Plant Circular RNA Database

Detail information of Zm00001d042793_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d042793_circ_g.1
					
						ID in PlantcircBase
						zma_circ_007732
					
						Alias
						zma_circ_0001245
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 179898052-179899958  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d042793						
					
						Parent gene annotation
						
							Transducin/WD40 repeat-like superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						leaf, 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
						Zm00001d042793_T010:3
Zm00001d042793_T012:3
Zm00001d042793_T001:3
Zm00001d042793_T011:3
Zm00001d042793_T005:3
Zm00001d042793_T006:3
Zm00001d042793_T002:3
Zm00001d042793_T003:3
Zm00001d042793_T009:3
Zm00001d042793_T004:3
Zm00001d042793_T007:3

General Information
CircRNA Name	Zm00001d042793_circ_g.1
ID in PlantcircBase	zma_circ_007732
Alias	zma_circ_0001245
Organism	Zea mays
Position	chr3: 179898052-179899958 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d042793
Parent gene annotation	Transducin/WD40 repeat-like superfamily protein
Parent gene strand	+
Alternative splicing	NA
Support reads	NA
Tissues	leaf, 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	Zm00001d042793_T010:3 Zm00001d042793_T012:3 Zm00001d042793_T001:3 Zm00001d042793_T011:3 Zm00001d042793_T005:3 Zm00001d042793_T006:3 Zm00001d042793_T002:3 Zm00001d042793_T003:3 Zm00001d042793_T009:3 Zm00001d042793_T004:3 Zm00001d042793_T007:3

			
						 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  
						
							TGCTATGGAGGTGCTGCAGGCATCATACGATGCCAGAGAATCTGAAGAGCCGCAATCTGGAATG
CTCTTCGAGAAACAGAGGCTTGTCACACAGATGGTGggggatcattatctcactggaagatggt
acattgaagtttctaagcttgcctcggattgcaaatgatgttccagccactggaaggccatttt
ccggaaca

									
								

					

						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
						
							GGGGATCATTATCTCACTGGAAGATGGTACATTGAAGTTTCTAAGCTTGCCTCGGATTGCAAAT
GATGTTCCAGCCACTGGAAGGCCATTTTCCGGAACAAAAACTCAGGGTGTTGCAACTTATCAGT
TGTCAGAATATTTGATTTGGAGTGTCCATGCTTCAGAACCTACAGGTGTGTTTCAGTACCATTT
TCATAGCCACAGCCCATATCCTGCCCAGTGGTACTGACTACTGGGTAACAAAATTCCTATGTAG
CAGCTGTCACTTCGGAGTCTAAACTAAAACGAGGGAGAGATTACCGTGTAAAATAAAACAATTA
TTTAAAATATTGGTATCACATGTGTTTGATCTAAATTTTAAAGGTGAAGTTGTTGCCAATAGAA
ATTTAAGATCTTCCTGCAGAACTTTGTTAATAGGAATTATTGTTTTGTGAAATTATTAGTTTGC
AGTTTGACAGTTGATACATAGTTCAATTGATAATAGTGGAGTAAACTGCCTGTAGATTTTGTAG
ATAATAGGCATAACACCCTGCAACTTGGATAGTATGACAGGAGAATTTTTTTACAAGTCTGAAA
TGTATTGTATGAAACAGAAAAAGAGAGCTGGGATCAGTACCTTACATGAGAAAAATTATTACAC
CAGGAAGTATCTATCTTAACTCGACCTTTGGGGGGGGGGGGAGTATCTATCTTAACTGACATAA
CCACCAGACAGAAAGGTGGATGCAACTTTGAGATTTTGAGCTTGTTCGGCTGCCATTTTCATCC
AGCTGCAGCTGCAAACAAACACTGTTCCTACAGCAGCAAGCAGCAGGCGGCTGCAGCAGCTGCC
ACTGTAGAAACTAGCAGCCGAACAAGCCGCCACTGTAGAAACTAGCAGCCGAACAAGCCCTTTC
CTGACCGACCCCTGCCAGTGTATTAATATACACTGCTTCCAGTCGGCTACCAAAACAGTGGCAA
CTTGTCTTCTTTTAGTATTAGTCCTAGATCGTTTTCTGATTATGCAGTAACTTCTGTTTTGCCT
CAAGTGTCAGATGCTTGCAGTGTTCTTTAAATTCATAATATATGTTTGCTGATGTCCAGGTTGT
GTGGCTTACTGTGGGGCAGATGGTACTGCTGTGTACTTCCAGGTGAACTTTCTAGTTGATATCA
TCAACAACATTTCTTTTCGTTTGAGTTGCAGTGTTCTAAACAAAAATTTAACTTGCTGTAGCTA
AAATCGAGATTCTGGGATAAGGAGCCTGGGCGTAACCGTGTTCCTTATTTCCTCTGTGGATCAT
TATCAGAGGATGGAGAAAATATTAAGATTGGCAGCAGGCTGCAAACATCTCCATTACCAAATGT
GCCTGTGGGGACCAAAAAGGGTTCAAAACCATCCCAAAGTATAGTTCAGGCGCTTGCTACAAGC
GATGTCACTAGCCTGCTGACATATCAGCTCAACTCCCCCACAGGAAACAATGATGCCGTAAATC
TAGAAGCTCATGATGATCAAGATGATGGACGCAGCAAAGAGCAAGGAGCAGGTGCTGTAAATCA
AGAACTTGATGGTGAACAAGATGATGGACACCGTGAAGAACAAGCAGCAGGCATGGTAACCACA
GAATTTGGCGATGATCAAGCCGATGGACACAGCGAAGAACAAGGAGCTGGTGCAATAATCTCAG
CCACTCCTGCAAAGGAAGAGAATGATGGAACATGGAACGACAAGGGTGTTCAATCCCCTAAAGA
CCTTAATGTCGTCCCTCCGAATTCTGTCGCTTTGAATCAAGTGCGGTGGAACATGAACAAGGGT
AGCCAGAGATGGCTGTGCTATGGAGGTGCTGCAGGCATCATACGATGCCAGAGAATCTGAAGAG
CCGCAATCTGGAATGCTCTTCGAGAAACAGAGGCTTGTCACACAGATGGTG
						
