Plant Circular RNA Database

Detail information of Zm00001d043915_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d043915_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007833
					
						Alias
						zma_circ_0001329
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 213749787-213751861  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d043915						
					
						Parent gene annotation
						
							Homeobox-DDT domain protein RLT1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d043915_circ_g.1 Zm00001d043915_circ_g.3 						
					
						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  
						
							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
						Zm00001d043915_T002:5
Zm00001d043915_T004:3
Zm00001d043915_T003:5
Zm00001d043915_T001:5

General Information
CircRNA Name	Zm00001d043915_circ_g.2
ID in PlantcircBase	zma_circ_007833
Alias	zma_circ_0001329
Organism	Zea mays
Position	chr3: 213749787-213751861 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	find_circ
Parent gene	Zm00001d043915
Parent gene annotation	Homeobox-DDT domain protein RLT1
Parent gene strand	-
Alternative splicing	Zm00001d043915_circ_g.1 Zm00001d043915_circ_g.3
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	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	Zm00001d043915_T002:5 Zm00001d043915_T004:3 Zm00001d043915_T003:5 Zm00001d043915_T001:5

			
						 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  
						
							TTAAAAGTTTCCTACGGATATACCTTTAAGAGTTTTTGATCATGCCAAGAAAATATCTCCGCAT
CATAAGATCGCACAGGCTGCTTTTGTTGCTCTGGAActcgaaaggaatcaagctgctgcaatgt
gtcgctgtcaagatacagcattgagggcaaccctttgttttgagcagctaattccattgattcc
aaacgctc

									
								

					

						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
						
							CTCGAAAGGAATCAAGCTGCTGCAATGTGTCGCTGTCAAGATACAGCATTGAGGGCAACCCTTT
GTTTTGAGCAGCTAATTCCATTGATTCCAAACGCTCATCTTCCACCAGTTCCATATACTCCCGT
GCAATCCTACGTGCAGTAGCCCTTTCATTGGCAGCCTTTTGCCTTGCTGCTTCTTTTTCTTTTC
GGAGTTCCTCCTTTTGCCTTTGTTTCTCTGCCTGCACAGGTGTAGACAGAAGAAATAAGCTATT
TAATATTATTTACTACACTACATTTACAGTTAACATTCTAGAAACCTAGAAACTAACTCGTCTA
GATTGCTTCTGCAAAAACTTCTCCATACGCTCATGTTCGCGCCTTTGCTCTCTTTGGAACCTCT
CTTCTTCTCGCTGCCTCTCACGCAGTAATCTCTCCTCCTCTTTTCTTCTCTCACGATCAAGTCT
CTCCATTTCCTTGCGCCTTTGCTCCTCTCTCTGCACAGACATCACATTGCAAACGAATTTAAAG
AGGAAGGCATCTACAATTATATAGAATCAGTAATACCTTTTTATTCAACATATCTTGTTTCTCA
AGCTCCTTCCTAATTCGTCTTTCGTGAGCTTCAACTTCCTTTGCAATCTTTGCTTCTTCACTAT
GCTGAAGAAAATCCCAGACAAATTTAAAATGTATACGACTATAAAGCTGAAGGGCAACATGAGT
ATATGAACTCAGAAATCATACTTTTCGTTTTCTTTCCACGCGAGAAGTATCTTCATCATGATAA
GCTATTATTTCAGATGATACAGGTGGGTTTTCAAATGCAGCAACCTGAGAAATATCAAACTGTC
CTTCAACAGGAACAGAACTAAGGTTGCTATTAGACTGAGTCATCTCATAATCTGTTGGTGCTGC
TGGAAACACTTGGGGCCTGCTGGACGGAGGCAACAGGCTAGAACCAGATGTGTGACCTTGAAAA
GCATAACTAGGCGCAGCCTCCTCAGATCCATGGAGAAGTTGTGATCCTGATGTGATAGAAGGTA
TCCTAGCATTTGAAACTTCCACTGGAGTGTCATAGTAGTGAGATCGGGTTGCCCTCTCATATGT
ATCACTTGGTTGCTCAGGAAGGAACTGATACTCATGAACAGCCCGTGATCCAACATGAGGTTGA
ACTATGGCTGAATTACCAACTGGTGATTTTCTCTTCCCAGTAAACGAATTTGGAACAAATGGGG
ATTCCATATTAGGTAAAAATGCTGAAGCCTGGGGGAGGGGGACAGGAGATAAAAAAAGGTGATA
CTTAGAAAATAAAGAGGACCATAGAAGCCTTAATATGGTAGCTATGGCACAGGGAGTAGTCTCA
CCCAGAAATCTAATACAGGTTAATGCAAATATCATTAGGGGAACAAAGTAGCTCTTCTTAACTA
AACCATAGGAAACATAACCATCCATGTGTAGCTTGATGTGCAGAACTAATGCAGAGAAAAGGGG
GCCACCAAGTACTACATAATAGTCATGTCATGCCAATATCTGTTGCAACCAAGTTACCAAATTC
TTAGTAGCCTCGCCACATTACCTACAGCACACCTGCACTATGTACTACTCAATGGCCAAGTCTT
AAGTCTTGACCACTTTGGGGTGCTCATAGAACTGGTAAAACATGATTTATGGTTTTAATCTTCA
TAGGCATTCTTATCATTTAAAAGATAGAAATACATGTCCTATTCCGAACTGACTTAGAGGCATG
ATGCACATGCACTCATTTGAGTAGGGCATCGAAGTTTAGCGCTAATAAATCAGCATAGCAACTG
CAGTGCTAATAATTGCATCTTATATCCATAGGAGAAAATTAAATAAAACTCACACCACCATCAT
TTTAGCACTGAAGCAATTTCACTTGAAAAAGCAAGAACATTCAAATCAGAAAACCCAGTTTATG
CAATGGCATGAATCCACAACAGATATATATATATATAAGAGATACAAACTTACATTTAAAAGTT
TCCTACGGATATACCTTTAAGAGTTTTTGATCATGCCAAGAAAATATCTCCGCATCATAAGATC
GCACAGGCTGCTTTTGTTGCTCTGGAA
						
