Plant Circular RNA Database

Detail information of Zm00001d025044_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d025044_circ_g.4
					
						ID in PlantcircBase
						zma_circ_010267
					
						Alias
						zma_circ_0000002
					
						Organism
						
							Zea mays						
					
						Position
						
							chr10: 101422294-101424367  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d025044						
					
						Parent gene annotation
						
							Vacuolar protein sorting-associated protein 54 chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d025044_circ_g.2 Zm00001d025044_circ_g.3 Zm00001d025044_circ_g.5 Zm00001d025044_circ_g.6 Zm00001d025044_circ_g.7 Zm00001d025044_circ_g.8 Zm00001d025044_circ_g.9 						
					
						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
						Zm00001d025044_T003:4
Zm00001d025044_T017:4
Zm00001d025044_T037:4
Zm00001d025044_T040:2
Zm00001d025044_T012:4
Zm00001d025044_T038:4
Zm00001d025044_T002:4
Zm00001d025044_T035:4
Zm00001d025044_T004:4
Zm00001d025044_T029:4
Zm00001d025044_T005:4
Zm00001d025044_T015:4
Zm00001d025044_T027:4
Zm00001d025044_T021:4
Zm00001d025044_T008:4
Zm00001d025044_T010:4
Zm00001d025044_T030:4
Zm00001d025044_T039:4
Zm00001d025044_T013:4
Zm00001d025044_T019:4
Zm00001d025044_T034:4
Zm00001d025044_T023:4
Zm00001d025044_T025:4

General Information
CircRNA Name	Zm00001d025044_circ_g.4
ID in PlantcircBase	zma_circ_010267
Alias	zma_circ_0000002
Organism	Zea mays
Position	chr10: 101422294-101424367 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d025044
Parent gene annotation	Vacuolar protein sorting-associated protein 54 chloroplastic
Parent gene strand	+
Alternative splicing	Zm00001d025044_circ_g.2 Zm00001d025044_circ_g.3 Zm00001d025044_circ_g.5 Zm00001d025044_circ_g.6 Zm00001d025044_circ_g.7 Zm00001d025044_circ_g.8 Zm00001d025044_circ_g.9
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	Zm00001d025044_T003:4 Zm00001d025044_T017:4 Zm00001d025044_T037:4 Zm00001d025044_T040:2 Zm00001d025044_T012:4 Zm00001d025044_T038:4 Zm00001d025044_T002:4 Zm00001d025044_T035:4 Zm00001d025044_T004:4 Zm00001d025044_T029:4 Zm00001d025044_T005:4 Zm00001d025044_T015:4 Zm00001d025044_T027:4 Zm00001d025044_T021:4 Zm00001d025044_T008:4 Zm00001d025044_T010:4 Zm00001d025044_T030:4 Zm00001d025044_T039:4 Zm00001d025044_T013:4 Zm00001d025044_T019:4 Zm00001d025044_T034:4 Zm00001d025044_T023:4 Zm00001d025044_T025:4

			
						 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  
						
							ACCATCACTATCTTTGGAGGTGGTCCAACGTGTTGTGGAAATATTGAAGCTTTTCAACACTAGG
ACTTGCCAACTTGTTCTCGGTGCAGGGGCCATGCAGggctgatgtcttgagagaaaacactgaa
gcagttttcgcggcttgtgatgctgcccatggacgatgggctaagctactaggtgttcgtgctg
gattacat

									
								

					

						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: 754
Transcript exons: 101422294-101422465,101422561-101422644,101423601-101423
944,101424214-101424367
GGCTGATGTCTTGAGAGAAAACACTGAAGCAGTTTTCGCGGCTTGTGATGCTGCCCATGGACGA
TGGGCTAAGCTACTAGGTGTTCGTGCTGGATTACATCCCAGGTTAAGGCTTGAAGAATTCTTGA
TCATCTACAGCATAACAGAAGAATTTATAGCTGCTACAGAAAAGATTGGAGGCAGGTTGGGTTA
CAACATTCGTGGAATCCTACAACAACAATCAAAGCAATTTGTTGATTATCAGCATAATGTTCGG
ATGACAAAAATCAAGGCAGTTCTTGACCAAGAGACGTGGGTTGCTGTGGATGTTCCTGAAGAGT
TTCAAGCAATCGTTCTTTCACTTTCATCCACTTACTCTTCTGTTAATGGCATGGAGATGCCTAG
CACTGATGATAACTCAAAGTTCAGTGATCATCAGCCTACAAGTCAAGAACTGACATATTCTGCT
GAAAATAATGCTGATAATGGCAAAGTAACATCCGGGACTGGTGAAAACCAGGTTGAATCCACTT
CTCAGAGTGCAAATAATGTTGCCGGGAATCTGAAATCCACCTTGCAAACAATTGTACATGGAGG
TGTTGGCTATCATATGGTAAACTGCGGTTTGATACTGTTGAAGATGTTATCTGAATATGTTGAC
ATCAGTAAATGTTTACCATCACTATCTTTGGAGGTGGTCCAACGTGTTGTGGAAATATTGAAGC
TTTTCAACACTAGGACTTGCCAACTTGTTCTCGGTGCAGGGGCCATGCAG
						
