Plant Circular RNA Database

Detail information of Zm00001d041108_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d041108_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007608
					
						Alias
						zma_circ_0001521
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 97777264-97779717  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d041108						
					
						Parent gene annotation
						
							Probable Ufm1-specific protease
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d041108_circ_g.1 Zm00001d041108_circ_g.2 Zm00001d041108_circ_g.4 Zm00001d041108_circ_g.5 						
					
						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
						Zm00001d041108_T005:5
Zm00001d041108_T004:5
Zm00001d041108_T020:5
Zm00001d041108_T002:5
Zm00001d041108_T009:5
Zm00001d041108_T019:5
Zm00001d041108_T003:5
Zm00001d041108_T013:3
Zm00001d041108_T017:5
Zm00001d041108_T012:4
Zm00001d041108_T010:5
Zm00001d041108_T011:5
Zm00001d041108_T014:5
Zm00001d041108_T007:3
Zm00001d041108_T018:5
Zm00001d041108_T001:3
Zm00001d041108_T008:5
Zm00001d041108_T015:5
Zm00001d041108_T016:5
Zm00001d041108_T021:5

General Information
CircRNA Name	Zm00001d041108_circ_g.3
ID in PlantcircBase	zma_circ_007608
Alias	zma_circ_0001521
Organism	Zea mays
Position	chr3: 97777264-97779717 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d041108
Parent gene annotation	Probable Ufm1-specific protease
Parent gene strand	+
Alternative splicing	Zm00001d041108_circ_g.1 Zm00001d041108_circ_g.2 Zm00001d041108_circ_g.4 Zm00001d041108_circ_g.5
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	Zm00001d041108_T005:5 Zm00001d041108_T004:5 Zm00001d041108_T020:5 Zm00001d041108_T002:5 Zm00001d041108_T009:5 Zm00001d041108_T019:5 Zm00001d041108_T003:5 Zm00001d041108_T013:3 Zm00001d041108_T017:5 Zm00001d041108_T012:4 Zm00001d041108_T010:5 Zm00001d041108_T011:5 Zm00001d041108_T014:5 Zm00001d041108_T007:3 Zm00001d041108_T018:5 Zm00001d041108_T001:3 Zm00001d041108_T008:5 Zm00001d041108_T015:5 Zm00001d041108_T016:5 Zm00001d041108_T021:5

			
						 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  
						
							GTAAAGTTTTATGTTTATTGCAGTATCCGGAGGTGTTATGTCTTTGATTGATGGTTCATATGAG
TATTATCATTATCTTCACGATGGTATTGATGACAATcctcagcacctgccagcctcatagtaat
caccttgaagcttgacatactatgctactcatcaatagactttccagtggcggctgctgtatct
gaacttgt

									
								

					

						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: 512
Transcript exons: 97777264-97777436,97778909-97778999,97779116-97779238,97
779495-97779542,97779641-97779717
CCTCAGCACCTGCCAGCCTCATAGTAATCACCTTGAAGCTTGACATACTATGCTACTCATCAAT
AGACTTTCCAGTGGCGGCTGCTGTATCTGAACTTGTTATTCCAGGATTAGCAGATCAGATGATT
GTAATGAAGAGAATTATTGCTTCAGAGATAACTCAACAAGCACAGCTTCAACCATTCCATTTTA
TTCCTTCTGGTTGGCATGTTCCAGTAACAGCTATATACAATACAAGATATGGTGAGACTGAGGA
GAGGCAAAGTGAGCTGCGAAAAGAACTGCATTTAAGGCTAGGACTTCCCTTAGATCGGCCTTTG
TTGCGAATTTCTAATGCATTGACTTTCGGTGGCATGGGAAGGAGGAAGAAAAGCATGCCAAGAA
GTGGTTCTTCGCTGCTTCGAGACATCCACAGAGAACTTCCATCTAGTGGTGTATCCGGAGGTGT
TATGTCTTTGATTGATGGTTCATATGAGTATTATCATTATCTTCACGATGGTATTGATGACAAT
						
					