					

			
		

Sequences
Splice junction sequence	TTAAAAGTTTCCTACGGATATACCTTTAAGAGTTTTTGATCATGCCAAGAAAATATCTCCGCAT CATAAGATCGCACAGGCTGCTTTTGTTGCTCTGGAActcgaaaggaatcaagctgctgcaatgt gtcgctgtcaagatacagcattgagggcaaccctttgttttgagcagctaattccattgattcc aaacgctc
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	CTCGAAAGGAATCAAGCTGCTGCAATGTGTCGCTGTCAAGATACAGCATTGAGGGCAACCCTTT GTTTTGAGCAGCTAATTCCATTGATTCCAAACGCTCATCTTCCACCAGTTCCATATACTCCCGT GCAATCCTACGTGCAGTAGCCCTTTCATTGGCAGCCTTTTGCCTTGCTGCTTCTTTTTCTTTTC GGAGTTCCTCCTTTTGCCTTTGTTTCTCTGCCTGCACAGGTGTAGACAGAAGAAATAAGCTATT TAATATTATTTACTACACTACATTTACAGTTAACATTCTAGAAACCTAGAAACTAACTCGTCTA GATTGCTTCTGCAAAAACTTCTCCATACGCTCATGTTCGCGCCTTTGCTCTCTTTGGAACCTCT CTTCTTCTCGCTGCCTCTCACGCAGTAATCTCTCCTCCTCTTTTCTTCTCTCACGATCAAGTCT CTCCATTTCCTTGCGCCTTTGCTCCTCTCTCTGCACAGACATCACATTGCAAACGAATTTAAAG AGGAAGGCATCTACAATTATATAGAATCAGTAATACCTTTTTATTCAACATATCTTGTTTCTCA AGCTCCTTCCTAATTCGTCTTTCGTGAGCTTCAACTTCCTTTGCAATCTTTGCTTCTTCACTAT GCTGAAGAAAATCCCAGACAAATTTAAAATGTATACGACTATAAAGCTGAAGGGCAACATGAGT ATATGAACTCAGAAATCATACTTTTCGTTTTCTTTCCACGCGAGAAGTATCTTCATCATGATAA GCTATTATTTCAGATGATACAGGTGGGTTTTCAAATGCAGCAACCTGAGAAATATCAAACTGTC CTTCAACAGGAACAGAACTAAGGTTGCTATTAGACTGAGTCATCTCATAATCTGTTGGTGCTGC TGGAAACACTTGGGGCCTGCTGGACGGAGGCAACAGGCTAGAACCAGATGTGTGACCTTGAAAA GCATAACTAGGCGCAGCCTCCTCAGATCCATGGAGAAGTTGTGATCCTGATGTGATAGAAGGTA TCCTAGCATTTGAAACTTCCACTGGAGTGTCATAGTAGTGAGATCGGGTTGCCCTCTCATATGT ATCACTTGGTTGCTCAGGAAGGAACTGATACTCATGAACAGCCCGTGATCCAACATGAGGTTGA ACTATGGCTGAATTACCAACTGGTGATTTTCTCTTCCCAGTAAACGAATTTGGAACAAATGGGG ATTCCATATTAGGTAAAAATGCTGAAGCCTGGGGGAGGGGGACAGGAGATAAAAAAAGGTGATA CTTAGAAAATAAAGAGGACCATAGAAGCCTTAATATGGTAGCTATGGCACAGGGAGTAGTCTCA CCCAGAAATCTAATACAGGTTAATGCAAATATCATTAGGGGAACAAAGTAGCTCTTCTTAACTA AACCATAGGAAACATAACCATCCATGTGTAGCTTGATGTGCAGAACTAATGCAGAGAAAAGGGG GCCACCAAGTACTACATAATAGTCATGTCATGCCAATATCTGTTGCAACCAAGTTACCAAATTC TTAGTAGCCTCGCCACATTACCTACAGCACACCTGCACTATGTACTACTCAATGGCCAAGTCTT AAGTCTTGACCACTTTGGGGTGCTCATAGAACTGGTAAAACATGATTTATGGTTTTAATCTTCA TAGGCATTCTTATCATTTAAAAGATAGAAATACATGTCCTATTCCGAACTGACTTAGAGGCATG ATGCACATGCACTCATTTGAGTAGGGCATCGAAGTTTAGCGCTAATAAATCAGCATAGCAACTG CAGTGCTAATAATTGCATCTTATATCCATAGGAGAAAATTAAATAAAACTCACACCACCATCAT TTTAGCACTGAAGCAATTTCACTTGAAAAAGCAAGAACATTCAAATCAGAAAACCCAGTTTATG CAATGGCATGAATCCACAACAGATATATATATATATAAGAGATACAAACTTACATTTAAAAGTT TCCTACGGATATACCTTTAAGAGTTTTTGATCATGCCAAGAAAATATCTCCGCATCATAAGATC GCACAGGCTGCTTTTGTTGCTCTGGAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.147558298