					

			
		

Sequences
Splice junction sequence	TGCTATGGAGGTGCTGCAGGCATCATACGATGCCAGAGAATCTGAAGAGCCGCAATCTGGAATG CTCTTCGAGAAACAGAGGCTTGTCACACAGATGGTGggggatcattatctcactggaagatggt acattgaagtttctaagcttgcctcggattgcaaatgatgttccagccactggaaggccatttt ccggaaca
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	GGGGATCATTATCTCACTGGAAGATGGTACATTGAAGTTTCTAAGCTTGCCTCGGATTGCAAAT GATGTTCCAGCCACTGGAAGGCCATTTTCCGGAACAAAAACTCAGGGTGTTGCAACTTATCAGT TGTCAGAATATTTGATTTGGAGTGTCCATGCTTCAGAACCTACAGGTGTGTTTCAGTACCATTT TCATAGCCACAGCCCATATCCTGCCCAGTGGTACTGACTACTGGGTAACAAAATTCCTATGTAG CAGCTGTCACTTCGGAGTCTAAACTAAAACGAGGGAGAGATTACCGTGTAAAATAAAACAATTA TTTAAAATATTGGTATCACATGTGTTTGATCTAAATTTTAAAGGTGAAGTTGTTGCCAATAGAA ATTTAAGATCTTCCTGCAGAACTTTGTTAATAGGAATTATTGTTTTGTGAAATTATTAGTTTGC AGTTTGACAGTTGATACATAGTTCAATTGATAATAGTGGAGTAAACTGCCTGTAGATTTTGTAG ATAATAGGCATAACACCCTGCAACTTGGATAGTATGACAGGAGAATTTTTTTACAAGTCTGAAA TGTATTGTATGAAACAGAAAAAGAGAGCTGGGATCAGTACCTTACATGAGAAAAATTATTACAC CAGGAAGTATCTATCTTAACTCGACCTTTGGGGGGGGGGGGAGTATCTATCTTAACTGACATAA CCACCAGACAGAAAGGTGGATGCAACTTTGAGATTTTGAGCTTGTTCGGCTGCCATTTTCATCC AGCTGCAGCTGCAAACAAACACTGTTCCTACAGCAGCAAGCAGCAGGCGGCTGCAGCAGCTGCC ACTGTAGAAACTAGCAGCCGAACAAGCCGCCACTGTAGAAACTAGCAGCCGAACAAGCCCTTTC CTGACCGACCCCTGCCAGTGTATTAATATACACTGCTTCCAGTCGGCTACCAAAACAGTGGCAA CTTGTCTTCTTTTAGTATTAGTCCTAGATCGTTTTCTGATTATGCAGTAACTTCTGTTTTGCCT CAAGTGTCAGATGCTTGCAGTGTTCTTTAAATTCATAATATATGTTTGCTGATGTCCAGGTTGT GTGGCTTACTGTGGGGCAGATGGTACTGCTGTGTACTTCCAGGTGAACTTTCTAGTTGATATCA TCAACAACATTTCTTTTCGTTTGAGTTGCAGTGTTCTAAACAAAAATTTAACTTGCTGTAGCTA AAATCGAGATTCTGGGATAAGGAGCCTGGGCGTAACCGTGTTCCTTATTTCCTCTGTGGATCAT TATCAGAGGATGGAGAAAATATTAAGATTGGCAGCAGGCTGCAAACATCTCCATTACCAAATGT GCCTGTGGGGACCAAAAAGGGTTCAAAACCATCCCAAAGTATAGTTCAGGCGCTTGCTACAAGC GATGTCACTAGCCTGCTGACATATCAGCTCAACTCCCCCACAGGAAACAATGATGCCGTAAATC TAGAAGCTCATGATGATCAAGATGATGGACGCAGCAAAGAGCAAGGAGCAGGTGCTGTAAATCA AGAACTTGATGGTGAACAAGATGATGGACACCGTGAAGAACAAGCAGCAGGCATGGTAACCACA GAATTTGGCGATGATCAAGCCGATGGACACAGCGAAGAACAAGGAGCTGGTGCAATAATCTCAG CCACTCCTGCAAAGGAAGAGAATGATGGAACATGGAACGACAAGGGTGTTCAATCCCCTAAAGA CCTTAATGTCGTCCCTCCGAATTCTGTCGCTTTGAATCAAGTGCGGTGGAACATGAACAAGGGT AGCCAGAGATGGCTGTGCTATGGAGGTGCTGCAGGCATCATACGATGCCAGAGAATCTGAAGAG CCGCAATCTGGAATGCTCTTCGAGAAACAGAGGCTTGTCACACAGATGGTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.027850481

