Plant Circular RNA Database

Detail information of Zm00001d035001_circ_ag.4

			
						 General Information
					
						CircRNA Name
						Zm00001d035001_circ_ag.4
					
						ID in PlantcircBase
						zma_circ_008867
					
						Alias
						zma_circ_0002340
					
						Organism
						
							Zea mays						
					
						Position
						
							chr6: 1392336-1396153  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							Zm00001d035002_circ_igg.1 Zm00001d035001_circ_g.1 Zm00001d035001_circ_ag.1 Zm00001d035001_circ_ag.2 Zm00001d035001_circ_ag.3 Zm00001d035001_circ_ag.5 Zm00001d035001_circ_ag.6 						
					
						Support reads
						NA
					
						Tissues
						leaf, root
					
						Exon boundary  
						
							NA-NA							"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
						NA

General Information
CircRNA Name	Zm00001d035001_circ_ag.4
ID in PlantcircBase	zma_circ_008867
Alias	zma_circ_0002340
Organism	Zea mays
Position	chr6: 1392336-1396153 JBrowse»
Reference genome	AGPv4.38
Type	ag-circRNA
Identification method	find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	Zm00001d035002_circ_igg.1 Zm00001d035001_circ_g.1 Zm00001d035001_circ_ag.1 Zm00001d035001_circ_ag.2 Zm00001d035001_circ_ag.3 Zm00001d035001_circ_ag.5 Zm00001d035001_circ_ag.6
Support reads	NA
Tissues	leaf, root
Exon boundary	NA-NA "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	NA

			
						 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  
						
							AGGAGGAGCAGGACCCCGCGCGGCAGGAGTAGGGCAGGTCGATGCCTTCCTCCTCGGCGTAGTC
CAGGATGTAGACGTCGTCGGGCACCTGCAGCTCCACctccccctccggcgtgatcagcttcacg
ttgtaggtggcctgcgcgcgcagcctgcccctgctgctggcgctacggcccatgatgcccacct
tggccgca

									
								

					

