Plant Circular RNA Database

Detail information of Zm00001d043312_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d043312_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007780
					
						Alias
						Zm03circ00082, zma_circ_0001237
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 196052660-196055886  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d043312						
					
						Parent gene annotation
						
							Ubiquitin carboxyl-terminal hydrolase 13
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d043312_circ_g.1 Zm00001d043312_circ_g.2 Zm00001d043312_circ_g.4 Zm00001d043312_circ_g.5 Zm00001d043312_circ_g.6 Zm00001d043312_circ_g.7 Zm00001d043312_circ_g.8 Zm00001d043312_circ_g.9 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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
						Zm00001d043312_T007:6
Zm00001d043312_T002:5
Zm00001d043312_T004:6
Zm00001d043312_T005:6
Zm00001d043312_T011:2
Zm00001d043312_T010:3
Zm00001d043312_T001:6
Zm00001d043312_T009:6
Zm00001d043312_T008:6

General Information
CircRNA Name	Zm00001d043312_circ_g.3
ID in PlantcircBase	zma_circ_007780
Alias	Zm03circ00082, zma_circ_0001237
Organism	Zea mays
Position	chr3: 196052660-196055886 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d043312
Parent gene annotation	Ubiquitin carboxyl-terminal hydrolase 13
Parent gene strand	+
Alternative splicing	Zm00001d043312_circ_g.1 Zm00001d043312_circ_g.2 Zm00001d043312_circ_g.4 Zm00001d043312_circ_g.5 Zm00001d043312_circ_g.6 Zm00001d043312_circ_g.7 Zm00001d043312_circ_g.8 Zm00001d043312_circ_g.9
Support reads	NA
Tissues	leaf, endosperm, 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	Zm00001d043312_T007:6 Zm00001d043312_T002:5 Zm00001d043312_T004:6 Zm00001d043312_T005:6 Zm00001d043312_T011:2 Zm00001d043312_T010:3 Zm00001d043312_T001:6 Zm00001d043312_T009:6 Zm00001d043312_T008:6

			
						 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  
						
							TAAAGAGCAAATTGGAAGACACATGCACTTTGATCTTGTGGACTTTGACAGAGTTAATAGCTTC
CGTGCACCTAAGAACATGTCAATCAACGAAGTCAAGataaatgaccgttatgagttcccacttc
aattggatcttgatagagatgatggaaaatatctttctccagacgcggatagaagtgtgcgtaa
cctatata

									
								

					

