Plant Circular RNA Database

Detail information of Zm00001d043376_circ_g.6

			
						 General Information
					
						CircRNA Name
						Zm00001d043376_circ_g.6
					
						ID in PlantcircBase
						zma_circ_007789
					
						Alias
						Zm03circ00086, zma_circ_0001252, GRMZM2G460078_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 198084779-198085747  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d043376						
					
						Parent gene annotation
						
							Long-chain-fatty-acid-CoA ligase-like protein  
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d043376_circ_g.1 Zm00001d043376_circ_g.2 Zm00001d043376_circ_g.3 Zm00001d043376_circ_g.4 Zm00001d043376_circ_g.5 						
					
						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
						Zm00001d043376_T005:5
Zm00001d043376_T004:5
Zm00001d043376_T001:5
Zm00001d043376_T006:5
Zm00001d043376_T002:5
Zm00001d043376_T003:5

General Information
CircRNA Name	Zm00001d043376_circ_g.6
ID in PlantcircBase	zma_circ_007789
Alias	Zm03circ00086, zma_circ_0001252, GRMZM2G460078_C2
Organism	Zea mays
Position	chr3: 198084779-198085747 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d043376
Parent gene annotation	Long-chain-fatty-acid-CoA ligase-like protein
Parent gene strand	-
Alternative splicing	Zm00001d043376_circ_g.1 Zm00001d043376_circ_g.2 Zm00001d043376_circ_g.3 Zm00001d043376_circ_g.4 Zm00001d043376_circ_g.5
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	Zm00001d043376_T005:5 Zm00001d043376_T004:5 Zm00001d043376_T001:5 Zm00001d043376_T006:5 Zm00001d043376_T002:5 Zm00001d043376_T003:5

			
						 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  
						
							ATACTGTAATGGCCTCTGTACTTTTACTCGCATCGTTGGGATATGATTCTCGCCATCTCTGCCA
TATCCCGCTTACACTGAATTTTGGTATAAACTCAACctctggtcttttccaatactccttgaaa
agagatggacttctaatgcagagctcgccaactccagttgtagtttcagccccgtcctccataa
tgatcttg

									
								

					

						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: 480
Transcript exons: 198084779-198084880,198084979-198085056,198085131-198085
223,198085435-198085533,198085640-198085747
CTCTGGTCTTTTCCAATACTCCTTGAAAAGAGATGGACTTCTAATGCAGAGCTCGCCAACTCCA
GTTGTAGTTTCAGCCCCGTCCTCCATAATGATCTTGGCCTCAATGCGTGGAAGAGGTTTACCAA
CTGTACCTTCTTTTCGGATACCATGCAATGGATTAGACAGTGCCATGACAAACTCAGTCATACC
ATAGCGTTCCAAAAGACGATGGCCTGTCACTTCCTCCCACCTCTTCATAAGTGGGGAAGGAAGA
GCTGATGATCCACACATCATTAACCTCAGATGCTTTGCAGCGTAAGAAGAGGCCGACTTTTGAT
CAGGATCCATACTATCATACCCTTGCAGCAGACGTGTATACATGGTTGGAACTCCAGTAAATAC
TGTAATGGCCTCTGTACTTTTACTCGCATCGTTGGGATATGATTCTCGCCATCTCTGCCATATC
CCGCTTACACTGAATTTTGGTATAAACTCAAC
						
					