						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
						
							CTCCCCCTCCGGCGTGATCAGCTTCACGTTGTAGGTGGCCTGCGCGCGCAGCCTGCCCCTGCTG
CTGGCGCTACGGCCCATGATGCCCACCTTGGCCGCAGGCAGCGCCACGGCGGTGGGCGCCGGCG
CGGCACGGAGGGAGGACGGCGAGAAGAAGAAGGCCGGCGCGCGGGGGCTGCCTAGGACGGTGGC
CATTGTTGTCGAGGGGTCGGGGTACGGTGGTGTGGCGGCCGGTGCAGTTAGGGAGCTCTAGATG
GAGAGAGTGGGGCTGGGGAGAGCGGCTGCTGGATAGATGGCCAATAGATAGCTTCTCCTGCCCT
CCCCTGCCCTGCCCCAGATGACAATACCAATGCAAGGGATGGATAGGCTTATCTTCTTGCATTG
CCGCCCCAATTTTGGCCACCCGTTTTTATCGCCCTTCAAACTCACGGGAATTTTGCATGCTGCG
GAAATTCAAATTCACATTATTCATGTGTAATGTCGATATTCGCATATAAAATAATTCATGGTAA
CTGATTATTGTGCGCGTGTGTAGGCCACGAGTCCCTTCAGGTCGTGGGACACGTGGGGTCATGT
GGCGCACGAACGAACTTTATAGTTCGGTGTAACTTATCATTGTTTCTTTAGTTTTTTTTACTTA
AATTTAGTTCCGGCGGTTCCTGTTGAATTTTTGAGGAGTTCCTCCCTTTTCGAGAAAGAGCCCA
TAAAAAACCTCCCTTTTGGTAGTTTTTTCAAGGAGTTGTTGAATGAGCCCTACCAGAGGAGGCC
TTAGTCGCATAATCTTGGACAAGTTGTGATAGAGTTAGATGAGAACCAAATAGATCCACAGTCT
CCTCATTGCGACGGGGAGGCAGAGACAGGTGGTCCGAGGAACAAGTGTCATCGACGTCGAAGTG
GGCGACAAGCACTGGTGGTGGTGTAGTCGTGTAGAAGGGCGACAATGGTGGAGTAGGGCATTAG
CATTGAGAAGAGATAAGGTTTTTAGTGTCAATGATGGCATGTGAGGCCCACATGTTTGATTTTA
AACATTGTTTTTTTACTGTCAATGGGGGAGAGAAGTTCTTCCCCATCTAAGATTTATATATATT
ACTTCTGTCTGAGAGAAACACATGAGATTACATTAGTACGTGAAGTTCATCAAAGTATCCGAAG
GGACCAGCCAGTGGATAACATTCTTGGTAGCATAAGGACACGGGTAACAACTCGATCTCGCTTA
ACAATTTTTTGTGAATCTTACTTGTTTGTTTCCTCTCTTGAGCCACTTAGGGTAGAAGAAGCAC
TGGGTGATCTAGAGTGGATAGTAGCAATGCAAGAGTAATTCAATAACTTCACCCGGAATGAAGT
TTAGCCCTTTGTGGAAAGACCCAAGCAAAATGTCATTGGAACTAAGTGTGTTTTCCGCAACATG
CAAGATGAACATGGCTTGGTCACAAGAAACAAGGCGTGGTTGGTTGCTCAAGGCTTCACTCAAG
TAGAAGGGCTTGATTTTGGAGAGACATATGCACCAGTGGCAATGTTAGAGTCAATTAAAATTTT
GATTGCTTATGCAACTAACCATGATTTCAAGCTATATTAAATGGACGACAAGAGTGCATTTCTA
AATGGACCACTACAAGAGTTGGTCTATGTGAAGCAACCATCGGACTTTGAAGATCAAATAAGCC
TAACCATGTATTTCTCCTCCATAAGGTGCTCTATGGGCTTAAGCAATCTCCTAGAGCATAGTAT
AAATGCCTTAAGGAGTTATTGATTAAAAATGGCTTTCAAATAGGCAAAGCCGACTCTACTCTAT
TTACTCGCAAGTTTGATAATGAACTATTTGTGTGCCAAATATATGTCGATAACATTATACTTGG