						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
						
							ATAAATGACCGTTATGAGTTCCCACTTCAATTGGATCTTGATAGAGATGATGGAAAATATCTTT
CTCCAGACGCGGATAGAAGTGTGCGTAACCTATATACTCTTCATAGGTAATAGTTCGATAAGCA
CTTCATTTTCATGTATTGTTTTTGTCACTCGAAATAAAGACTACGTGAGCATTTACATCTTACC
GATATTAATTATCAACTATGCTCAGCTTATTTTAGATAAGTTCATATACTGTTTGTGTTTTCCA
GTTGTAAGTTATAATGATGGACTAGTTAACATGTTGAAAGTGTGGAAATATTTGCTCAGCTTTA
GTAATCTGATTTTCAGAATTACGTATTAGCTGTTTAGGTGCAGATTTATGGGTTTTCAATTTTT
GAGAGCTGTTTGGATCTTTTGTAGTAATATTTGTAGCTTCTCTTCAATGCAGTGTACTGGTTCA
TAGTGGTGGAGTTCATGGAGGACACTATTATGCCTTTATTCGTCCGAAGCTGTCTGATCAATGG
TACATTCTGTTTAACATTTGAATCGAATTGTTCTTATTTCGATACTTAAACAGAGATCTTTCGC
TGGTACTAGACCCATTCTGGTTTAAACTCTATCTGAAAAGACAATTCAAGCAACCTTTTGATTT
TTAAGTTCAGACGCAAAAAAAATCTTTTCATGTACCCTAATTCATATTAAATTTCTTATCGGTA
ATTGATATTTTGGTCGCTGATATAATTTTCACTCATGAGTCATGACCTCATAGTGGAAAGATAT
GCCTAAGAAAATTTCATTATGTGTCCTTTTTTGTGCTAAGGCTGTCCGCAACATATCGTGTAAA
ATAGAGGATTTGTACAGTAGATGACACTGTTTGCAGAGTGAAGTTTGAAATAGGGGTTGAGATA
GGTGATGAAATAGGATAGCTGCTGAAGACAACCTAAGGTGGGTATTCTTCAATGTATACAAATC
GTATAATCGAAAGTATCAAACTTAGTTGTGGGACTAAAACTCGGCCAGTAGGGAAAAGACCGCC
CCACGGTATTATATTAAGAAGAAGCTCACGGAGCCCCGACCGAGAATGGTCACGTAAGCTGCCC
CCCTGGTGTAGTATGAGGGTCCGCCCCCTGTAGGCCAGATTTTTACTCGTGCTTTGAGCCCTCC
CATAGGTCATTCCATCTCGTTTGCAGACAATCAGGGGAACCGGCGAGTGACTTTTTTTAACTTC
AACCTGAAATTCTCTCCCACTGGGGATTCAACCTCAGGACGAGTTCTACTTAGACCACCTAACC
AACTCAGTTAGAGGCCCTTTCGCCCTAGTCATGGGACTGTCTACTAATCTCGATTAGTCGTCGA
CTAGGCATAGTCGGCCCTAGTCGGCCTATATATTTCAGGACATATACGTAATATATATGCCTAT
ATATACTTATAATATAGTATATACACAATAAACAAAGGATCAAGACTACATTAGTGACTAGTTG
ATTTTTGCACTGTTCCACATCTGCACATAAACAGCAGTACAACACACATATGCACATAAACAGC
AGTACAACACCTTAGGATGGAGTATCAACAAGCAGCTATAGTAGTAGAGAGGTAGTACAACAAG
CAATCGGACTAGCGATGGGCAACAACATAGCAAGCAAGGGAACATCACTAGTGCTGCAGTGTGA
GGGATAGGGAGGAGGAAAGAAGATGGAGGGAAATGGCACATTTACAAATGTTGGAGTCATCATG
AAGAGGGGTGGCAGCTTCACCACAGAAACGACGTTGGATGAAGAATAGTGTGCAGGATATGAAG
AATGGTGTGTGGGGTAGGAGGAAAGGTGCATGGGGGAAGAATTGTGGTGGCATGGGAGAAGGAA
ACCAGTGTTGCCTCCATTCTCTGTTTTTGGTGGAGTTTGGGCACACTTTATGCTAACCTAACAG
GCCAAATTGGTAGGCCCAATTGAGTGTGAACAGTACAGGGAGTCAGAGATCTAGCTCGGTCGCC
CCCTCCTAGTTGGACGGCTAGGGGCGTGTTTGGTTTCTCTGCTCGTCTCCGTGTAATCTTGCTG
AGCAATGATTTCAAACAAACTAGTGCGTTTGAATTCCTTGCTTGCATGCCTTGAAACCTGTAAT
GACAAGATCTGGCTCATCGTTGTGGGGGAGCCAAAACGAGTCTCTTGGCAGGGAGAGTGAGGCG
AAGCGGGATACCAAACACGCCCTAGGTTTGTAGTCGAGCTAGTCGCCTCGTTGACCCTGGCCGA
GAGACCGACTAGACTGATTGATTAATTGTATCGTAATAAACAGATGACTTGTGAGCACTGGTAT
TCTTATCTAAGAATTATTTGCTCCACATTGGAATTGAAAAAGGTACAAGTTCGAGGATGAACGA
GTGACGAAAGAAGACATGAAACGAGCATTGGAGGAACAATATGGTGGTGAAGAAGAGGTAATAC
ATGCAGACACTAAACTTCTTCAATTAGCTTGGGTACATAACATTTATCTTTGTTGCAGCTCCCG
CATACCAACCCTGGGTTGGATACTGCACCGCTTAGATTTACCAAGCATTCAAATGCTTACATGC
TTGTTTACATTCGAGAAAGTGACAAAGATAACATTATCTGTGATTTGGATGATGAAGATATTTC
AGAACACCTTAAGGTATACTTTTTATTCAATTTTAAAAAATTATTAAATACTCTCCCGTCCCGT
GAATAAGTCAAACTTTTCTAGATTTGACAAGTTTTTAGGAAAAATATCAGCATTTGTGTCTACA
ACTAGAATTACTATAAAAATATGTTTCATAATTAATCTAATGACATTTATTTGGTATCGTAAAC
ATTTGTATTTTGTATATATTTTGGTCAAACTTTAATTTGATTGACTCCTCGTGAAGTGAGATTT
GTATTTTTTTAAGTTGAGTGAGTGGTAGAGTCCACATAGTTTGTCTTGATGTTACAGAAATATT
ATCAGGTTAGGTTGAGAAAGGAACATGAAGAGAAGGAGTACAAGAAAAAGGAGAAGGCTGAGGC
TCATATGTTCACTGCATTGAAGGTTTGGCTTGATTTTGTCTCTTACATAATCTGATCGGACTAT
TTCTCAGTTTTTACTAAAATGAAACAATCACTCAGGTGGCCCGAGACTTTGATATTAAAGAGCA
AATTGGAAGACACATGCACTTTGATCTTGTGGACTTTGACAGAGTTAATAGCTTCCGTGCACCT
AAGAACATGTCAATCAACGAAGTCAAG
						
