Plant Circular RNA Database

Detail information of Zm00001d021015_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d021015_circ_g.1
					
						ID in PlantcircBase
						zma_circ_009386
					
						Alias
						zma_circ_0002573
					
						Organism
						
							Zea mays						
					
						Position
						
							chr7: 140492080-140493702  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d021015						
					
						Parent gene annotation
						
							DNA topoisomerase 3-alpha
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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
						Zm00001d021015_T004:5
Zm00001d021015_T009:5
Zm00001d021015_T003:5
Zm00001d021015_T005:5
Zm00001d021015_T006:5
Zm00001d021015_T002:5
Zm00001d021015_T012:5
Zm00001d021015_T008:5
Zm00001d021015_T011:5

General Information
CircRNA Name	Zm00001d021015_circ_g.1
ID in PlantcircBase	zma_circ_009386
Alias	zma_circ_0002573
Organism	Zea mays
Position	chr7: 140492080-140493702 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d021015
Parent gene annotation	DNA topoisomerase 3-alpha
Parent gene strand	+
Alternative splicing	NA
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	Zm00001d021015_T004:5 Zm00001d021015_T009:5 Zm00001d021015_T003:5 Zm00001d021015_T005:5 Zm00001d021015_T006:5 Zm00001d021015_T002:5 Zm00001d021015_T012:5 Zm00001d021015_T008:5 Zm00001d021015_T011:5

			
						 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  
						
							ATGTGGTCGGTATATGAAGTACATTTCCACTCAGCCAATGAGGTTGTACTGTATAACTTGTGAG
GATGTCTATTATCTTCCTCAGAACGGTTCAATTAAGttatcctcgtacagagagcactgcatat
ccgtcatcatttgattttcgaggtgcacttgctgcactattaaataatcctctatggtccaatg
atgtccgg

									
								

					

						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: 970
Transcript exons: 140492080-140492358,140492555-140492723,140492808-140492
936,140493067-140493279,140493523-140493702
TTATCCTCGTACAGAGAGCACTGCATATCCGTCATCATTTGATTTTCGAGGTGCACTTGCTGCA
CTATTAAATAATCCTCTATGGTCCAATGATGTCCGGAAATTACTGGATGCTGGTTTTGTTAAGC
CTCGTCAAGGTCATGATGCTGGGGACCATCCTCCAATCACTCCAATGAGGTCAGCAACAGAAGC
ATCTTTGGGAACTGATGCTTGGAGGCTGTACCAATACATATGCCAGCACTTCATTGGAACTGTT
AGTCCTGATTGTAGATATACAAGGACTGCCATTGAGTTCACTTCAGGTGGTGAAACATTCCACT
GTGTTGGGTATCGAGTCACTTCTAAAGGATTTACATCTATCATGCCATGGCTGGCTGTCAGCGA
GAACAGTCTTCCTGCATTTAAAAAGGGAGACTCTGTTAGTATTCATAAGGCTGACATATATGAG
GGAAGCACTACACCACCTGATTACCTCACTGAAAGTGAATTGATTTCCCTCATGGAGAAGAATG
GCATAGGTACAGATGCATCAATTCCTGTACATATAAACAACATTTGTGAACGTAATTATGTTCA
GGTGAATTCTGGAAGAAGGTTAGTACCAACACCCCTGGGAACTACGTTGATAAGAGGGTATCAG
TGTATTGATGCTGATCTCTGCTTGCCAGATATCAGAAGCTTTATTGAGCAACAGATTACTCTAA
TTGCAAAAGGAAAAGCTGATCATCTTCGAGTTGTTCAACATGTCATTCAGCAATTTATGAAAAA
GTACTCTTACTTTGTGAAAAAGATTGAAAACATGGATGCTCTGTTCGAGGCACAGTTTTCACCT
TTGGCAGACTCTGGGCGCCTACTAAGCAAGTGTGGAAAATGTGGTCGGTATATGAAGTACATTT
CCACTCAGCCAATGAGGTTGTACTGTATAACTTGTGAGGATGTCTATTATCTTCCTCAGAACGG
TTCAATTAAG
						
					

