Plant Circular RNA Database

Detail information of Zm00001d037346_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d037346_circ_g.4
					
						ID in PlantcircBase
						zma_circ_009024
					
						Alias
						Zm06circ00049
					
						Organism
						
							Zea mays						
					
						Position
						
							chr6: 122242564-122245094  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d037346						
					
						Parent gene annotation
						
							Chromatin structure-remodeling complex protein SYD
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d037346_circ_g.5 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d037346_T010:5
Zm00001d037346_T002:3
Zm00001d037346_T007:5
Zm00001d037346_T006:5
Zm00001d037346_T017:5
Zm00001d037346_T001:3
Zm00001d037346_T011:5
Zm00001d037346_T005:5
Zm00001d037346_T009:5
Zm00001d037346_T012:5
Zm00001d037346_T008:5
Zm00001d037346_T016:5
Zm00001d037346_T003:5
Zm00001d037346_T013:5
Zm00001d037346_T004:5
Zm00001d037346_T014:5

General Information
CircRNA Name	Zm00001d037346_circ_g.4
ID in PlantcircBase	zma_circ_009024
Alias	Zm06circ00049
Organism	Zea mays
Position	chr6: 122242564-122245094 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d037346
Parent gene annotation	Chromatin structure-remodeling complex protein SYD
Parent gene strand	+
Alternative splicing	Zm00001d037346_circ_g.5
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d037346_T010:5 Zm00001d037346_T002:3 Zm00001d037346_T007:5 Zm00001d037346_T006:5 Zm00001d037346_T017:5 Zm00001d037346_T001:3 Zm00001d037346_T011:5 Zm00001d037346_T005:5 Zm00001d037346_T009:5 Zm00001d037346_T012:5 Zm00001d037346_T008:5 Zm00001d037346_T016:5 Zm00001d037346_T003:5 Zm00001d037346_T013:5 Zm00001d037346_T004:5 Zm00001d037346_T014:5

			
						 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  
						
							AGATTTCTGATTCTTTCATGTTTGATATTTACTCAAGTGTAATTTCCTCTTCGCAGCATTATCT
GGAAAGTAATGAAAAGTACTATCAACTGGCACACAGgagagcgttaattcatccgaagatcttt
ctgcaaagaccaagagcgtcattgaattgaaaaagcttcagcttctgccacttcaacgtcgtgt
acgcaggt

									
								

					