					

						Genomic sequence
						
							GGCTGATGTCTTGAGAGAAAACACTGAAGCAGTTTTCGCGGCTTGTGATGCTGCCCATGGACGA
TGGGCTAAGCTACTAGGTGTTCGTGCTGGATTACATCCCAGGTTAAGGCTTGAAGAATTCTTGA
TCATCTACAGCATAACAGAAGAATTTATAGCTGCTACAGAAAAGGTTACATCTTCTTGTTTGGA
ATAAATACACAAAATCAGCTGCATTAATTGCATATAAGCAAGTTGTAATGTTATCTTAGCCTCT
TATTCTTGTAGATTGGAGGCAGGTTGGGTTACAACATTCGTGGAATCCTACAACAACAATCAAA
GCAATTTGTTGATTATCAGCATAATGTTCGGGTCAGTAAAACAATGTTACAGTTCTATTGTCGA
AGTTAAACCCTATTATTCAAATTTCACCTATTTGATTAGAAGCTTCCAAAATAATCATTGATCA
TCATTATTGGAAGGAACAAAAAGCACCCAACTTTCCCTTCTTAATTAGGGATGACTGGTTGTCC
ACCAAGCTGAATACAGCACATATGTTCAATTCAAGTATAACTTTGTACCCTTTTTTTACATTAA
CAGTAGTTGATCTTTACTGAAACTCCCCCTATTACAAATTATGAGTCATTCTAATTTTATAGGT
ATATAGTTTTGTTATTCTTCTAGATATATACTATGTCTAGATACTACTACCTCCGTCTTGAATA
TTTGTCGCCCTCTAATTTATTTTTGAACTAAAACGCGACAAATAAAAAAGAACTGAGGGAGTAG
TTTTTATTATGTATCTAGAAAAGCCAGAATGACTTATGACTTATAATTTGGAACAAATGGAGTG
TTTCTGAGATCAAAATGGTGGTGGAATGAAAGATTTTAATTAATGAAGTTCATCTTCTCTAGAT
ACTCAAATTATGTGAGTTTTGGATTATCCAAGGTTGCGAAAGGGCCTCCAGCCGAGTTGGTTAG
GTGGTCTGAGTAACACTCCTTAGGTCCTGGGTTCGACTCCCCGTAGGAGCGAATTTCAGGTTGC
GGTTAAAAAATCCCCTCGTCTGTCCCACGCCAAAGCACAGGTCTAAGTCTCAGCCCCGGTCGCG
GTCGTTCTCACATGGGCTTCGATGCCGCAGTGTATGGGTGAGACAGGGGTTCGGGGGTCCTTCG
ATCTGTGTGAGAAGGTCTTCTTCTTAATACAATACTCGGGGGCTGTCTTACCCCCCGCAGTTTT
TTTGGATTATCCAAGGTGCTTGATAGTTAGGGCTAGTTAAACTAAATTGTGTTTCCCCTATTGT
TTCAAACTGAAACCTTTTTTTTTCAAGATGACAAAAATCAAGGCAGTTCTTGACCAAGAGACGT
GGGTTGCTGTGGATGTTCCTGAAGAGTTTCAAGCAATCGTTCTTTCACTTTCATCCACTTACTC
TTCTGTTAATGGCATGGAGATGCCTAGCACTGATGATAACTCAAAGTTCAGTGATCATCAGCCT
ACAAGTCAAGAACTGACATATTCTGCTGAAAATAATGCTGATAATGGCAAAGTAACATCCGGGA
CTGGTGAAAACCAGGTTGAATCCACTTCTCAGAGTGCAAATAATGTTGCCGGGAATCTGAAATC
CACCTTGCAAACAATTGTACATGGAGGTGTTGGCTATCATATGGTAAACTGGTTAGTCATCTAT
ATTTACCTTCCAATAATTTGAAACTTGGTCTCTACTTATGAATTTTGCACTGCTGAAATGAAAT
GTGTTCAGTAGCCATCAATCTGTAAATTTAGTTTAAATAAAATAAATGTAGTATTTGATGCAGC
CATGTCTTTTATTGATTTGTTCTTGTTATTTTTAGAGTTCATTATTCTAAGTTATTACATTAAT
ATAAAGCATATTTATTCTTTTGGAATCCATGCCTCTCTCTTACAATGCTTTATTGGTTCTGCAG
CGGTTTGATACTGTTGAAGATGTTATCTGAATATGTTGACATCAGTAAATGTTTACCATCACTA
TCTTTGGAGGTGGTCCAACGTGTTGTGGAAATATTGAAGCTTTTCAACACTAGGACTTGCCAAC
TTGTTCTCGGTGCAGGGGCCATGCAG
						