					

			
		

Sequences
Splice junction sequence	TAAAGAGCAAATTGGAAGACACATGCACTTTGATCTTGTGGACTTTGACAGAGTTAATAGCTTC CGTGCACCTAAGAACATGTCAATCAACGAAGTCAAGataaatgaccgttatgagttcccacttc aattggatcttgatagagatgatggaaaatatctttctccagacgcggatagaagtgtgcgtaa cctatata
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	ATAAATGACCGTTATGAGTTCCCACTTCAATTGGATCTTGATAGAGATGATGGAAAATATCTTT CTCCAGACGCGGATAGAAGTGTGCGTAACCTATATACTCTTCATAGGTAATAGTTCGATAAGCA CTTCATTTTCATGTATTGTTTTTGTCACTCGAAATAAAGACTACGTGAGCATTTACATCTTACC GATATTAATTATCAACTATGCTCAGCTTATTTTAGATAAGTTCATATACTGTTTGTGTTTTCCA GTTGTAAGTTATAATGATGGACTAGTTAACATGTTGAAAGTGTGGAAATATTTGCTCAGCTTTA GTAATCTGATTTTCAGAATTACGTATTAGCTGTTTAGGTGCAGATTTATGGGTTTTCAATTTTT GAGAGCTGTTTGGATCTTTTGTAGTAATATTTGTAGCTTCTCTTCAATGCAGTGTACTGGTTCA TAGTGGTGGAGTTCATGGAGGACACTATTATGCCTTTATTCGTCCGAAGCTGTCTGATCAATGG TACATTCTGTTTAACATTTGAATCGAATTGTTCTTATTTCGATACTTAAACAGAGATCTTTCGC TGGTACTAGACCCATTCTGGTTTAAACTCTATCTGAAAAGACAATTCAAGCAACCTTTTGATTT TTAAGTTCAGACGCAAAAAAAATCTTTTCATGTACCCTAATTCATATTAAATTTCTTATCGGTA ATTGATATTTTGGTCGCTGATATAATTTTCACTCATGAGTCATGACCTCATAGTGGAAAGATAT GCCTAAGAAAATTTCATTATGTGTCCTTTTTTGTGCTAAGGCTGTCCGCAACATATCGTGTAAA ATAGAGGATTTGTACAGTAGATGACACTGTTTGCAGAGTGAAGTTTGAAATAGGGGTTGAGATA GGTGATGAAATAGGATAGCTGCTGAAGACAACCTAAGGTGGGTATTCTTCAATGTATACAAATC GTATAATCGAAAGTATCAAACTTAGTTGTGGGACTAAAACTCGGCCAGTAGGGAAAAGACCGCC CCACGGTATTATATTAAGAAGAAGCTCACGGAGCCCCGACCGAGAATGGTCACGTAAGCTGCCC CCCTGGTGTAGTATGAGGGTCCGCCCCCTGTAGGCCAGATTTTTACTCGTGCTTTGAGCCCTCC CATAGGTCATTCCATCTCGTTTGCAGACAATCAGGGGAACCGGCGAGTGACTTTTTTTAACTTC AACCTGAAATTCTCTCCCACTGGGGATTCAACCTCAGGACGAGTTCTACTTAGACCACCTAACC AACTCAGTTAGAGGCCCTTTCGCCCTAGTCATGGGACTGTCTACTAATCTCGATTAGTCGTCGA CTAGGCATAGTCGGCCCTAGTCGGCCTATATATTTCAGGACATATACGTAATATATATGCCTAT ATATACTTATAATATAGTATATACACAATAAACAAAGGATCAAGACTACATTAGTGACTAGTTG