						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
						
							GAGAGCGTTAATTCATCCGAAGATCTTTCTGCAAAGACCAAGAGCGTCATTGAATTGAAAAAGC
TTCAGCTTCTGCCACTTCAACGTCGTGTACGCAGGTTGGTTGTCGTTGGAGAACCCCCCCAATC
ATTGTTATTCTTTTGTTAATCTGACTATATGTCTGTTTAACATTTTAACTATGTGATCCCTGTT
TCTCTTTTTCTATTCTTTCATGCAGTGAATTTTTGCTGGATTTTTTCAAGCCTAATACATCCGA
CTTAGAGCGCATAAAATCACTGAAGAAACATAGGCATGGGCGGCGGGTGAAACAGCTTGAAAAA
ATTGAACAGAAAATGAAGGAAGAAAGGCAAAAGAGAATTCGTGAGAGACAGAAGGAATTCTTTG
CTGATATTGAAGCTTACAGGTTGGATAACAATCTCTGTTGCTTTCATCATTTCTTTGAACCATT
TGAAGTCATCTCTAAGCGATGTCTTTTGCAGAGAGAAACTCGAGGATAACTTCAAGGTTAAGAG
AGAGCGCTTGAAGGGGTTCAATCGATACATAAAAGAATTTCACAAAAGGAAAGAAAGAATTCAT
CGGGAGAAACTGGATAGGATCCAACGCGAGAAAATCAACCTGCTTAAGAACAATGATGTTGAAG
GTTATCTTAGAATGGTCAAGGTGAGTTTTGTCTTGCTTTATTTTGATTTAATGGTATCTTGATC
TTAGCCCTTCATTTTTTTCTCGAACACGCAGGAGAGATGCACATCATTATAATAAGAGAGGAAA
GGTCCAAAATGGAACGAAATACAACGCCCTGGAGGGCAGAAAAACAAACACTGGACCTGACCAC
CAAGACCTAACACCCATGCCTCCTCTCCAACAACAAATAAGGCGAAACAAAGCAAAGGAGAGGG
CTGGCAGGCCCGACTAGACCCTATTTAAGGCGACAATAAGCCCCAGACTGTCTATATGCTTAGC
TCCCGCCTTATCCCAACTGATCAACTCATCTAAAAACAACCTTTTAACCAAGCTAATGGAAGGG
TTCACTTCATCAAAAACAGCCTTACTACGAATAAGCCATATGCACCAAGCCCTAAGAATTATGA
CGCTATTGAAGCCCTTCCTCCTGCACTTGTGCATTTTTTTAAGAGCCTTTCCCCACCACACAGC
AAAGGATTGTTCATCATTCTCCGGAGTGAGATCACCTAGCCTTATGGGCGACAAAATATGATGC
CAAAATTGTCTGGCAAAACTGTAGGTGCAGAGGATATGCTGGGCTGTTTCTTGCTCTTGATCAC
ATAGGGGACAACACACCTGGTACCGCATTCCTCTCCTTTGGAGCCTGTCAGCAGTCCAACACTT
ATTCCTTATTGCTAACCAAAGGAAAAACTTGCATTTTGGGGGAGCCCAAGTCTTCCACAATCTT
TTCCATGGCTCAAAGGAGATGGAACCCATGAAGAAGGCTCTGTAGCAAGACTTGGATGAGAATT
GTCCAGAAGCAGTGTGCATCCATACATGTCTGTCCGCCTCCTGTGAAAGCATTACCACTCCAAG
AACATCCCATAACTTCAAATAGCATACCAATCAGCGAAAGATGACTCCCAATATCACTAACCCA
CTGTCAGTTGTCAAGTGCCTGAGCTACAGTCCTGGTAGAGATGACTCTACGACCAACCATACAG
ACAACGGCTGGTGCAATATCATGGATAGCATTCCCATTCAACCATTTATCTGACCAAAATAGAG
TATTGGTCCCATTTCCTACCACAGATAATACCGACAGATTAAAGAACTGTCTGACCTGCTGCTG
TATAGGAAGACTCATCCCATGCCAAGGTCTGGACGGATCAGTTTTTTACAGCCATAACCATTTA
GCCTGTAAGGCCCAACTTTTGAATTGTAAATTAGAAACTACAAGCCTGCCAAGTTTTAGAGGCC
TTGTAACTATCTCCCATGGAACAAGACAGCTTCCACCGTTTACATTCTCACTTTCTTTCCATAG
AAACCCCCTCCGGATTTTATCGATAGGTTTGATCACCCATTTGGGACGCCAATAGCACTCATTC
ATAAACCGGTGACGGGTACAAATAGCATAAAGAAATGTAACCAACGTTTATTGGAAAAAAGCAA
CACCAAAGATTTGGGACCAAAAGCGGTTATGGCCATGAGGATATATACAGGAATGGCCGAAAGC
ACATGCCTCACCAAAGCTGTCATTTAATCTCTACTTATTTTCTGATAAATATTGCTACATTGTA
GGATGCAAAATCTGATCGTGTCAAGCAACTATTGCGTGAAACTGAGAAATATCTTCAGAAACTT
GGGAACAAATTACAGAGTGCAAAGTCCACAGATGGCCGCTCATCTTTTGTTACTGATAAGAGTG
ACACTGCAAACGACATTGAAGATGAGAGCTACCAGCCACAGGTTACATAGTTTTCTGGTATATA
GATTTCTGATTCTTTCATGTTTGATATTTACTCAAGTGTAATTTCCTCTTCGCAGCATTATCTG
GAAAGTAATGAAAAGTACTATCAACTGGCACACAG
						