CAGTACTAATGATGAGTTTTGTGGGGAATTTAGCAGGGTAATGATGAATATGTTTGAGATGTCT
ATGATGGGTGAGTTAAAGTTCTTCTGAGGATTCCAAGTAAAACAATTAAAGAAAGAGACTTTTC
TATGCCAAACCAAGTATATTTGGTTCATACACCTAACCTAGGCCTTTGGTATCCTAAAGACTCC
ACTTTCAATTTGCTTCGCTACTCTGACTCAGATTACATCAGTTGTAAAGTAGATAAAAAGTACC
ATCGAGACTTGCCAATTCGTTGGGCGGTCCTTAGTGTCGTGGAGTTCCAAGAAACAAAATTGTG
TTGCACTTTCCACTGCCGAGGCTGAGTATATAGCAGCTGATGTTTGTTGCGCCCAATTTTTATG
GATGAAGCAAACCTTGAGGGATTTTGGTTGTGAGTTTAGCAAAATTCCGCTACTTTGTGTTAAT
GAGAGTGCCATAAAACTTTCAAACAATCACGTGCAACACTTTAGAACTAAACACATTGACATTA
GACATCACTTCTTAAGATACCATGAGGACAAAGGAGATATCAAAATATGGCATGTGAGTGCTGA
GAACCAACTAGCCGATATCTTCATCATACCCCTAAATGAGACTAGGTTTGTTTTCTCAGAAGTG
AACTAAATATCTTGGACTCTCGTAACATGTCTTGGAAAGTGTGTGCTTAAAATTTGGATGTTTC
ATGTGCTGTAAAACTTTTTAAAATGACTAATTTCTATATATTTATACAAATTTTTTTGTTAAGT
TAGGCAAAATAGATGCCATAATGAAGATCGCCAAAGGGTTTCTCTGATAATTTTCGGTTGATAG
AGTGAGTTGAATAGGCCATTCAACCAAATTCTTCTCTGGTCAGACTTGGTTCAACCGGGGAAAA
ACTCGGTTCAACCGACTTTTGACCTGCTTTGCCAGTCAACCCTGCCATCTGTCAGTTTGGCCTC
GCAGACTGCTCTTCTAGAAAGTCGGTTCAACCGAGATTAAACCCAATTCAACTTAGTTTGCGCA
GAGAGTCGACCGGGTTTATTTCTTTTTTTCTCTTCTCTCTCTCTTCTCATTCCTTAGTCGAGTT
ATTTGAAAAGGAGACGCCGCCCCTTCTCTATCCCCCTCTCAAACCCTCCCCTCAACCAAAATAT
TGAGCCAAATCCATTGAAACTTGGAGGACTTCATCATGTTGAGGTCCTCCACCTATTCCCTCCA
TTGATTTGAAGTTTCGCGAGTGGAATCGATAGATCGAGGTAAAGCTCTCTTCTCTATCTTTTGC
CCTGATCTTTGGTTATAGCTAAGGTCTTGTGAATCCCTTTGAGTAAAAGGATCTTGTGGATGTA
AGAAACATATTGCTCTAAGGGATTTCTCTAATTTATTGACGTACTCGACGAAAAAGGGTAATGA
ATCGTTCATGTGAGGTTGACCCGAATAGTTGAACGGCATATATTCCGTTCACTCTCTCTTCCTA
TCATTTGTTGAATCACCATTTGGTTATTCTTTTTATCTTATACCTGTGTTTTTAGTTCAAGAAT
GAAGAACTAGCCGGCGATAAATATTTAAAAAATATTTGAAAACAGAGGTAATAGTTTACAATAC
AGTTTGAAACGGACAAAAAAATTACATGCACAGCCAGTATTGAGACATCTTCTACTCTCCTGTG
CTTGCAAGTCGACGTGATAATTGGCGGTGCTTTATTAATTTGCTTAGGAGATAAGGTCATCCTC
CTTGTGCGTCTCGATGACGACGTCGGAGGTGGGGTACGCCACGCAGGTGAGCACCCAGCCGGCG
GCGATCTGGCCGTCGTCGAGGTAGCTCTGGTCGGACTGGTCCACGGAGCCGGAGACGACCTTGC
CGGCGCAGGAGGAGCAGGACCCCGCGCGGCAGGAGTAGGGCAGGTCGATGCCTTCCTCCTCGGC
GTAGTCCAGGATGTAGACGTCGTCGGGCACCTGCAGCTCCAC
						