ATTTTTGCACTGTTCCACATCTGCACATAAACAGCAGTACAACACACATATGCACATAAACAGC AGTACAACACCTTAGGATGGAGTATCAACAAGCAGCTATAGTAGTAGAGAGGTAGTACAACAAG CAATCGGACTAGCGATGGGCAACAACATAGCAAGCAAGGGAACATCACTAGTGCTGCAGTGTGA GGGATAGGGAGGAGGAAAGAAGATGGAGGGAAATGGCACATTTACAAATGTTGGAGTCATCATG AAGAGGGGTGGCAGCTTCACCACAGAAACGACGTTGGATGAAGAATAGTGTGCAGGATATGAAG AATGGTGTGTGGGGTAGGAGGAAAGGTGCATGGGGGAAGAATTGTGGTGGCATGGGAGAAGGAA ACCAGTGTTGCCTCCATTCTCTGTTTTTGGTGGAGTTTGGGCACACTTTATGCTAACCTAACAG GCCAAATTGGTAGGCCCAATTGAGTGTGAACAGTACAGGGAGTCAGAGATCTAGCTCGGTCGCC CCCTCCTAGTTGGACGGCTAGGGGCGTGTTTGGTTTCTCTGCTCGTCTCCGTGTAATCTTGCTG AGCAATGATTTCAAACAAACTAGTGCGTTTGAATTCCTTGCTTGCATGCCTTGAAACCTGTAAT GACAAGATCTGGCTCATCGTTGTGGGGGAGCCAAAACGAGTCTCTTGGCAGGGAGAGTGAGGCG AAGCGGGATACCAAACACGCCCTAGGTTTGTAGTCGAGCTAGTCGCCTCGTTGACCCTGGCCGA GAGACCGACTAGACTGATTGATTAATTGTATCGTAATAAACAGATGACTTGTGAGCACTGGTAT TCTTATCTAAGAATTATTTGCTCCACATTGGAATTGAAAAAGGTACAAGTTCGAGGATGAACGA GTGACGAAAGAAGACATGAAACGAGCATTGGAGGAACAATATGGTGGTGAAGAAGAGGTAATAC ATGCAGACACTAAACTTCTTCAATTAGCTTGGGTACATAACATTTATCTTTGTTGCAGCTCCCG CATACCAACCCTGGGTTGGATACTGCACCGCTTAGATTTACCAAGCATTCAAATGCTTACATGC TTGTTTACATTCGAGAAAGTGACAAAGATAACATTATCTGTGATTTGGATGATGAAGATATTTC AGAACACCTTAAGGTATACTTTTTATTCAATTTTAAAAAATTATTAAATACTCTCCCGTCCCGT GAATAAGTCAAACTTTTCTAGATTTGACAAGTTTTTAGGAAAAATATCAGCATTTGTGTCTACA ACTAGAATTACTATAAAAATATGTTTCATAATTAATCTAATGACATTTATTTGGTATCGTAAAC ATTTGTATTTTGTATATATTTTGGTCAAACTTTAATTTGATTGACTCCTCGTGAAGTGAGATTT GTATTTTTTTAAGTTGAGTGAGTGGTAGAGTCCACATAGTTTGTCTTGATGTTACAGAAATATT ATCAGGTTAGGTTGAGAAAGGAACATGAAGAGAAGGAGTACAAGAAAAAGGAGAAGGCTGAGGC TCATATGTTCACTGCATTGAAGGTTTGGCTTGATTTTGTCTCTTACATAATCTGATCGGACTAT TTCTCAGTTTTTACTAAAATGAAACAATCACTCAGGTGGCCCGAGACTTTGATATTAAAGAGCA AATTGGAAGACACATGCACTTTGATCTTGTGGACTTTGACAGAGTTAATAGCTTCCGTGCACCT AAGAACATGTCAATCAACGAAGTCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.030725971