						Genomic sequence
						
							CCTCAGCACCTGCCAGCCTCATAGTAATCACCTTGAAGCTTGACATACTATGCTACTCATCAAT
AGACTTTCCAGTGGCGGCTGCTGTATCTGAACTTGTTATTCCAGGATTAGCAGATCAGATGATT
GTAATGAAGAGAATTATTGCTTCAGAGATAACTCAACAAGCACAGGTGTGTGATTTGTTTAATG
TCACAATTGATTAATTGCCTTTACTTAAGCAACACATTTTTGTTTTTGTTGAACCACATATGGC
TTTGGCTGTTACAAATTACTTGAAACCTTGGTCGGACAAAAAACACAATATTTTTGCTGCATAT
TTTGGAGTTTAAAAGCTTTGTCAGTGCATATCATGCAGATAAATTTTTCTTGAACGACATTGAA
GATTTGTGTCATTTAATTAAGAAAGAAAAAAACAAGGAAACACTAGTAGGCATCCAAAGAAGTA
TAGTTACAAACGTGCTATGTACATTAGAACCTAGGGATGGCAACAGACACATTACCCACGGGTG
GGGCCTACACATATACGGATCAAGCACTATGACTATTCAGAGGACAAGTTAAATAGGGCAAGCA
AGGTCTTCTTTCAATTACGCCTAAGGCCTATCTTTGTTTTAGTCCTATAGGAGGACCCTTTAGA
GCTCAATTGGTTCAATTACGCCTAAGGCCTATCCAGATCACGACACGGCGCGCCACCAAGGGGG
TGGCATTCCGGCCCTTGCCCATTTAATTTGGATGCGGTGTCAAGTGAGTAAGGATCGGGTCGTC
GCTTCCTTAGTGGCGCGCTACATCTGTGCCCGGGTGTAGTGACAAATGTGCAAGGGTCTTCGCA
TCTGTCTCGACGAGTAAGGAAGCTAGTTGAGCCGACTAGGATCCATGTAGGTAGTTGGAACATA
GGGTCCCTTACAGGTAAGCTACGAGAGTTAGTCGATGCAGTGAGAATGAGGCGTGTTAGTATCC
TTTGTGTCCAAGAGACAAAATGGAAAGGAAAAAAAGCGAAGGAGGTGGAGAACACTGGTTTCAA
ACTATGGTACTCAGGAACAGTGGCAAACAAAAATGGAGTAGGTATCCTGATTGATAAGACCCTC
AAGGATGGAGTGGTGGACGTCAAAAGGAACCAGTCTTGGAAAATTGAAACGACCGAGCCGGGTG
TGCATTAAGTCAACCAACGAGATTATTCTGAACTAGAGCTCTCTAGCAAACACGCAACAGACCA
AGAGGTGTTGCACCGTTTCATCTTCTTGATCACAAAGAGGACAGCAATCTGGATGATCCAAGCC
CCTCCTCAGTCCTCACCAAGCGATCGACGCCCAACATCTTTTCTGGGCCACTATCCAAAGGAAA
AAAATTGCACCTTGGTGGAGCCTAGGCCTTGTGAATTTGATTATCAGCGTATTGGTGTATTATG
GATTAGACTATGACTACTAAATAAAAAAAGAAGTAAAACATACTATTCTGGATCTGTTTGGTAT
TTTCTTGGTTGCATGTTTGATGTTTGTCTTTCAACGCATGCAAATCAAATCATGTTCTCTTAAT
CATTAACACTGATTCTTTTATAGTATGTCATTCATTATAAATATGATAATTAAAAGCTTTAGTT
TCTTATTAGAATGTTTTATCAAATGTTTCTTGACATTGTTTGCAGCTTCAACCATTCCATTTTA
TTCCTTCTGGTTGGCATGTTCCAGTAACAGCTATATACAATACAAGATATGGTGAGACTGAGGA
GAGGCAAAGTATGAAAAATTCTATTTCTGAAAAGTTCATAAATTCTTTCTTGAAGCACGAGAGT
GAATATAGGACCTTAATACTGCCTCTGTCTCTATCTAAAAATATCCTTTATTATTTACAGGTGA
GCTGCGAAAAGAACTGCATTTAAGGCTAGGACTTCCCTTAGATCGGCCTTTGTTGCGAATTTCT
AATGCATTGACTTTCGGTGGCATGGGAAGGAGGAAGAAAAGCATGCCAAGAAGTGGTATTCACC
ATGCATATGTTGCGACATATGCTTCATTACTCTGTTTTCCCCCTAAATTACATGTGGGATCTTG
TGGTAACTTTGTGCAAAAAATGTTTCAAAGTATAATATATATAAGAACTGCAAAATATCATATT
ATACTATGTGAGAAGTTAATAACTTCATCTAACATGAAGATAAGAACTTATCTTTGTATATGTA
ATTCCTCAGGAAGTAGAATTTGTTTTCATCCATTGTGGTATGTTATCACATTCAGGTTCTTCGC
TGCTTCGAGACATCCACAGAGAACTTCCATCTAGTGGTGGTTAGTTGTATCTCTATTTCTTGCT
TTAAGCAAAATAAGAAATTTGGTGAATGTATTCTAGAAGGAGATAGTGACGTAAAGTTTTATGT
TTATTGCAGTATCCGGAGGTGTTATGTCTTTGATTGATGGTTCATATGAGTATTATCATTATCT
TCACGATGGTATTGATGACAAT
						