						Genomic sequence
						
							CTCTGGTCTTTTCCAATACTCCTTGAAAAGAGATGGACTTCTAATGCAGAGCTCGCCAACTCCA
GTTGTAGTTTCAGCCCCGTCCTCCATAATGATCTTGGCCTGAGTCAGAAAGATGACTTAAAACT
ATGAAGCAATGCAGAATACACAGAATAACCAATGCTTTAATGATACTAACTCCCATGAATTGTT
CATCATACCTCAATGCGTGGAAGAGGTTTACCAACTGTACCTTCTTTTCGGATACCATGCAATG
GATTAGACAGTGCCATGACAAACTGTAACCAATATTAAGTCTATCAGGAGTCATACAGTTAATT
AGTGTATTGACTAGATGGGGAATATTTTTTACCTCAGTCATACCATAGCGTTCCAAAAGACGAT
GGCCTGTCACTTCCTCCCACCTCTTCATAAGTGGGGAAGGAAGAGCTGATGATCCACACATCTG
CAGCAATTCAATGAGTATTAATGATAAAATCTTTATAATTCATGCATCAGTTCCATGATAGAAC
TGAAAAAGGTCTATAGAACTCACTAAGAATACAGATGTAAGAGTAAAACACAAACCAGCAAATC
ACACTTCGATGCACAGCAAGTGAAAAAATGATAAATGATAAATGTATAAAGACTTAAACACTGT
TTCCAATGAACATTACCATTAACCTCAGATGCTTTGCAGCGTAAGAAGAGGCCGACTTTTGATC
AGGATCCATACTATCATACCCTTGCAGCAGACGTGTATACATGGTTGGAACCTGCCATAAAAGA
AGTATCAAATTACCTTAACTTATCAAACAATATGAAGAAAAATAGTTTGGCATGAATCTGAAGA
TACTGTTATGCTATGACAGCAAATCATACTCCAGTAAATACTGTAATGGCCTCTGTACTTTTAC
TCGCATCGTTGGGATATGATTCTCGCCATCTCTGCCATATCCCGCTTACACTGAATTTTGGTAT
AAACTCAAC
						
					

			
		

Sequences
Splice junction sequence	ATACTGTAATGGCCTCTGTACTTTTACTCGCATCGTTGGGATATGATTCTCGCCATCTCTGCCA TATCCCGCTTACACTGAATTTTGGTATAAACTCAACctctggtcttttccaatactccttgaaa agagatggacttctaatgcagagctcgccaactccagttgtagtttcagccccgtcctccataa tgatcttg
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: 480 Transcript exons: 198084779-198084880,198084979-198085056,198085131-198085 223,198085435-198085533,198085640-198085747 CTCTGGTCTTTTCCAATACTCCTTGAAAAGAGATGGACTTCTAATGCAGAGCTCGCCAACTCCA GTTGTAGTTTCAGCCCCGTCCTCCATAATGATCTTGGCCTCAATGCGTGGAAGAGGTTTACCAA CTGTACCTTCTTTTCGGATACCATGCAATGGATTAGACAGTGCCATGACAAACTCAGTCATACC ATAGCGTTCCAAAAGACGATGGCCTGTCACTTCCTCCCACCTCTTCATAAGTGGGGAAGGAAGA GCTGATGATCCACACATCATTAACCTCAGATGCTTTGCAGCGTAAGAAGAGGCCGACTTTTGAT CAGGATCCATACTATCATACCCTTGCAGCAGACGTGTATACATGGTTGGAACTCCAGTAAATAC TGTAATGGCCTCTGTACTTTTACTCGCATCGTTGGGATATGATTCTCGCCATCTCTGCCATATC CCGCTTACACTGAATTTTGGTATAAACTCAAC
Genomic sequence	CTCTGGTCTTTTCCAATACTCCTTGAAAAGAGATGGACTTCTAATGCAGAGCTCGCCAACTCCA GTTGTAGTTTCAGCCCCGTCCTCCATAATGATCTTGGCCTGAGTCAGAAAGATGACTTAAAACT ATGAAGCAATGCAGAATACACAGAATAACCAATGCTTTAATGATACTAACTCCCATGAATTGTT CATCATACCTCAATGCGTGGAAGAGGTTTACCAACTGTACCTTCTTTTCGGATACCATGCAATG GATTAGACAGTGCCATGACAAACTGTAACCAATATTAAGTCTATCAGGAGTCATACAGTTAATT AGTGTATTGACTAGATGGGGAATATTTTTTACCTCAGTCATACCATAGCGTTCCAAAAGACGAT GGCCTGTCACTTCCTCCCACCTCTTCATAAGTGGGGAAGGAAGAGCTGATGATCCACACATCTG CAGCAATTCAATGAGTATTAATGATAAAATCTTTATAATTCATGCATCAGTTCCATGATAGAAC TGAAAAAGGTCTATAGAACTCACTAAGAATACAGATGTAAGAGTAAAACACAAACCAGCAAATC ACACTTCGATGCACAGCAAGTGAAAAAATGATAAATGATAAATGTATAAAGACTTAAACACTGT TTCCAATGAACATTACCATTAACCTCAGATGCTTTGCAGCGTAAGAAGAGGCCGACTTTTGATC AGGATCCATACTATCATACCCTTGCAGCAGACGTGTATACATGGTTGGAACCTGCCATAAAAGA AGTATCAAATTACCTTAACTTATCAAACAATATGAAGAAAAATAGTTTGGCATGAATCTGAAGA TACTGTTATGCTATGACAGCAAATCATACTCCAGTAAATACTGTAATGGCCTCTGTACTTTTAC TCGCATCGTTGGGATATGATTCTCGCCATCTCTGCCATATCCCGCTTACACTGAATTTTGGTAT AAACTCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.253496396

