Plant Circular RNA Database

Detail information of Zm00001d010716_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d010716_circ_g.2
					
						ID in PlantcircBase
						zma_circ_009690
					
						Alias
						zma_circ_0002818
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 125530556-125532164  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d010716						
					
						Parent gene annotation
						
							TRAF-like superfamily protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d010716_circ_g.1 Zm00001d010716_circ_g.3 						
					
						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  
						
							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
						Zm00001d010716_T013:3
Zm00001d010716_T021:3
Zm00001d010716_T029:3
Zm00001d010716_T015:3
Zm00001d010716_T020:3
Zm00001d010716_T026:3
Zm00001d010716_T008:3
Zm00001d010716_T016:3
Zm00001d010716_T002:4
Zm00001d010716_T044:3
Zm00001d010716_T003:3
Zm00001d010716_T004:3
Zm00001d010716_T012:3
Zm00001d010716_T006:3
Zm00001d010716_T018:2
Zm00001d010716_T009:3
Zm00001d010716_T038:3
Zm00001d010716_T017:3
Zm00001d010716_T053:3
Zm00001d010716_T024:3
Zm00001d010716_T027:3
Zm00001d010716_T047:3
Zm00001d010716_T025:3
Zm00001d010716_T014:3
Zm00001d010716_T005:3
Zm00001d010716_T019:3
Zm00001d010716_T023:3
Zm00001d010716_T001:3
Zm00001d010716_T010:3
Zm00001d010716_T028:3
Zm00001d010716_T022:3
Zm00001d010716_T052:3
Zm00001d010716_T030:3

General Information
CircRNA Name	Zm00001d010716_circ_g.2
ID in PlantcircBase	zma_circ_009690
Alias	zma_circ_0002818
Organism	Zea mays
Position	chr8: 125530556-125532164 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d010716
Parent gene annotation	TRAF-like superfamily protein
Parent gene strand	-
Alternative splicing	Zm00001d010716_circ_g.1 Zm00001d010716_circ_g.3
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	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	Zm00001d010716_T013:3 Zm00001d010716_T021:3 Zm00001d010716_T029:3 Zm00001d010716_T015:3 Zm00001d010716_T020:3 Zm00001d010716_T026:3 Zm00001d010716_T008:3 Zm00001d010716_T016:3 Zm00001d010716_T002:4 Zm00001d010716_T044:3 Zm00001d010716_T003:3 Zm00001d010716_T004:3 Zm00001d010716_T012:3 Zm00001d010716_T006:3 Zm00001d010716_T018:2 Zm00001d010716_T009:3 Zm00001d010716_T038:3 Zm00001d010716_T017:3 Zm00001d010716_T053:3 Zm00001d010716_T024:3 Zm00001d010716_T027:3 Zm00001d010716_T047:3 Zm00001d010716_T025:3 Zm00001d010716_T014:3 Zm00001d010716_T005:3 Zm00001d010716_T019:3 Zm00001d010716_T023:3 Zm00001d010716_T001:3 Zm00001d010716_T010:3 Zm00001d010716_T028:3 Zm00001d010716_T022:3 Zm00001d010716_T052:3 Zm00001d010716_T030:3

			
						 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  
						
							AAAACGTCGGTATATTTGTTCCACATTTGTCATATAGATGCGGATCAATTCTCTCCGGTAAGGA
CGATCAAGGCAACGAAAAGGTCTATCCACTTTCTCCctaaatatatgagatagcacaaatgtct
ctagtatcttctgaccaagctcagttagacgtctttcctcacgctccatagaaacattgtaaac
ctcaccag

									
								

					

						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: 633
Transcript exons: 125530556-125530665,125531520-125531883,125532006-125532
164
CTAAATATATGAGATAGCACAAATGTCTCTAGTATCTTCTGACCAAGCTCAGTTAGACGTCTTT
CCTCACGCTCCATAGAAACATTGTAAACCTCACCAGAACTTCCATCCTTCATGCGGGGTTGGGA
AGTTTTATCATCCTTGGGGGCTAAAGGTTGACAAGGCAAGGGTTCTAAGGCAGCTCTCTCAAGC
AAAGCTATGACATCATCAGCCAAAATAAACATGTCCATGTCAACATGGACCATAGGCGCAGGTA
GTTCTTCCAAATCTGCTAATTTTGTTTTGCCTTTCCTGCCCTTCATCTGGTATTCAAGTGCCTT
CAGACTCGTATACAAGGAGTCCATCACTAATGTGGAAGTAACTTCTTTCTCTACAAAGAATTGC
TTCACTAACATTTTCAATATGGTGTCAGTCTTTTCCCTGGACATGCGATGCCTGGTGTTTGGGT
CAATTGCTGACCAGAAAGCACGAAAACTGGACCATTTTATTTTGTCCTCAATGAGCTTGCTTAA
TTTACTTCTTCGCTCCTCAATAAAACGTCGGTATATTTGTTCCACATTTGTCATATAGATGCGG
ATCAATTCTCTCCGGTAAGGACGATCAAGGCAACGAAAAGGTCTATCCACTTTCTCC
						
