Plant Circular RNA Database

Detail information of Zm00001d037156_circ_g.3

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d037156_circ_g.3
					

						ID in PlantcircBase
						zma_circ_009009
					

						Alias
						Zm06circ00041, zma_circ_0002147, GRMZM2G330024_C1
					

						Organism
						
							Zea mays						
					

						Position
						
							chr6: 114077315-114077674  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						CIRI2, find_circ
					

						Parent gene
						
							Zm00001d037156						
					

						Parent gene annotation
						
							Putative PHD-finger domain containing protein family  
							
					

						Parent gene strand
						-
					

						Alternative splicing
						
							Zm00001d037156_circ_g.2 						
					

						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
						Zm00001d037156_T106:1
Zm00001d037156_T036:1
Zm00001d037156_T003:1
Zm00001d037156_T024:1
Zm00001d037156_T030:1
Zm00001d037156_T034:1
Zm00001d037156_T010:1
Zm00001d037156_T006:1
Zm00001d037156_T012:1
Zm00001d037156_T084:1
Zm00001d037156_T094:1
Zm00001d037156_T064:1
Zm00001d037156_T040:1
Zm00001d037156_T046:1
Zm00001d037156_T060:1
Zm00001d037156_T001:1
Zm00001d037156_T082:1
Zm00001d037156_T072:1
Zm00001d037156_T093:1
Zm00001d037156_T073:1
Zm00001d037156_T026:1
Zm00001d037156_T032:1
Zm00001d037156_T028:1
Zm00001d037156_T019:1
Zm00001d037156_T020:1
Zm00001d037156_T038:1
Zm00001d037156_T055:1
Zm00001d037156_T083:1
Zm00001d037156_T005:1
Zm00001d037156_T004:1
Zm00001d037156_T086:1
Zm00001d037156_T018:1
Zm00001d037156_T066:1
Zm00001d037156_T049:1
Zm00001d037156_T087:1
Zm00001d037156_T008:1
Zm00001d037156_T099:1
Zm00001d037156_T098:1
Zm00001d037156_T062:1
Zm00001d037156_T102:1
Zm00001d037156_T100:1
Zm00001d037156_T104:1
Zm00001d037156_T044:1
Zm00001d037156_T097:1
Zm00001d037156_T076:1
Zm00001d037156_T043:1
Zm00001d037156_T023:1
Zm00001d037156_T074:1
Zm00001d037156_T014:1
Zm00001d037156_T090:1
Zm00001d037156_T068:1
Zm00001d037156_T015:1
Zm00001d037156_T081:1
Zm00001d037156_T092:1
Zm00001d037156_T052:1
Zm00001d037156_T047:1
Zm00001d037156_T070:1
Zm00001d037156_T051:1
Zm00001d037156_T108:1
Zm00001d037156_T079:1

					

			
		

General Information
CircRNA Name	Zm00001d037156_circ_g.3
ID in PlantcircBase	zma_circ_009009
Alias	Zm06circ00041, zma_circ_0002147, GRMZM2G330024_C1
Organism	Zea mays
Position	chr6: 114077315-114077674 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d037156
Parent gene annotation	Putative PHD-finger domain containing protein family
Parent gene strand	-
Alternative splicing	Zm00001d037156_circ_g.2
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	Zm00001d037156_T106:1 Zm00001d037156_T036:1 Zm00001d037156_T003:1 Zm00001d037156_T024:1 Zm00001d037156_T030:1 Zm00001d037156_T034:1 Zm00001d037156_T010:1 Zm00001d037156_T006:1 Zm00001d037156_T012:1 Zm00001d037156_T084:1 Zm00001d037156_T094:1 Zm00001d037156_T064:1 Zm00001d037156_T040:1 Zm00001d037156_T046:1 Zm00001d037156_T060:1 Zm00001d037156_T001:1 Zm00001d037156_T082:1 Zm00001d037156_T072:1 Zm00001d037156_T093:1 Zm00001d037156_T073:1 Zm00001d037156_T026:1 Zm00001d037156_T032:1 Zm00001d037156_T028:1 Zm00001d037156_T019:1 Zm00001d037156_T020:1 Zm00001d037156_T038:1 Zm00001d037156_T055:1 Zm00001d037156_T083:1 Zm00001d037156_T005:1 Zm00001d037156_T004:1 Zm00001d037156_T086:1 Zm00001d037156_T018:1 Zm00001d037156_T066:1 Zm00001d037156_T049:1 Zm00001d037156_T087:1 Zm00001d037156_T008:1 Zm00001d037156_T099:1 Zm00001d037156_T098:1 Zm00001d037156_T062:1 Zm00001d037156_T102:1 Zm00001d037156_T100:1 Zm00001d037156_T104:1 Zm00001d037156_T044:1 Zm00001d037156_T097:1 Zm00001d037156_T076:1 Zm00001d037156_T043:1 Zm00001d037156_T023:1 Zm00001d037156_T074:1 Zm00001d037156_T014:1 Zm00001d037156_T090:1 Zm00001d037156_T068:1 Zm00001d037156_T015:1 Zm00001d037156_T081:1 Zm00001d037156_T092:1 Zm00001d037156_T052:1 Zm00001d037156_T047:1 Zm00001d037156_T070:1 Zm00001d037156_T051:1 Zm00001d037156_T108:1 Zm00001d037156_T079:1