						Genomic sequence
						
							TTATCCTCGTACAGAGAGCACTGCATATCCGTCATCATTTGATTTTCGAGGTGCACTTGCTGCA
CTATTAAATAATCCTCTATGGTCCAATGATGTCCGGAAATTACTGGATGCTGGTTTTGTTAAGC
CTCGTCAAGGTCATGATGCTGGGGACCATCCTCCAATCACTCCAATGAGGTCAGCAACAGAAGC
ATCTTTGGGAACTGATGCTTGGAGGCTGTACCAATACATATGCCAGCACTTCATTGGAACTGTT
AGTCCTGATTGTAGATATACAAGGTAGTTTGTCTCCTTATTGTTTCATAGCTAGATAAATCATT
TGTGTCTTTGTTCTGTTACAGTTCACAAGCTTCTTATAAACTATAACTAAGCTAGTTATTGATA
TTTCCTTGCACTATGCTCTTATCTGGATATCTAGTGCTTTTCTATTATTTGAAATGCAAAATAT
CCCTTTCTAAATAAACATGTTTTTCAGGACTGCCATTGAGTTCACTTCAGGTGGTGAAACATTC
CACTGTGTTGGGTATCGAGTCACTTCTAAAGGATTTACATCTATCATGCCATGGCTGGCTGTCA
GCGAGAACAGTCTTCCTGCATTTAAAAAGGGAGACTCTGTTAGTATTCATAAGGCTGACATATA
TGAGGTAAGGTCTATCAGTTTGCTCAAACCACATGCACTTAACTTTTATCAGGATATGATGTTG
ATCAATCATAATTCTTTGTTGAAGGGAAGCACTACACCACCTGATTACCTCACTGAAAGTGAAT
TGATTTCCCTCATGGAGAAGAATGGCATAGGTACAGATGCATCAATTCCTGTACATATAAACAA
CATTTGTGAACGTAATTATGTTCAGGTTAGTTGAGCTGTTTTCTACGAGATCTTCAGAGCATCA
TATGCTGTGAATCTTTTGCATGCAAGTCTACTATTAAGTATGTAAATGTACAAAAAGCTGAATG
CCTCTAAGGCTCTAATCTTTCTTGAAGGTGAATTCTGGAAGAAGGTTAGTACCAACACCCCTGG
GAACTACGTTGATAAGAGGGTATCAGTGTATTGATGCTGATCTCTGCTTGCCAGATATCAGAAG
CTTTATTGAGCAACAGATTACTCTAATTGCAAAAGGAAAAGCTGATCATCTTCGAGTTGTTCAA
CATGTCATTCAGCAATTTATGAAAAAGTACTCTTACTTTGTGAAAAAGGTGACATTTCTTGTTG
ATAATAATAATCTATGAGACTGTTGCTGTCTTCCATGGTATTTGGCAAAGTTTATACTCCAAAA
TGGTCAATAGTACTTTACATTTGCAGATATCTTTATTCTTTTAGTTTTAATACATATTTAAGAT
TCCCTGTTCTTAACAACCAAAATTCATTGATATAAGACATCAGCTATGTACTGCTATAATGCTA
TTTCAACTTCTTTAGAATGAATGTACTTCTTGCAGATTGAAAACATGGATGCTCTGTTCGAGGC
ACAGTTTTCACCTTTGGCAGACTCTGGGCGCCTACTAAGCAAGTGTGGAAAATGTGGTCGGTAT
ATGAAGTACATTTCCACTCAGCCAATGAGGTTGTACTGTATAACTTGTGAGGATGTCTATTATC
TTCCTCAGAACGGTTCAATTAAG
						
					

			
		