Conservation Information
Conserved circRNAs	NA
PMCS	0.027850481

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							179899853-179899900(+)
179899864-179898114(+)
179898062-179899883(-)
						
						Potential amino acid sequence
						
							MAVLWRCCRHHTMPENLKSRNLECSSRNRGLSHRWWGIIISLEDGTLKFLSLPRIANDVPATGR
PFSGTKTQGVATYQLSEYLIWSVHASEPTGCVAYCGADGTAVYFQLKSRFWDKEPGRNRVPYFL
CGSLSEDGENIKIGSRLQTSPLPNVPVGTKKGSKPSQSIVQALATSDVTSLLTYQLNSPTGNND
AVNLEAHDDQDDGRSKEQGAGAVNQELDGEQDDGHREEQAAGMVTTEFGDDQADGHSEEQGAGA
IISATPAKEENDGTWNDKGVQSPKDLNVVPPNSVALNQVRWNMNKGSQRWLCYGGAAGIIRCQR
I*(+)
MEVLQASYDARESEEPQSGMLFEKQRLVTQMVGDHYLTGRWYIEVSKLASDCK*(+)
MIPHHLCDKPLFLEEHSRLRLFRFSGIV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	179899853-179899900(+) 179899864-179898114(+) 179898062-179899883(-)
Potential amino acid sequence	MAVLWRCCRHHTMPENLKSRNLECSSRNRGLSHRWWGIIISLEDGTLKFLSLPRIANDVPATGR PFSGTKTQGVATYQLSEYLIWSVHASEPTGCVAYCGADGTAVYFQLKSRFWDKEPGRNRVPYFL CGSLSEDGENIKIGSRLQTSPLPNVPVGTKKGSKPSQSIVQALATSDVTSLLTYQLNSPTGNND AVNLEAHDDQDDGRSKEQGAGAVNQELDGEQDDGHREEQAAGMVTTEFGDDQADGHSEEQGAGA IISATPAKEENDGTWNDKGVQSPKDLNVVPPNSVALNQVRWNMNKGSQRWLCYGGAAGIIRCQR I(+) MEVLQASYDARESEEPQSGMLFEKQRLVTQMVGDHYLTGRWYIEVSKLASDCK(+) MIPHHLCDKPLFLEEHSRLRLFRFSGIV*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d042793_circ_g.1

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