					

			
		

Sequences
Splice junction sequence	ACCATCACTATCTTTGGAGGTGGTCCAACGTGTTGTGGAAATATTGAAGCTTTTCAACACTAGG ACTTGCCAACTTGTTCTCGGTGCAGGGGCCATGCAGggctgatgtcttgagagaaaacactgaa gcagttttcgcggcttgtgatgctgcccatggacgatgggctaagctactaggtgttcgtgctg gattacat
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: 754 Transcript exons: 101422294-101422465,101422561-101422644,101423601-101423 944,101424214-101424367 GGCTGATGTCTTGAGAGAAAACACTGAAGCAGTTTTCGCGGCTTGTGATGCTGCCCATGGACGA TGGGCTAAGCTACTAGGTGTTCGTGCTGGATTACATCCCAGGTTAAGGCTTGAAGAATTCTTGA TCATCTACAGCATAACAGAAGAATTTATAGCTGCTACAGAAAAGATTGGAGGCAGGTTGGGTTA CAACATTCGTGGAATCCTACAACAACAATCAAAGCAATTTGTTGATTATCAGCATAATGTTCGG ATGACAAAAATCAAGGCAGTTCTTGACCAAGAGACGTGGGTTGCTGTGGATGTTCCTGAAGAGT TTCAAGCAATCGTTCTTTCACTTTCATCCACTTACTCTTCTGTTAATGGCATGGAGATGCCTAG CACTGATGATAACTCAAAGTTCAGTGATCATCAGCCTACAAGTCAAGAACTGACATATTCTGCT GAAAATAATGCTGATAATGGCAAAGTAACATCCGGGACTGGTGAAAACCAGGTTGAATCCACTT CTCAGAGTGCAAATAATGTTGCCGGGAATCTGAAATCCACCTTGCAAACAATTGTACATGGAGG TGTTGGCTATCATATGGTAAACTGCGGTTTGATACTGTTGAAGATGTTATCTGAATATGTTGAC ATCAGTAAATGTTTACCATCACTATCTTTGGAGGTGGTCCAACGTGTTGTGGAAATATTGAAGC TTTTCAACACTAGGACTTGCCAACTTGTTCTCGGTGCAGGGGCCATGCAG
Genomic sequence	GGCTGATGTCTTGAGAGAAAACACTGAAGCAGTTTTCGCGGCTTGTGATGCTGCCCATGGACGA TGGGCTAAGCTACTAGGTGTTCGTGCTGGATTACATCCCAGGTTAAGGCTTGAAGAATTCTTGA TCATCTACAGCATAACAGAAGAATTTATAGCTGCTACAGAAAAGGTTACATCTTCTTGTTTGGA ATAAATACACAAAATCAGCTGCATTAATTGCATATAAGCAAGTTGTAATGTTATCTTAGCCTCT TATTCTTGTAGATTGGAGGCAGGTTGGGTTACAACATTCGTGGAATCCTACAACAACAATCAAA GCAATTTGTTGATTATCAGCATAATGTTCGGGTCAGTAAAACAATGTTACAGTTCTATTGTCGA AGTTAAACCCTATTATTCAAATTTCACCTATTTGATTAGAAGCTTCCAAAATAATCATTGATCA TCATTATTGGAAGGAACAAAAAGCACCCAACTTTCCCTTCTTAATTAGGGATGACTGGTTGTCC ACCAAGCTGAATACAGCACATATGTTCAATTCAAGTATAACTTTGTACCCTTTTTTTACATTAA CAGTAGTTGATCTTTACTGAAACTCCCCCTATTACAAATTATGAGTCATTCTAATTTTATAGGT ATATAGTTTTGTTATTCTTCTAGATATATACTATGTCTAGATACTACTACCTCCGTCTTGAATA TTTGTCGCCCTCTAATTTATTTTTGAACTAAAACGCGACAAATAAAAAAGAACTGAGGGAGTAG TTTTTATTATGTATCTAGAAAAGCCAGAATGACTTATGACTTATAATTTGGAACAAATGGAGTG TTTCTGAGATCAAAATGGTGGTGGAATGAAAGATTTTAATTAATGAAGTTCATCTTCTCTAGAT ACTCAAATTATGTGAGTTTTGGATTATCCAAGGTTGCGAAAGGGCCTCCAGCCGAGTTGGTTAG GTGGTCTGAGTAACACTCCTTAGGTCCTGGGTTCGACTCCCCGTAGGAGCGAATTTCAGGTTGC GGTTAAAAAATCCCCTCGTCTGTCCCACGCCAAAGCACAGGTCTAAGTCTCAGCCCCGGTCGCG GTCGTTCTCACATGGGCTTCGATGCCGCAGTGTATGGGTGAGACAGGGGTTCGGGGGTCCTTCG ATCTGTGTGAGAAGGTCTTCTTCTTAATACAATACTCGGGGGCTGTCTTACCCCCCGCAGTTTT TTTGGATTATCCAAGGTGCTTGATAGTTAGGGCTAGTTAAACTAAATTGTGTTTCCCCTATTGT TTCAAACTGAAACCTTTTTTTTTCAAGATGACAAAAATCAAGGCAGTTCTTGACCAAGAGACGT GGGTTGCTGTGGATGTTCCTGAAGAGTTTCAAGCAATCGTTCTTTCACTTTCATCCACTTACTC TTCTGTTAATGGCATGGAGATGCCTAGCACTGATGATAACTCAAAGTTCAGTGATCATCAGCCT ACAAGTCAAGAACTGACATATTCTGCTGAAAATAATGCTGATAATGGCAAAGTAACATCCGGGA CTGGTGAAAACCAGGTTGAATCCACTTCTCAGAGTGCAAATAATGTTGCCGGGAATCTGAAATC CACCTTGCAAACAATTGTACATGGAGGTGTTGGCTATCATATGGTAAACTGGTTAGTCATCTAT ATTTACCTTCCAATAATTTGAAACTTGGTCTCTACTTATGAATTTTGCACTGCTGAAATGAAAT GTGTTCAGTAGCCATCAATCTGTAAATTTAGTTTAAATAAAATAAATGTAGTATTTGATGCAGC CATGTCTTTTATTGATTTGTTCTTGTTATTTTTAGAGTTCATTATTCTAAGTTATTACATTAAT ATAAAGCATATTTATTCTTTTGGAATCCATGCCTCTCTCTTACAATGCTTTATTGGTTCTGCAG CGGTTTGATACTGTTGAAGATGTTATCTGAATATGTTGACATCAGTAAATGTTTACCATCACTA TCTTTGGAGGTGGTCCAACGTGTTGTGGAAATATTGAAGCTTTTCAACACTAGGACTTGCCAAC TTGTTCTCGGTGCAGGGGCCATGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.165288896