Sequences
Splice junction sequence	ATGTGGTCGGTATATGAAGTACATTTCCACTCAGCCAATGAGGTTGTACTGTATAACTTGTGAG GATGTCTATTATCTTCCTCAGAACGGTTCAATTAAGttatcctcgtacagagagcactgcatat ccgtcatcatttgattttcgaggtgcacttgctgcactattaaataatcctctatggtccaatg atgtccgg
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: 970 Transcript exons: 140492080-140492358,140492555-140492723,140492808-140492 936,140493067-140493279,140493523-140493702 TTATCCTCGTACAGAGAGCACTGCATATCCGTCATCATTTGATTTTCGAGGTGCACTTGCTGCA CTATTAAATAATCCTCTATGGTCCAATGATGTCCGGAAATTACTGGATGCTGGTTTTGTTAAGC CTCGTCAAGGTCATGATGCTGGGGACCATCCTCCAATCACTCCAATGAGGTCAGCAACAGAAGC ATCTTTGGGAACTGATGCTTGGAGGCTGTACCAATACATATGCCAGCACTTCATTGGAACTGTT AGTCCTGATTGTAGATATACAAGGACTGCCATTGAGTTCACTTCAGGTGGTGAAACATTCCACT GTGTTGGGTATCGAGTCACTTCTAAAGGATTTACATCTATCATGCCATGGCTGGCTGTCAGCGA GAACAGTCTTCCTGCATTTAAAAAGGGAGACTCTGTTAGTATTCATAAGGCTGACATATATGAG GGAAGCACTACACCACCTGATTACCTCACTGAAAGTGAATTGATTTCCCTCATGGAGAAGAATG GCATAGGTACAGATGCATCAATTCCTGTACATATAAACAACATTTGTGAACGTAATTATGTTCA GGTGAATTCTGGAAGAAGGTTAGTACCAACACCCCTGGGAACTACGTTGATAAGAGGGTATCAG TGTATTGATGCTGATCTCTGCTTGCCAGATATCAGAAGCTTTATTGAGCAACAGATTACTCTAA TTGCAAAAGGAAAAGCTGATCATCTTCGAGTTGTTCAACATGTCATTCAGCAATTTATGAAAAA GTACTCTTACTTTGTGAAAAAGATTGAAAACATGGATGCTCTGTTCGAGGCACAGTTTTCACCT TTGGCAGACTCTGGGCGCCTACTAAGCAAGTGTGGAAAATGTGGTCGGTATATGAAGTACATTT CCACTCAGCCAATGAGGTTGTACTGTATAACTTGTGAGGATGTCTATTATCTTCCTCAGAACGG TTCAATTAAG
Genomic sequence	TTATCCTCGTACAGAGAGCACTGCATATCCGTCATCATTTGATTTTCGAGGTGCACTTGCTGCA CTATTAAATAATCCTCTATGGTCCAATGATGTCCGGAAATTACTGGATGCTGGTTTTGTTAAGC CTCGTCAAGGTCATGATGCTGGGGACCATCCTCCAATCACTCCAATGAGGTCAGCAACAGAAGC ATCTTTGGGAACTGATGCTTGGAGGCTGTACCAATACATATGCCAGCACTTCATTGGAACTGTT AGTCCTGATTGTAGATATACAAGGTAGTTTGTCTCCTTATTGTTTCATAGCTAGATAAATCATT TGTGTCTTTGTTCTGTTACAGTTCACAAGCTTCTTATAAACTATAACTAAGCTAGTTATTGATA TTTCCTTGCACTATGCTCTTATCTGGATATCTAGTGCTTTTCTATTATTTGAAATGCAAAATAT CCCTTTCTAAATAAACATGTTTTTCAGGACTGCCATTGAGTTCACTTCAGGTGGTGAAACATTC CACTGTGTTGGGTATCGAGTCACTTCTAAAGGATTTACATCTATCATGCCATGGCTGGCTGTCA GCGAGAACAGTCTTCCTGCATTTAAAAAGGGAGACTCTGTTAGTATTCATAAGGCTGACATATA TGAGGTAAGGTCTATCAGTTTGCTCAAACCACATGCACTTAACTTTTATCAGGATATGATGTTG ATCAATCATAATTCTTTGTTGAAGGGAAGCACTACACCACCTGATTACCTCACTGAAAGTGAAT TGATTTCCCTCATGGAGAAGAATGGCATAGGTACAGATGCATCAATTCCTGTACATATAAACAA CATTTGTGAACGTAATTATGTTCAGGTTAGTTGAGCTGTTTTCTACGAGATCTTCAGAGCATCA TATGCTGTGAATCTTTTGCATGCAAGTCTACTATTAAGTATGTAAATGTACAAAAAGCTGAATG CCTCTAAGGCTCTAATCTTTCTTGAAGGTGAATTCTGGAAGAAGGTTAGTACCAACACCCCTGG GAACTACGTTGATAAGAGGGTATCAGTGTATTGATGCTGATCTCTGCTTGCCAGATATCAGAAG CTTTATTGAGCAACAGATTACTCTAATTGCAAAAGGAAAAGCTGATCATCTTCGAGTTGTTCAA CATGTCATTCAGCAATTTATGAAAAAGTACTCTTACTTTGTGAAAAAGGTGACATTTCTTGTTG ATAATAATAATCTATGAGACTGTTGCTGTCTTCCATGGTATTTGGCAAAGTTTATACTCCAAAA TGGTCAATAGTACTTTACATTTGCAGATATCTTTATTCTTTTAGTTTTAATACATATTTAAGAT TCCCTGTTCTTAACAACCAAAATTCATTGATATAAGACATCAGCTATGTACTGCTATAATGCTA TTTCAACTTCTTTAGAATGAATGTACTTCTTGCAGATTGAAAACATGGATGCTCTGTTCGAGGC ACAGTTTTCACCTTTGGCAGACTCTGGGCGCCTACTAAGCAAGTGTGGAAAATGTGGTCGGTAT ATGAAGTACATTTCCACTCAGCCAATGAGGTTGTACTGTATAACTTGTGAGGATGTCTATTATC TTCCTCAGAACGGTTCAATTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.189278921