			
						 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  
						
							CAACTTGAGCGGAGTCCAGTTCAGATACACTTTTGTCATTCTGTATGGAGCTGATGCTTTTGAC
AGAAGAATGCTTTGCACAAAATGCTCGCATCTCAACctttctaagaattccggaaacatctcca
gaatcgctcataagattcccatctgaagagggttgatcagcagccatatctgcactttgtgttt
cttgagtc

						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: 360
Transcript exons: 114077315-114077674
CTTTCTAAGAATTCCGGAAACATCTCCAGAATCGCTCATAAGATTCCCATCTGAAGAGGGTTGA
TCAGCAGCCATATCTGCACTTTGTGTTTCTTGAGTCCTTCCAAGAACGGGTGAAATGGTAGCCA
CTTCATTTGTATGTGCTTCGTTTAGGCTACAAGAACTAGTAGTAATTGTGCTGTTCACAAATTT
GTCCTTGTTACTGCGCGTAAATCTCACTTGCTGTTCCTTCCCAGTAACAGGCTTTCCATCATGC
AGCTCAACTTGAGCGGAGTCCAGTTCAGATACACTTTTGTCATTCTGTATGGAGCTGATGCTTT
TGACAGAAGAATGCTTTGCACAAAATGCTCGCATCTCAAC
						
						Genomic sequence
						
							CTTTCTAAGAATTCCGGAAACATCTCCAGAATCGCTCATAAGATTCCCATCTGAAGAGGGTTGA
TCAGCAGCCATATCTGCACTTTGTGTTTCTTGAGTCCTTCCAAGAACGGGTGAAATGGTAGCCA
CTTCATTTGTATGTGCTTCGTTTAGGCTACAAGAACTAGTAGTAATTGTGCTGTTCACAAATTT
GTCCTTGTTACTGCGCGTAAATCTCACTTGCTGTTCCTTCCCAGTAACAGGCTTTCCATCATGC
AGCTCAACTTGAGCGGAGTCCAGTTCAGATACACTTTTGTCATTCTGTATGGAGCTGATGCTTT
TGACAGAAGAATGCTTTGCACAAAATGCTCGCATCTCAAC

Sequences
Splice junction sequence	CAACTTGAGCGGAGTCCAGTTCAGATACACTTTTGTCATTCTGTATGGAGCTGATGCTTTTGAC AGAAGAATGCTTTGCACAAAATGCTCGCATCTCAACctttctaagaattccggaaacatctcca gaatcgctcataagattcccatctgaagagggttgatcagcagccatatctgcactttgtgttt cttgagtc
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: 360 Transcript exons: 114077315-114077674 CTTTCTAAGAATTCCGGAAACATCTCCAGAATCGCTCATAAGATTCCCATCTGAAGAGGGTTGA TCAGCAGCCATATCTGCACTTTGTGTTTCTTGAGTCCTTCCAAGAACGGGTGAAATGGTAGCCA CTTCATTTGTATGTGCTTCGTTTAGGCTACAAGAACTAGTAGTAATTGTGCTGTTCACAAATTT GTCCTTGTTACTGCGCGTAAATCTCACTTGCTGTTCCTTCCCAGTAACAGGCTTTCCATCATGC AGCTCAACTTGAGCGGAGTCCAGTTCAGATACACTTTTGTCATTCTGTATGGAGCTGATGCTTT TGACAGAAGAATGCTTTGCACAAAATGCTCGCATCTCAAC
Genomic sequence	CTTTCTAAGAATTCCGGAAACATCTCCAGAATCGCTCATAAGATTCCCATCTGAAGAGGGTTGA TCAGCAGCCATATCTGCACTTTGTGTTTCTTGAGTCCTTCCAAGAACGGGTGAAATGGTAGCCA CTTCATTTGTATGTGCTTCGTTTAGGCTACAAGAACTAGTAGTAATTGTGCTGTTCACAAATTT GTCCTTGTTACTGCGCGTAAATCTCACTTGCTGTTCCTTCCCAGTAACAGGCTTTCCATCATGC AGCTCAACTTGAGCGGAGTCCAGTTCAGATACACTTTTGTCATTCTGTATGGAGCTGATGCTTT TGACAGAAGAATGCTTTGCACAAAATGCTCGCATCTCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.143918919

