWPANCVYNYLERMNGVTTIYTIPCVADGVG YGHQIESHHPVSIPSIEGITIPQGTHGYILKVLQEDTTLVRWEGPVSGYRGILRTFISAFIASY EVSYQKEHSSFDMISSILCEVYDGEESLCMQFWDKDSFVDGPIRSVLHMLEEEYPFQISELIRF LSAVCHGTWPANCVYNYLERMNGVTTIYTIPCVADGVGYGHQIESHHPVSIPSIEGITIPQGTH GYILKVLQEDTTLVRWEGPVSGYRGILRTFISAFIASYEVSYQKEHSSFDMISSILCEVYDGEE SLCMQFWDKDSFVDGPIRSVLHMLEEEYPFQISELIRFLSAVCHGTWPANCVYNYLERMNGVTT IYTIPCVADGVGYGHQIESHHPVSIPSIEGITIPQGTHGYILKVLQEDTTLVRWE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d030340_circ_g.5

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