					

			
		

Sequences
Splice junction sequence	AGGAGGAGCAGGACCCCGCGCGGCAGGAGTAGGGCAGGTCGATGCCTTCCTCCTCGGCGTAGTC CAGGATGTAGACGTCGTCGGGCACCTGCAGCTCCACctccccctccggcgtgatcagcttcacg ttgtaggtggcctgcgcgcgcagcctgcccctgctgctggcgctacggcccatgatgcccacct tggccgca
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	CTCCCCCTCCGGCGTGATCAGCTTCACGTTGTAGGTGGCCTGCGCGCGCAGCCTGCCCCTGCTG CTGGCGCTACGGCCCATGATGCCCACCTTGGCCGCAGGCAGCGCCACGGCGGTGGGCGCCGGCG CGGCACGGAGGGAGGACGGCGAGAAGAAGAAGGCCGGCGCGCGGGGGCTGCCTAGGACGGTGGC CATTGTTGTCGAGGGGTCGGGGTACGGTGGTGTGGCGGCCGGTGCAGTTAGGGAGCTCTAGATG GAGAGAGTGGGGCTGGGGAGAGCGGCTGCTGGATAGATGGCCAATAGATAGCTTCTCCTGCCCT CCCCTGCCCTGCCCCAGATGACAATACCAATGCAAGGGATGGATAGGCTTATCTTCTTGCATTG CCGCCCCAATTTTGGCCACCCGTTTTTATCGCCCTTCAAACTCACGGGAATTTTGCATGCTGCG GAAATTCAAATTCACATTATTCATGTGTAATGTCGATATTCGCATATAAAATAATTCATGGTAA CTGATTATTGTGCGCGTGTGTAGGCCACGAGTCCCTTCAGGTCGTGGGACACGTGGGGTCATGT GGCGCACGAACGAACTTTATAGTTCGGTGTAACTTATCATTGTTTCTTTAGTTTTTTTTACTTA AATTTAGTTCCGGCGGTTCCTGTTGAATTTTTGAGGAGTTCCTCCCTTTTCGAGAAAGAGCCCA TAAAAAACCTCCCTTTTGGTAGTTTTTTCAAGGAGTTGTTGAATGAGCCCTACCAGAGGAGGCC TTAGTCGCATAATCTTGGACAAGTTGTGATAGAGTTAGATGAGAACCAAATAGATCCACAGTCT CCTCATTGCGACGGGGAGGCAGAGACAGGTGGTCCGAGGAACAAGTGTCATCGACGTCGAAGTG GGCGACAAGCACTGGTGGTGGTGTAGTCGTGTAGAAGGGCGACAATGGTGGAGTAGGGCATTAG CATTGAGAAGAGATAAGGTTTTTAGTGTCAATGATGGCATGTGAGGCCCACATGTTTGATTTTA AACATTGTTTTTTTACTGTCAATGGGGGAGAGAAGTTCTTCCCCATCTAAGATTTATATATATT ACTTCTGTCTGAGAGAAACACATGAGATTACATTAGTACGTGAAGTTCATCAAAGTATCCGAAG GGACCAGCCAGTGGATAACATTCTTGGTAGCATAAGGACACGGGTAACAACTCGATCTCGCTTA ACAATTTTTTGTGAATCTTACTTGTTTGTTTCCTCTCTTGAGCCACTTAGGGTAGAAGAAGCAC TGGGTGATCTAGAGTGGATAGTAGCAATGCAAGAGTAATTCAATAACTTCACCCGGAATGAAGT TTAGCCCTTTGTGGAAAGACCCAAGCAAAATGTCATTGGAACTAAGTGTGTTTTCCGCAACATG CAAGATGAACATGGCTTGGTCACAAGAAACAAGGCGTGGTTGGTTGCTCAAGGCTTCACTCAAG TAGAAGGGCTTGATTTTGGAGAGACATATGCACCAGTGGCAATGTTAGAGTCAATTAAAATTTT GATTGCTTATGCAACTAACCATGATTTCAAGCTATATTAAATGGACGACAAGAGTGCATTTCTA AATGGACCACTACAAGAGTTGGTCTATGTGAAGCAACCATCGGACTTTGAAGATCAAATAAGCC TAACCATGTATTTCTCCTCCATAAGGTGCTCTATGGGCTTAAGCAATCTCCTAGAGCATAGTAT AAATGCCTTAAGGAGTTATTGATTAAAAATGGCTTTCAAATAGGCAAAGCCGACTCTACTCTAT TTACTCGCAAGTTTGATAATGAACTATTTGTGTGCCAAATATATGTCGATAACATTATACTTGG