					

			
		

Sequences
Splice junction sequence	AGATTTCTGATTCTTTCATGTTTGATATTTACTCAAGTGTAATTTCCTCTTCGCAGCATTATCT GGAAAGTAATGAAAAGTACTATCAACTGGCACACAGgagagcgttaattcatccgaagatcttt ctgcaaagaccaagagcgtcattgaattgaaaaagcttcagcttctgccacttcaacgtcgtgt acgcaggt
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	GAGAGCGTTAATTCATCCGAAGATCTTTCTGCAAAGACCAAGAGCGTCATTGAATTGAAAAAGC TTCAGCTTCTGCCACTTCAACGTCGTGTACGCAGGTTGGTTGTCGTTGGAGAACCCCCCCAATC ATTGTTATTCTTTTGTTAATCTGACTATATGTCTGTTTAACATTTTAACTATGTGATCCCTGTT TCTCTTTTTCTATTCTTTCATGCAGTGAATTTTTGCTGGATTTTTTCAAGCCTAATACATCCGA CTTAGAGCGCATAAAATCACTGAAGAAACATAGGCATGGGCGGCGGGTGAAACAGCTTGAAAAA ATTGAACAGAAAATGAAGGAAGAAAGGCAAAAGAGAATTCGTGAGAGACAGAAGGAATTCTTTG CTGATATTGAAGCTTACAGGTTGGATAACAATCTCTGTTGCTTTCATCATTTCTTTGAACCATT TGAAGTCATCTCTAAGCGATGTCTTTTGCAGAGAGAAACTCGAGGATAACTTCAAGGTTAAGAG AGAGCGCTTGAAGGGGTTCAATCGATACATAAAAGAATTTCACAAAAGGAAAGAAAGAATTCAT CGGGAGAAACTGGATAGGATCCAACGCGAGAAAATCAACCTGCTTAAGAACAATGATGTTGAAG GTTATCTTAGAATGGTCAAGGTGAGTTTTGTCTTGCTTTATTTTGATTTAATGGTATCTTGATC TTAGCCCTTCATTTTTTTCTCGAACACGCAGGAGAGATGCACATCATTATAATAAGAGAGGAAA GGTCCAAAATGGAACGAAATACAACGCCCTGGAGGGCAGAAAAACAAACACTGGACCTGACCAC CAAGACCTAACACCCATGCCTCCTCTCCAACAACAAATAAGGCGAAACAAAGCAAAGGAGAGGG CTGGCAGGCCCGACTAGACCCTATTTAAGGCGACAATAAGCCCCAGACTGTCTATATGCTTAGC TCCCGCCTTATCCCAACTGATCAACTCATCTAAAAACAACCTTTTAACCAAGCTAATGGAAGGG TTCACTTCATCAAAAACAGCCTTACTACGAATAAGCCATATGCACCAAGCCCTAAGAATTATGA CGCTATTGAAGCCCTTCCTCCTGCACTTGTGCATTTTTTTAAGAGCCTTTCCCCACCACACAGC AAAGGATTGTTCATCATTCTCCGGAGTGAGATCACCTAGCCTTATGGGCGACAAAATATGATGC CAAAATTGTCTGGCAAAACTGTAGGTGCAGAGGATATGCTGGGCTGTTTCTTGCTCTTGATCAC ATAGGGGACAACACACCTGGTACCGCATTCCTCTCCTTTGGAGCCTGTCAGCAGTCCAACACTT ATTCCTTATTGCTAACCAAAGGAAAAACTTGCATTTTGGGGGAGCCCAAGTCTTCCACAATCTT TTCCATGGCTCAAAGGAGATGGAACCCATGAAGAAGGCTCTGTAGCAAGACTTGGATGAGAATT GTCCAGAAGCAGTGTGCATCCATACATGTCTGTCCGCCTCCTGTGAAAGCATTACCACTCCAAG AACATCCCATAACTTCAAATAGCATACCAATCAGCGAAAGATGACTCCCAATATCACTAACCCA CTGTCAGTTGTCAAGTGCCTGAGCTACAGTCCTGGTAGAGATGACTCTACGACCAACCATACAG ACAACGGCTGGTGCAATATCATGGATAGCATTCCCATTCAACCATTTATCTGACCAAAATAGAG TATTGGTCCCATTTCCTACCACAGATAATACCGACAGATTAAAGAACTGTCTGACCTGCTGCTG TATAGGAAGACTCATCCCATGCCAAGGTCTGGACGGATCAGTTTTTTACAGCCATAACCATTTA GCCTGTAAGGCCCAACTTTTGAATTGTAAATTAGAAACTACAAGCCTGCCAAGTTTTAGAGGCC TTGTAACTATCTCCCATGGAACAAGACAGCTTCCACCGTTTACATTCTCACTTTCTTTCCATAG AAACCCCCTCCGGATTTTATCGATAGGTTTGATCACCCATTTGGGACGCCAATAGCACTCATTC ATAAACCGGTGACGGGTACAAATAGCATAAAGAAATGTAACCAACGTTTATTGGAAAAAAGCAA CACCAAAGATTTGGGACCAAAAGCGGTTATGGCCATGAGGATATATACAGGAATGGCCGAAAGC ACATGCCTCACCAAAGCTGTCATTTAATCTCTACTTATTTTCTGATAAATATTGCTACATTGTA GGATGCAAAATCTGATCGTGTCAAGCAACTATTGCGTGAAACTGAGAAATATCTTCAGAAACTT GGGAACAAATTACAGAGTGCAAAGTCCACAGATGGCCGCTCATCTTTTGTTACTGATAAGAGTG ACACTGCAAACGACATTGAAGATGAGAGCTACCAGCCACAGGTTACATAGTTTTCTGGTATATA GATTTCTGATTCTTTCATGTTTGATATTTACTCAAGTGTAATTTCCTCTTCGCAGCATTATCTG GAAAGTAATGAAAAGTACTATCAACTGGCACACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.127221197