Conservation Information
Conserved circRNAs	NA
PMCS	0.165288896

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							101423602-101422296(+)
101422353-101424329(-)
101422427-101424277(-)
						
						Potential amino acid sequence
						
							MTKIKAVLDQETWVAVDVPEEFQAIVLSLSSTYSSVNGMEMPSTDDNSKFSDHQPTSQELTYSA
ENNADNGKVTSGTGENQVESTSQSANNVAGNLKSTLQTIVHGGVGYHMVNCGLILLKMLSEYVD
ISKCLPSLSLEVVQRVVEILKLFNTRTCQLVLGAGAMQG*(+)
MGSITSRENCFSVFSQDISPAWPLHREQVGKS*(-)
MIKNSSSLNLGCNPARTPSSLAHRPWAASQAAKTASVFSLKTSALHGPCTENKLASPSVEKLQY
FHNTLDHLQR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	101423602-101422296(+) 101422353-101424329(-) 101422427-101424277(-)
Potential amino acid sequence	MTKIKAVLDQETWVAVDVPEEFQAIVLSLSSTYSSVNGMEMPSTDDNSKFSDHQPTSQELTYSA ENNADNGKVTSGTGENQVESTSQSANNVAGNLKSTLQTIVHGGVGYHMVNCGLILLKMLSEYVD ISKCLPSLSLEVVQRVVEILKLFNTRTCQLVLGAGAMQG(+) MGSITSRENCFSVFSQDISPAWPLHREQVGKS(-) MIKNSSSLNLGCNPARTPSSLAHRPWAASQAAKTASVFSLKTSALHGPCTENKLASPSVEKLQY FHNTLDHLQR*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d025044_circ_g.4

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