CAGTACTAATGATGAGTTTTGTGGGGAATTTAGCAGGGTAATGATGAATATGTTTGAGATGTCT ATGATGGGTGAGTTAAAGTTCTTCTGAGGATTCCAAGTAAAACAATTAAAGAAAGAGACTTTTC TATGCCAAACCAAGTATATTTGGTTCATACACCTAACCTAGGCCTTTGGTATCCTAAAGACTCC ACTTTCAATTTGCTTCGCTACTCTGACTCAGATTACATCAGTTGTAAAGTAGATAAAAAGTACC ATCGAGACTTGCCAATTCGTTGGGCGGTCCTTAGTGTCGTGGAGTTCCAAGAAACAAAATTGTG TTGCACTTTCCACTGCCGAGGCTGAGTATATAGCAGCTGATGTTTGTTGCGCCCAATTTTTATG GATGAAGCAAACCTTGAGGGATTTTGGTTGTGAGTTTAGCAAAATTCCGCTACTTTGTGTTAAT GAGAGTGCCATAAAACTTTCAAACAATCACGTGCAACACTTTAGAACTAAACACATTGACATTA GACATCACTTCTTAAGATACCATGAGGACAAAGGAGATATCAAAATATGGCATGTGAGTGCTGA GAACCAACTAGCCGATATCTTCATCATACCCCTAAATGAGACTAGGTTTGTTTTCTCAGAAGTG AACTAAATATCTTGGACTCTCGTAACATGTCTTGGAAAGTGTGTGCTTAAAATTTGGATGTTTC ATGTGCTGTAAAACTTTTTAAAATGACTAATTTCTATATATTTATACAAATTTTTTTGTTAAGT TAGGCAAAATAGATGCCATAATGAAGATCGCCAAAGGGTTTCTCTGATAATTTTCGGTTGATAG AGTGAGTTGAATAGGCCATTCAACCAAATTCTTCTCTGGTCAGACTTGGTTCAACCGGGGAAAA ACTCGGTTCAACCGACTTTTGACCTGCTTTGCCAGTCAACCCTGCCATCTGTCAGTTTGGCCTC GCAGACTGCTCTTCTAGAAAGTCGGTTCAACCGAGATTAAACCCAATTCAACTTAGTTTGCGCA GAGAGTCGACCGGGTTTATTTCTTTTTTTCTCTTCTCTCTCTCTTCTCATTCCTTAGTCGAGTT ATTTGAAAAGGAGACGCCGCCCCTTCTCTATCCCCCTCTCAAACCCTCCCCTCAACCAAAATAT TGAGCCAAATCCATTGAAACTTGGAGGACTTCATCATGTTGAGGTCCTCCACCTATTCCCTCCA TTGATTTGAAGTTTCGCGAGTGGAATCGATAGATCGAGGTAAAGCTCTCTTCTCTATCTTTTGC CCTGATCTTTGGTTATAGCTAAGGTCTTGTGAATCCCTTTGAGTAAAAGGATCTTGTGGATGTA AGAAACATATTGCTCTAAGGGATTTCTCTAATTTATTGACGTACTCGACGAAAAAGGGTAATGA ATCGTTCATGTGAGGTTGACCCGAATAGTTGAACGGCATATATTCCGTTCACTCTCTCTTCCTA TCATTTGTTGAATCACCATTTGGTTATTCTTTTTATCTTATACCTGTGTTTTTAGTTCAAGAAT GAAGAACTAGCCGGCGATAAATATTTAAAAAATATTTGAAAACAGAGGTAATAGTTTACAATAC AGTTTGAAACGGACAAAAAAATTACATGCACAGCCAGTATTGAGACATCTTCTACTCTCCTGTG CTTGCAAGTCGACGTGATAATTGGCGGTGCTTTATTAATTTGCTTAGGAGATAAGGTCATCCTC CTTGTGCGTCTCGATGACGACGTCGGAGGTGGGGTACGCCACGCAGGTGAGCACCCAGCCGGCG GCGATCTGGCCGTCGTCGAGGTAGCTCTGGTCGGACTGGTCCACGGAGCCGGAGACGACCTTGC CGGCGCAGGAGGAGCAGGACCCCGCGCGGCAGGAGTAGGGCAGGTCGATGCCTTCCTCCTCGGC GTAGTCCAGGATGTAGACGTCGTCGGGCACCTGCAGCTCCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.459085842

Conservation Information
Conserved circRNAs	NA
PMCS	0.459085842

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d035001_circ_ag.4

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