					

			
		

Sequences
Splice junction sequence	GTAAAGTTTTATGTTTATTGCAGTATCCGGAGGTGTTATGTCTTTGATTGATGGTTCATATGAG TATTATCATTATCTTCACGATGGTATTGATGACAATcctcagcacctgccagcctcatagtaat caccttgaagcttgacatactatgctactcatcaatagactttccagtggcggctgctgtatct gaacttgt
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: 512 Transcript exons: 97777264-97777436,97778909-97778999,97779116-97779238,97 779495-97779542,97779641-97779717 CCTCAGCACCTGCCAGCCTCATAGTAATCACCTTGAAGCTTGACATACTATGCTACTCATCAAT AGACTTTCCAGTGGCGGCTGCTGTATCTGAACTTGTTATTCCAGGATTAGCAGATCAGATGATT GTAATGAAGAGAATTATTGCTTCAGAGATAACTCAACAAGCACAGCTTCAACCATTCCATTTTA TTCCTTCTGGTTGGCATGTTCCAGTAACAGCTATATACAATACAAGATATGGTGAGACTGAGGA GAGGCAAAGTGAGCTGCGAAAAGAACTGCATTTAAGGCTAGGACTTCCCTTAGATCGGCCTTTG TTGCGAATTTCTAATGCATTGACTTTCGGTGGCATGGGAAGGAGGAAGAAAAGCATGCCAAGAA GTGGTTCTTCGCTGCTTCGAGACATCCACAGAGAACTTCCATCTAGTGGTGTATCCGGAGGTGT TATGTCTTTGATTGATGGTTCATATGAGTATTATCATTATCTTCACGATGGTATTGATGACAAT
Genomic sequence	CCTCAGCACCTGCCAGCCTCATAGTAATCACCTTGAAGCTTGACATACTATGCTACTCATCAAT AGACTTTCCAGTGGCGGCTGCTGTATCTGAACTTGTTATTCCAGGATTAGCAGATCAGATGATT GTAATGAAGAGAATTATTGCTTCAGAGATAACTCAACAAGCACAGGTGTGTGATTTGTTTAATG TCACAATTGATTAATTGCCTTTACTTAAGCAACACATTTTTGTTTTTGTTGAACCACATATGGC TTTGGCTGTTACAAATTACTTGAAACCTTGGTCGGACAAAAAACACAATATTTTTGCTGCATAT TTTGGAGTTTAAAAGCTTTGTCAGTGCATATCATGCAGATAAATTTTTCTTGAACGACATTGAA GATTTGTGTCATTTAATTAAGAAAGAAAAAAACAAGGAAACACTAGTAGGCATCCAAAGAAGTA TAGTTACAAACGTGCTATGTACATTAGAACCTAGGGATGGCAACAGACACATTACCCACGGGTG GGGCCTACACATATACGGATCAAGCACTATGACTATTCAGAGGACAAGTTAAATAGGGCAAGCA AGGTCTTCTTTCAATTACGCCTAAGGCCTATCTTTGTTTTAGTCCTATAGGAGGACCCTTTAGA GCTCAATTGGTTCAATTACGCCTAAGGCCTATCCAGATCACGACACGGCGCGCCACCAAGGGGG TGGCATTCCGGCCCTTGCCCATTTAATTTGGATGCGGTGTCAAGTGAGTAAGGATCGGGTCGTC GCTTCCTTAGTGGCGCGCTACATCTGTGCCCGGGTGTAGTGACAAATGTGCAAGGGTCTTCGCA TCTGTCTCGACGAGTAAGGAAGCTAGTTGAGCCGACTAGGATCCATGTAGGTAGTTGGAACATA GGGTCCCTTACAGGTAAGCTACGAGAGTTAGTCGATGCAGTGAGAATGAGGCGTGTTAGTATCC TTTGTGTCCAAGAGACAAAATGGAAAGGAAAAAAAGCGAAGGAGGTGGAGAACACTGGTTTCAA ACTATGGTACTCAGGAACAGTGGCAAACAAAAATGGAGTAGGTATCCTGATTGATAAGACCCTC AAGGATGGAGTGGTGGACGTCAAAAGGAACCAGTCTTGGAAAATTGAAACGACCGAGCCGGGTG TGCATTAAGTCAACCAACGAGATTATTCTGAACTAGAGCTCTCTAGCAAACACGCAACAGACCA AGAGGTGTTGCACCGTTTCATCTTCTTGATCACAAAGAGGACAGCAATCTGGATGATCCAAGCC CCTCCTCAGTCCTCACCAAGCGATCGACGCCCAACATCTTTTCTGGGCCACTATCCAAAGGAAA AAAATTGCACCTTGGTGGAGCCTAGGCCTTGTGAATTTGATTATCAGCGTATTGGTGTATTATG GATTAGACTATGACTACTAAATAAAAAAAGAAGTAAAACATACTATTCTGGATCTGTTTGGTAT TTTCTTGGTTGCATGTTTGATGTTTGTCTTTCAACGCATGCAAATCAAATCATGTTCTCTTAAT CATTAACACTGATTCTTTTATAGTATGTCATTCATTATAAATATGATAATTAAAAGCTTTAGTT TCTTATTAGAATGTTTTATCAAATGTTTCTTGACATTGTTTGCAGCTTCAACCATTCCATTTTA TTCCTTCTGGTTGGCATGTTCCAGTAACAGCTATATACAATACAAGATATGGTGAGACTGAGGA GAGGCAAAGTATGAAAAATTCTATTTCTGAAAAGTTCATAAATTCTTTCTTGAAGCACGAGAGT GAATATAGGACCTTAATACTGCCTCTGTCTCTATCTAAAAATATCCTTTATTATTTACAGGTGA GCTGCGAAAAGAACTGCATTTAAGGCTAGGACTTCCCTTAGATCGGCCTTTGTTGCGAATTTCT AATGCATTGACTTTCGGTGGCATGGGAAGGAGGAAGAAAAGCATGCCAAGAAGTGGTATTCACC ATGCATATGTTGCGACATATGCTTCATTACTCTGTTTTCCCCCTAAATTACATGTGGGATCTTG TGGTAACTTTGTGCAAAAAATGTTTCAAAGTATAATATATATAAGAACTGCAAAATATCATATT ATACTATGTGAGAAGTTAATAACTTCATCTAACATGAAGATAAGAACTTATCTTTGTATATGTA ATTCCTCAGGAAGTAGAATTTGTTTTCATCCATTGTGGTATGTTATCACATTCAGGTTCTTCGC TGCTTCGAGACATCCACAGAGAACTTCCATCTAGTGGTGGTTAGTTGTATCTCTATTTCTTGCT TTAAGCAAAATAAGAAATTTGGTGAATGTATTCTAGAAGGAGATAGTGACGTAAAGTTTTATGT TTATTGCAGTATCCGGAGGTGTTATGTCTTTGATTGATGGTTCATATGAGTATTATCATTATCT TCACGATGGTATTGATGACAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.078524085