Conservation Information
Conserved circRNAs	NA
PMCS	0.127221197

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							122242897-122242618(+)
122244807-122242571(+)
122242615-122244919(-)
						
						Potential amino acid sequence
						
							MKEERQKRIRERQKEFFADIEAYREKLEDNFKDAKSDRVKQLLRETEKYLQKLGNKLQSAKSTD
GRSSFVTDKSDTANDIEDESYQPQHYLESNEKYYQLAHRRALIHPKIFLQRPRASLN*(+)
MQNLIVSSNYCVKLRNIFRNLGTNYRVQSPQMAAHLLLLIRVTLQTTLKMRATSHSIIWKVMKS
TINWHTGER*(+)
MTLLVFAERSSDELTLSCVPVDSTFHYFPDNAVAGSSHLQCRLQCHSYQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	122242897-122242618(+) 122244807-122242571(+) 122242615-122244919(-)
Potential amino acid sequence	MKEERQKRIRERQKEFFADIEAYREKLEDNFKDAKSDRVKQLLRETEKYLQKLGNKLQSAKSTD GRSSFVTDKSDTANDIEDESYQPQHYLESNEKYYQLAHRRALIHPKIFLQRPRASLN(+) MQNLIVSSNYCVKLRNIFRNLGTNYRVQSPQMAAHLLLLIRVTLQTTLKMRATSHSIIWKVMKS TINWHTGER(+) MTLLVFAERSSDELTLSCVPVDSTFHYFPDNAVAGSSHLQCRLQCHSYQ*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d037346_circ_g.4

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