					

						Genomic sequence
						
							CTAAATATATGAGATAGCACAAATGTCTCTAGTATCTTCTGACCAAGCTCAGTTAGACGTCTTT
CCTCACGCTCCATAGAAACATTGTAAACCTCACCAGAACTTCCATCCTACGAAAACGAGCATCA
CAAAAAAAATGAGTAAAATGCACTTCTGGTCCTTCAACTTGTCTGCCTGTGTCAACACGGTCCA
TAAACTTTTAAAGTATGTCTTTTAAGGACCCAATCTTTGTTCGGGTCTCTATTACGTCCTAACG
GATTGTTGTGTCCCACATATCAGTTGCCGTTGTCTGTTGGATCCCACCCACCCTTCTATCTCCT
TCCTCGACGACTAACATGTGGGCCATAACAACCCGTTAGGACCTGATAGAGACCCGAACAAATA
TTGATCTTTTAAGAGGCATACTTTAAAAGTTTATGGACCGTGTTGACACAGCCAGACAAGTTTA
AGGGTCGGAACTCGGAAGTGTACTTCGCTCCAAATAAATGATTCTATGCAATAGTGATTTCATT
TCTCAAAATATAACAGAATCAAGCAAGGCTATGTGCTTATAAAGAATATAGCAAGTAGTCAATA
CCATGCGATGAAAACAAGCAAACTGTTGACCAACCTACCAAGATAGTGCAGAGAACATACTAAT
TGCATGCTCAAATATCTGTTTGTATAAACAGAACATATCTCAGAAAATATCACATGCTAGGGTG
TTCTGACTGGAAATGAAACCCCTATCCAATATTTGTGCATGTGATGAGAGTAGTAGTAAACGCA
ATTATTAACTTGTTCATTAAACCAATCCAGACGAGTTCAAAAGATTTACCTGCAAGTAAGCATG
AGAAACTAGCAAGAAAATTGTCCTAACATAATTGATCCGAGGTTCTAGGGCCAAGAAAGTAGAC
ACCTACTAAGATGAGCAAAAAGTGGAAATAAAACCAAGCTATAACATATCAAATTATATATTCC
CTACCTTCATGCGGGGTTGGGAAGTTTTATCATCCTTGGGGGCTAAAGGTTGACAAGGCAAGGG
TTCTAAGGCAGCTCTCTCAAGCAAAGCTATGACATCATCAGCCAAAATAAACATGTCCATGTCA
ACATGGACCATAGGCGCAGGTAGTTCTTCCAAATCTGCTAATTTTGTTTTGCCTTTCCTGCCCT
TCATCTGGTATTCAAGTGCCTTCAGACTCGTATACAAGGAGTCCATCACTAATGTGGAAGTAAC
TTCTTTCTCTACAAAGAATTGCTTCACTAACATTTTCAATATGGTGTCAGTCTTTTCCCTGGAC
ATGCGATGCCTGGTGTTTGGGTCAATTGCTGACCAGAAAGCACGAAAACTGCAAGACCAACAAA
GATTTCAATGGGAGGAAGTATATAAAATATATAACAACCGCAAGTGACACTGAGTCACTGGCCA
GTTTATTATGACAGATTAATCTAGGAAAGCCAACTGTCTAACCTGGACCATTTTATTTTGTCCT
CAATGAGCTTGCTTAATTTACTTCTTCGCTCCTCAATAAAACGTCGGTATATTTGTTCCACATT
TGTCATATAGATGCGGATCAATTCTCTCCGGTAAGGACGATCAAGGCAACGAAAAGGTCTATCC
ACTTTCTCC
						
					

			
		