Conservation Information
Conserved circRNAs	NA
PMCS	0.189278921

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							140492253-140492118(+)
140493669-140492118(+)
						
						Potential amino acid sequence
						
							MRSATEASLGTDAWRLYQYICQHFIGTVSPDCRYTRTAIEFTSGGETFHCVGYRVTSKGFTSIM
PWLAVSENSLPAFKKGDSVSIHKADIYEGSTTPPDYLTESELISLMEKNGIGTDASIPVHINNI
CERNYVQLNASKALIFLEGEFWKKIENMDALFEAQFSPLADSGRLLSKCGKCGRYMKYISTQPM
RLYCITCEDVYYLPQNGSIKLSSYREHCISVII*(+)
MSIIFLRTVQLSYPRTESTAYPSSFDFRGALAALLNNPLWSNDVRKLLDAGFVKPRQGHDAGDH
PPITPMRSATEASLGTDAWRLYQYICQHFIGTVSPDCRYTRTAIEFTSGGETFHCVGYRVTSKG
FTSIMPWLAVSENSLPAFKKGDSVSIHKADIYEGSTTPPDYLTESELISLMEKNGIGTDASIPV
HINNICERNYVQLNASKALIFLEGEFWKKIENMDALFEAQFSPLADSGRLLSKCGKCGRYMKYI
STQPMRLYCITCEDVYYLPQNGSIKLSSYREHCISVII*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	140492253-140492118(+) 140493669-140492118(+)
Potential amino acid sequence	MRSATEASLGTDAWRLYQYICQHFIGTVSPDCRYTRTAIEFTSGGETFHCVGYRVTSKGFTSIM PWLAVSENSLPAFKKGDSVSIHKADIYEGSTTPPDYLTESELISLMEKNGIGTDASIPVHINNI CERNYVQLNASKALIFLEGEFWKKIENMDALFEAQFSPLADSGRLLSKCGKCGRYMKYISTQPM RLYCITCEDVYYLPQNGSIKLSSYREHCISVII(+) MSIIFLRTVQLSYPRTESTAYPSSFDFRGALAALLNNPLWSNDVRKLLDAGFVKPRQGHDAGDH PPITPMRSATEASLGTDAWRLYQYICQHFIGTVSPDCRYTRTAIEFTSGGETFHCVGYRVTSKG FTSIMPWLAVSENSLPAFKKGDSVSIHKADIYEGSTTPPDYLTESELISLMEKNGIGTDASIPV HINNICERNYVQLNASKALIFLEGEFWKKIENMDALFEAQFSPLADSGRLLSKCGKCGRYMKYI STQPMRLYCITCEDVYYLPQNGSIKLSSYREHCISVII(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d021015_circ_g.1

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