Conservation Information
Conserved circRNAs	NA
PMCS	0.078524085

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							97779669-97777303(+)
97777387-97777284(+)
97777311-97779655(-)
						
						Potential amino acid sequence
						
							MVHMSIIIIFTMVLMTILSTCQPHSNHLEA*(+)
MIVMKRIIASEITQQAQLQPFHFIPSGWHVPVTAIYNTRYGETEERQSELRKELHLRLGLPLDR
PLLRISNALTFGGMGRRKKSMPRSGSSLLRDIHRELPSSGVSGGVMSLIDGSYEYYHYLHDGID
DNPQHLPAS*(+)
MSSFKVITMRLAGAEDCHQYHREDNDNTHMNHQSKT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	97779669-97777303(+) 97777387-97777284(+) 97777311-97779655(-)
Potential amino acid sequence	MVHMSIIIIFTMVLMTILSTCQPHSNHLEA(+) MIVMKRIIASEITQQAQLQPFHFIPSGWHVPVTAIYNTRYGETEERQSELRKELHLRLGLPLDR PLLRISNALTFGGMGRRKKSMPRSGSSLLRDIHRELPSSGVSGGVMSLIDGSYEYYHYLHDGID DNPQHLPAS(+) MSSFKVITMRLAGAEDCHQYHREDNDNTHMNHQSKT*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d041108_circ_g.3

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