Sequences
Splice junction sequence	AAAACGTCGGTATATTTGTTCCACATTTGTCATATAGATGCGGATCAATTCTCTCCGGTAAGGA CGATCAAGGCAACGAAAAGGTCTATCCACTTTCTCCctaaatatatgagatagcacaaatgtct ctagtatcttctgaccaagctcagttagacgtctttcctcacgctccatagaaacattgtaaac ctcaccag
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: 633 Transcript exons: 125530556-125530665,125531520-125531883,125532006-125532 164 CTAAATATATGAGATAGCACAAATGTCTCTAGTATCTTCTGACCAAGCTCAGTTAGACGTCTTT CCTCACGCTCCATAGAAACATTGTAAACCTCACCAGAACTTCCATCCTTCATGCGGGGTTGGGA AGTTTTATCATCCTTGGGGGCTAAAGGTTGACAAGGCAAGGGTTCTAAGGCAGCTCTCTCAAGC AAAGCTATGACATCATCAGCCAAAATAAACATGTCCATGTCAACATGGACCATAGGCGCAGGTA GTTCTTCCAAATCTGCTAATTTTGTTTTGCCTTTCCTGCCCTTCATCTGGTATTCAAGTGCCTT CAGACTCGTATACAAGGAGTCCATCACTAATGTGGAAGTAACTTCTTTCTCTACAAAGAATTGC TTCACTAACATTTTCAATATGGTGTCAGTCTTTTCCCTGGACATGCGATGCCTGGTGTTTGGGT CAATTGCTGACCAGAAAGCACGAAAACTGGACCATTTTATTTTGTCCTCAATGAGCTTGCTTAA TTTACTTCTTCGCTCCTCAATAAAACGTCGGTATATTTGTTCCACATTTGTCATATAGATGCGG ATCAATTCTCTCCGGTAAGGACGATCAAGGCAACGAAAAGGTCTATCCACTTTCTCC
Genomic sequence	CTAAATATATGAGATAGCACAAATGTCTCTAGTATCTTCTGACCAAGCTCAGTTAGACGTCTTT CCTCACGCTCCATAGAAACATTGTAAACCTCACCAGAACTTCCATCCTACGAAAACGAGCATCA CAAAAAAAATGAGTAAAATGCACTTCTGGTCCTTCAACTTGTCTGCCTGTGTCAACACGGTCCA TAAACTTTTAAAGTATGTCTTTTAAGGACCCAATCTTTGTTCGGGTCTCTATTACGTCCTAACG GATTGTTGTGTCCCACATATCAGTTGCCGTTGTCTGTTGGATCCCACCCACCCTTCTATCTCCT TCCTCGACGACTAACATGTGGGCCATAACAACCCGTTAGGACCTGATAGAGACCCGAACAAATA TTGATCTTTTAAGAGGCATACTTTAAAAGTTTATGGACCGTGTTGACACAGCCAGACAAGTTTA AGGGTCGGAACTCGGAAGTGTACTTCGCTCCAAATAAATGATTCTATGCAATAGTGATTTCATT TCTCAAAATATAACAGAATCAAGCAAGGCTATGTGCTTATAAAGAATATAGCAAGTAGTCAATA CCATGCGATGAAAACAAGCAAACTGTTGACCAACCTACCAAGATAGTGCAGAGAACATACTAAT TGCATGCTCAAATATCTGTTTGTATAAACAGAACATATCTCAGAAAATATCACATGCTAGGGTG TTCTGACTGGAAATGAAACCCCTATCCAATATTTGTGCATGTGATGAGAGTAGTAGTAAACGCA ATTATTAACTTGTTCATTAAACCAATCCAGACGAGTTCAAAAGATTTACCTGCAAGTAAGCATG AGAAACTAGCAAGAAAATTGTCCTAACATAATTGATCCGAGGTTCTAGGGCCAAGAAAGTAGAC ACCTACTAAGATGAGCAAAAAGTGGAAATAAAACCAAGCTATAACATATCAAATTATATATTCC CTACCTTCATGCGGGGTTGGGAAGTTTTATCATCCTTGGGGGCTAAAGGTTGACAAGGCAAGGG TTCTAAGGCAGCTCTCTCAAGCAAAGCTATGACATCATCAGCCAAAATAAACATGTCCATGTCA ACATGGACCATAGGCGCAGGTAGTTCTTCCAAATCTGCTAATTTTGTTTTGCCTTTCCTGCCCT TCATCTGGTATTCAAGTGCCTTCAGACTCGTATACAAGGAGTCCATCACTAATGTGGAAGTAAC TTCTTTCTCTACAAAGAATTGCTTCACTAACATTTTCAATATGGTGTCAGTCTTTTCCCTGGAC ATGCGATGCCTGGTGTTTGGGTCAATTGCTGACCAGAAAGCACGAAAACTGCAAGACCAACAAA GATTTCAATGGGAGGAAGTATATAAAATATATAACAACCGCAAGTGACACTGAGTCACTGGCCA GTTTATTATGACAGATTAATCTAGGAAAGCCAACTGTCTAACCTGGACCATTTTATTTTGTCCT CAATGAGCTTGCTTAATTTACTTCTTCGCTCCTCAATAAAACGTCGGTATATTTGTTCCACATT TGTCATATAGATGCGGATCAATTCTCTCCGGTAAGGACGATCAAGGCAACGAAAAGGTCTATCC ACTTTCTCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.207249073