Conservation Information
Conserved circRNAs	NA
PMCS	0.147558298

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							213751022-213749930(+)
213751804-213749835(+)
213751011-213749789(-)
						
					

						Potential amino acid sequence
						
							MLKPLRVFDHAKKISPHHKIAQAAFVALELERNQAAAMCRCQDTALRATLCFEQLIPLIPNAHL
PPVPYTPVQSYVQ*(+)
MPRKYLRIIRSHRLLLLLWNSKGIKLLQCVAVKIQH*(+)
MESPFVPNSFTGKRKSPVGNSAIVQPHVGSRAVHEYQFLPEQPSDTYERATRSHYYDTPVEVSN
ARIPSITSGSQLLHGSEEAAPSYAFQGHTSGSSLLPPSSRPQVFPAAPTDYEMTQSNSNLSSVP
VEGQFDISQVAAFENPPVSSEIIAYHDEDTSRVERKRKHSEEAKIAKEVEAHERRIRKELEKQD
MLNKKREEQRRKEMERLDRERRKEEERLLRERQREEERFQREQRREHERMEKFLQKQSRRAEKQ
RQKEELRKEKEAARQKAANERATARRIAREYMELVEDERLESMELAAQNKGLPSMLYLDSDTLQ
QLDSFRVPEQQKQPVRSYDAEIFSWHDQKLLKASAFLPNMESPFVPNSFTGKRKSPVGNSAIVQ
PHVGSRAVHEYQFLPEQPSDTYERATRSHYYDTPVEVSNARIPSITSGSQLLHGSEEAAPSYAF
QGHTSGSSLLPPSSRPQVFPAAPTDYEMTQSNSNLSSVPVEGQFDISQVAAFENPPVSSEIIAY
HDEDTSRVERKRKHSEEAKIAKEVEAHERRIRKELEKQDMLNKKREEQRRKEMERLDRERRKEE
ERLLRERQREEERFQREQRREHERMEKFLQKQSRRAEKQRQKEELRKEKEAARQKAANERATAR
RIAREYMELVEDERLESMELAAQNKGLPSMLYLDSDTLQQLDSFRVPEQQKQPVRSYDAEIFSW
HDQKLLKASAFLPNMESPFVPNSFTGKRKSPVGNSAIVQPHVGSRAVHEYQFLPEQPSDTYERA
TRSHYYDTPVEVSNARIPSITSGSQLLHGSEEAAPSYAFQGHTSGSSLLPPSSRPQVFPAAPTD
YEMTQSNSNLSSVPVEGQFDISQVAAFENPPVSSEIIAYHDEDTSRVERKRKHSEEAKIAKEVE
AHERRIRKELEKQDMLNKKREEQRRKEMERLDRERRKEEERLLRERQREEERFQREQRREHERM
EKFLQKQSRRAEKQRQKEELRKEKEAARQKAANERATARRIAREYMELVEDERLESMELAAQNK
GLPSMLYLDSDTLQQLDSFRVPEQQKQPVRSYDAEIFSWHDQKLLKASAFLPNMESPFVPNSFT
GKRKSPVGNSAIVQPHVGSRAVHEYQFLPEQPSDTYERATRSHYYDTPVEVSNARIPSITSGSQ
LLHGSEEAAPSYAFQGHTSGSSLLPPSSRPQVFPAAPTDYEMTQSNSNLSSVPVEGQFDISQVA
AFENPPVSSEIIAYHDEDTSRVERKRKHSEEAKIAKEVEAHERRIRKELEKQDMLNKKREEQRR
KEMERLDRERRKEEERLLRERQREEERFQREQRREHERMEKFLQKQSRRAEKQRQKEELRKEKE