Conservation Information
Conserved circRNAs	NA
PMCS	0.030725971

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							196055044-196055883(+)
196055069-196052660(+)
						
						Potential amino acid sequence
						
							MKRALEEQYGGEEELPHTNPGLDTAPLRFTKHSNAYMLVYIRESDKDNIICDLDDEDISEHLKV
ARDFDIKEQIGRHMHFDLVDFDRVNSFRAPKNMSINEVKINDRYEFPLQLDLDRDDGKYLSPDA
DRSVRNLYTLHSVLVHSGGVHGGHYYAFIRPKLSDQWYKFEDERVTKEDMKRALEEQYGGEEEL
PHTNPGLDTAPLRFTKHSNAYMLVYIRESDKDNIICDLDDEDISEHLKVARDFDIKEQIGRHMH
FDLVDFDRVNSFRAPKNMSINEVKINDRYEFPLQLDLDRDDGKYLSPDADRSVRNLYTLHSVLV
HSGGVHGGHYYAFIRPKLSDQWYKFEDERVTKEDMKRALEEQYGGEEELPHTNPGLDTAPLRFT
KHSNAYMLVYIRESDKDNIICDLDDEDISEHLKVARDFDIKEQIGRHMHFDLVDFDRVNSFRAP
KNMSINEVKINDRYEFPLQLDLDRDDGKYLSPDADRSVRNLYTLHSVLVHSGGVHGGHYYAFIR
PKLSDQWYKFEDERVTKEDMKRALEEQYGGEEELPHTNPGLDTAPLRFTKHSNAYMLVYIRESD
KDNIICDLDDEDISEHLKVARDFDIKEQIGRHMHFDLVDFDRVNSFRAPKNMSINEVK(+)
MVVKKSSRIPTLGWILHRLDLPSIQMLTCLFTFEKVTKITLSVIWMMKIFQNTLRWPETLILKS
KLEDTCTLILWTLTELIASVHLRTCQSTKSR*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	196055044-196055883(+) 196055069-196052660(+)
Potential amino acid sequence	MKRALEEQYGGEEELPHTNPGLDTAPLRFTKHSNAYMLVYIRESDKDNIICDLDDEDISEHLKV ARDFDIKEQIGRHMHFDLVDFDRVNSFRAPKNMSINEVKINDRYEFPLQLDLDRDDGKYLSPDA DRSVRNLYTLHSVLVHSGGVHGGHYYAFIRPKLSDQWYKFEDERVTKEDMKRALEEQYGGEEEL PHTNPGLDTAPLRFTKHSNAYMLVYIRESDKDNIICDLDDEDISEHLKVARDFDIKEQIGRHMH FDLVDFDRVNSFRAPKNMSINEVKINDRYEFPLQLDLDRDDGKYLSPDADRSVRNLYTLHSVLV HSGGVHGGHYYAFIRPKLSDQWYKFEDERVTKEDMKRALEEQYGGEEELPHTNPGLDTAPLRFT KHSNAYMLVYIRESDKDNIICDLDDEDISEHLKVARDFDIKEQIGRHMHFDLVDFDRVNSFRAP KNMSINEVKINDRYEFPLQLDLDRDDGKYLSPDADRSVRNLYTLHSVLVHSGGVHGGHYYAFIR PKLSDQWYKFEDERVTKEDMKRALEEQYGGEEELPHTNPGLDTAPLRFTKHSNAYMLVYIRESD KDNIICDLDDEDISEHLKVARDFDIKEQIGRHMHFDLVDFDRVNSFRAPKNMSINEVK(+) MVVKKSSRIPTLGWILHRLDLPSIQMLTCLFTFEKVTKITLSVIWMMKIFQNTLRWPETLILKS KLEDTCTLILWTLTELIASVHLRTCQSTKSR*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b

circRNA

Detail information of Zm00001d043312_circ_g.3

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