Conservation Information
Conserved circRNAs	NA
PMCS	0.253496396

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							198085524-198085143(+)
198085526-198084781(-)
198085030-198085722(-)
						
						Potential amino acid sequence
						
							MVGTPVNTVMASVLLLASLGYDSRHLCHIPLTLNFGINSTSGLFQYSLKRDGLLMQSSPTPVVV
SAPSSIMILASMRGRGLPTVPSFRIPCNGLDSAMTNSVIP*(+)
MYTRLLQGYDSMDPDQKSASSYAAKHLRLMMCGSSALPSPLMKRWEEVTGHRLLERYGMTEFVM
ALSNPLHGIRKEGTVGKPLPRIEAKIIMEDGAETTTGVGELCIRSPSLFKEYWKRPEVEFIPKF
SVSGIWQRWRESYPNDASKSTEAITVFTGVPTMYTRLLQGYDSMDPDQKSASSYAAKHLRLMMC
GSSALPSPLMKRWEEVTGHRLLERYGMTEFVMALSNPLHGIRKEGTVGKPLPRIEAKIIMEDGA
ETTTGVGELCIRSPSLFKEYWKRPEVEFIPKFSVSGIWQRWRESYPNDASKSTEAITVFTGVPT
MYTRLLQGYDSMDPDQKSASSYAAKHLRLMMCGSSALPSPLMKRWEEVTGHRLLERYGMTEFVM
ALSNPLHGIRKEGTVGKPLPRIEAKIIMEDGAETTTGVGELCIRSPSLFKEYWKRPEVEFIPKF
SVSGIWQRWRESYPNDASKSTEAITVFTGVPTMYTRLLQGYDSMDPDQKSASSYAAKHLRLMMC
GSSALPSPLMKRWEEVTGHRLLERYGMTEFVMALSNPLHGIRKEGTVGKPLPRIEAKIIMEDGA
ETTTGVGELCIRSPSLFKEYWKRPE(-)
MVSEKKVQLVNLFHALRPRSLWRTGLKLQLELASSALEVHLFSRSIGKDQRLSLYQNSV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	198085524-198085143(+) 198085526-198084781(-) 198085030-198085722(-)
Potential amino acid sequence	MVGTPVNTVMASVLLLASLGYDSRHLCHIPLTLNFGINSTSGLFQYSLKRDGLLMQSSPTPVVV SAPSSIMILASMRGRGLPTVPSFRIPCNGLDSAMTNSVIP(+) MYTRLLQGYDSMDPDQKSASSYAAKHLRLMMCGSSALPSPLMKRWEEVTGHRLLERYGMTEFVM ALSNPLHGIRKEGTVGKPLPRIEAKIIMEDGAETTTGVGELCIRSPSLFKEYWKRPEVEFIPKF SVSGIWQRWRESYPNDASKSTEAITVFTGVPTMYTRLLQGYDSMDPDQKSASSYAAKHLRLMMC GSSALPSPLMKRWEEVTGHRLLERYGMTEFVMALSNPLHGIRKEGTVGKPLPRIEAKIIMEDGA ETTTGVGELCIRSPSLFKEYWKRPEVEFIPKFSVSGIWQRWRESYPNDASKSTEAITVFTGVPT MYTRLLQGYDSMDPDQKSASSYAAKHLRLMMCGSSALPSPLMKRWEEVTGHRLLERYGMTEFVM ALSNPLHGIRKEGTVGKPLPRIEAKIIMEDGAETTTGVGELCIRSPSLFKEYWKRPEVEFIPKF SVSGIWQRWRESYPNDASKSTEAITVFTGVPTMYTRLLQGYDSMDPDQKSASSYAAKHLRLMMC GSSALPSPLMKRWEEVTGHRLLERYGMTEFVMALSNPLHGIRKEGTVGKPLPRIEAKIIMEDGA ETTTGVGELCIRSPSLFKEYWKRPE(-) MVSEKKVQLVNLFHALRPRSLWRTGLKLQLELASSALEVHLFSRSIGKDQRLSLYQNSV(-)
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 Zm00001d043376_circ_g.6

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