AARQKAANERATARRIAREYMELVEDERLESMELAAQNKGLPSMLYLDSDTLQQLDSFR(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	213751022-213749930(+) 213751804-213749835(+) 213751011-213749789(-)
Potential amino acid sequence	MLKPLRVFDHAKKISPHHKIAQAAFVALELERNQAAAMCRCQDTALRATLCFEQLIPLIPNAHL PPVPYTPVQSYVQ(+) MPRKYLRIIRSHRLLLLLWNSKGIKLLQCVAVKIQH(+) MESPFVPNSFTGKRKSPVGNSAIVQPHVGSRAVHEYQFLPEQPSDTYERATRSHYYDTPVEVSN ARIPSITSGSQLLHGSEEAAPSYAFQGHTSGSSLLPPSSRPQVFPAAPTDYEMTQSNSNLSSVP VEGQFDISQVAAFENPPVSSEIIAYHDEDTSRVERKRKHSEEAKIAKEVEAHERRIRKELEKQD MLNKKREEQRRKEMERLDRERRKEEERLLRERQREEERFQREQRREHERMEKFLQKQSRRAEKQ RQKEELRKEKEAARQKAANERATARRIAREYMELVEDERLESMELAAQNKGLPSMLYLDSDTLQ QLDSFRVPEQQKQPVRSYDAEIFSWHDQKLLKASAFLPNMESPFVPNSFTGKRKSPVGNSAIVQ PHVGSRAVHEYQFLPEQPSDTYERATRSHYYDTPVEVSNARIPSITSGSQLLHGSEEAAPSYAF QGHTSGSSLLPPSSRPQVFPAAPTDYEMTQSNSNLSSVPVEGQFDISQVAAFENPPVSSEIIAY HDEDTSRVERKRKHSEEAKIAKEVEAHERRIRKELEKQDMLNKKREEQRRKEMERLDRERRKEE ERLLRERQREEERFQREQRREHERMEKFLQKQSRRAEKQRQKEELRKEKEAARQKAANERATAR RIAREYMELVEDERLESMELAAQNKGLPSMLYLDSDTLQQLDSFRVPEQQKQPVRSYDAEIFSW HDQKLLKASAFLPNMESPFVPNSFTGKRKSPVGNSAIVQPHVGSRAVHEYQFLPEQPSDTYERA TRSHYYDTPVEVSNARIPSITSGSQLLHGSEEAAPSYAFQGHTSGSSLLPPSSRPQVFPAAPTD YEMTQSNSNLSSVPVEGQFDISQVAAFENPPVSSEIIAYHDEDTSRVERKRKHSEEAKIAKEVE AHERRIRKELEKQDMLNKKREEQRRKEMERLDRERRKEEERLLRERQREEERFQREQRREHERM EKFLQKQSRRAEKQRQKEELRKEKEAARQKAANERATARRIAREYMELVEDERLESMELAAQNK GLPSMLYLDSDTLQQLDSFRVPEQQKQPVRSYDAEIFSWHDQKLLKASAFLPNMESPFVPNSFT GKRKSPVGNSAIVQPHVGSRAVHEYQFLPEQPSDTYERATRSHYYDTPVEVSNARIPSITSGSQ LLHGSEEAAPSYAFQGHTSGSSLLPPSSRPQVFPAAPTDYEMTQSNSNLSSVPVEGQFDISQVA AFENPPVSSEIIAYHDEDTSRVERKRKHSEEAKIAKEVEAHERRIRKELEKQDMLNKKREEQRR KEMERLDRERRKEEERLLRERQREEERFQREQRREHERMEKFLQKQSRRAEKQRQKEELRKEKE AARQKAANERATARRIAREYMELVEDERLESMELAAQNKGLPSMLYLDSDTLQQLDSFR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d043915_circ_g.2

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