Conservation Information
Conserved circRNAs	NA
PMCS	0.143918919

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							114077568-114077365(+)
114077620-114077375(+)
114077670-114077317(-)
114077339-114077532(-)
						
						Potential amino acid sequence
						
							MQLNLSGVQFRYTFVILYGADAFDRRMLCTKCSHLNLSKNSGNISRIAHKIPI*(+)
MELMLLTEECFAQNARISTFLRIPETSPESLIRFPSEEG*(+)
MRAFCAKHSSVKSISSIQNDKSVSELDSAQVELHDGKPVTGKEQQVRFTRSNKDKFVNSTITTS
SCSLNEAHTNEVATISPVLGRTQETQSADMAADQPSSDGNLMSDSGDVSGILRKVEMRAFCAKH
SSVKSISSIQNDKSVSELDSAQVELHDGKPVTGKEQQVRFTRSNKDKFVNSTITTSSCSLNEAH
TNEVATISPVLGRTQETQSADMAADQPSSDGNLMSDSGDVSGILRKVEMRAFCAKHSSVKSISS
IQNDKSVSELDSAQVELHDGKPVTGKEQQVRFTRSNKDKFVNSTITTSSCSLNEAHTNEVATIS
PVLGRTQETQSADMAADQPSSDGNLMSDSGDVSGILRKVEMRAFCAKHSSVKSISSIQNDKSVS
ELDSAQVELHDGKPVTGKEQQVRFTRSNKDKFVNSTITTSSCSLNEAHTNEVATISPVLGRTQE
TQSADMAADQPSSDGNLMSDSGDVSGILRK(-)
MFPEFLERLRCEHFVQSILLSKASAPYRMTKVYLNWTPLKLSCMMESLLLGRNSK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	114077568-114077365(+) 114077620-114077375(+) 114077670-114077317(-) 114077339-114077532(-)
Potential amino acid sequence	MQLNLSGVQFRYTFVILYGADAFDRRMLCTKCSHLNLSKNSGNISRIAHKIPI(+) MELMLLTEECFAQNARISTFLRIPETSPESLIRFPSEEG(+) MRAFCAKHSSVKSISSIQNDKSVSELDSAQVELHDGKPVTGKEQQVRFTRSNKDKFVNSTITTS SCSLNEAHTNEVATISPVLGRTQETQSADMAADQPSSDGNLMSDSGDVSGILRKVEMRAFCAKH SSVKSISSIQNDKSVSELDSAQVELHDGKPVTGKEQQVRFTRSNKDKFVNSTITTSSCSLNEAH TNEVATISPVLGRTQETQSADMAADQPSSDGNLMSDSGDVSGILRKVEMRAFCAKHSSVKSISS IQNDKSVSELDSAQVELHDGKPVTGKEQQVRFTRSNKDKFVNSTITTSSCSLNEAHTNEVATIS PVLGRTQETQSADMAADQPSSDGNLMSDSGDVSGILRKVEMRAFCAKHSSVKSISSIQNDKSVS ELDSAQVELHDGKPVTGKEQQVRFTRSNKDKFVNSTITTSSCSLNEAHTNEVATISPVLGRTQE TQSADMAADQPSSDGNLMSDSGDVSGILRK(-) MFPEFLERLRCEHFVQSILLSKASAPYRMTKVYLNWTPLKLSCMMESLLLGRNSK*(-)
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 Zm00001d037156_circ_g.3

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