Conservation Information
Conserved circRNAs	NA
PMCS	0.207249073

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							125532099-125530558(-)
						
						Potential amino acid sequence
						
							MTNVEQIYRRFIEERRSKLSKLIEDKIKWSSFRAFWSAIDPNTRHRMSREKTDTILKMLVKQFF
VEKEVTSTLVMDSLYTSLKALEYQMKGRKGKTKLADLEELPAPMVHVDMDMFILADDVIALLER
AALEPLPCQPLAPKDDKTSQPRMKDGSSGEVYNVSMEREERRLTELGQKILETFVLSHIFREKV
DRPFRCLDRPYRRELIRIYMTNVEQIYRRFIEERRSKLSKLIEDKIKWSSFRAFWSAIDPNTRH
RMSREKTDTILKMLVKQFFVEKEVTSTLVMDSLYTSLKALEYQMKGRKGKTKLADLEELPAPMV
HVDMDMFILADDVIALLERAALEPLPCQPLAPKDDKTSQPRMKDGSSGEVYNVSMEREERRLTE
LGQKILETFVLSHIFREKVDRPFRCLDRPYRRELIRIYMTNVEQIYRRFIEERRSKLSKLIEDK
IKWSSFRAFWSAIDPNTRHRMSREKTDTILKMLVKQFFVEKEVTSTLVMDSLYTSLKALEYQMK
GRKGKTKLADLEELPAPMVHVDMDMFILADDVIALLERAALEPLPCQPLAPKDDKTSQPRMKDG
SSGEVYNVSMEREERRLTELGQKILETFVLSHIFREKVDRPFRCLDRPYRRELIRIYMTNVEQI
YRRFIEERRSKLSKLIEDKIKWSSFRAFWSAIDPNTRHRMSREKTDTILKMLVKQFFVEKEVTS
TLVMDSLYTSLKALEYQMKGRKGKTKLADLEELPAPMVHVDMDMFILADDVIALLERAALEPLP
CQPLAPKDDKTSQPRMKDGSSGEVYNVSMEREERRLTELGQKILETFVLSHIF(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	125532099-125530558(-)
Potential amino acid sequence	MTNVEQIYRRFIEERRSKLSKLIEDKIKWSSFRAFWSAIDPNTRHRMSREKTDTILKMLVKQFF VEKEVTSTLVMDSLYTSLKALEYQMKGRKGKTKLADLEELPAPMVHVDMDMFILADDVIALLER AALEPLPCQPLAPKDDKTSQPRMKDGSSGEVYNVSMEREERRLTELGQKILETFVLSHIFREKV DRPFRCLDRPYRRELIRIYMTNVEQIYRRFIEERRSKLSKLIEDKIKWSSFRAFWSAIDPNTRH RMSREKTDTILKMLVKQFFVEKEVTSTLVMDSLYTSLKALEYQMKGRKGKTKLADLEELPAPMV HVDMDMFILADDVIALLERAALEPLPCQPLAPKDDKTSQPRMKDGSSGEVYNVSMEREERRLTE LGQKILETFVLSHIFREKVDRPFRCLDRPYRRELIRIYMTNVEQIYRRFIEERRSKLSKLIEDK IKWSSFRAFWSAIDPNTRHRMSREKTDTILKMLVKQFFVEKEVTSTLVMDSLYTSLKALEYQMK GRKGKTKLADLEELPAPMVHVDMDMFILADDVIALLERAALEPLPCQPLAPKDDKTSQPRMKDG SSGEVYNVSMEREERRLTELGQKILETFVLSHIFREKVDRPFRCLDRPYRRELIRIYMTNVEQI YRRFIEERRSKLSKLIEDKIKWSSFRAFWSAIDPNTRHRMSREKTDTILKMLVKQFFVEKEVTS TLVMDSLYTSLKALEYQMKGRKGKTKLADLEELPAPMVHVDMDMFILADDVIALLERAALEPLP CQPLAPKDDKTSQPRMKDGSSGEVYNVSMEREERRLTELGQKILETFVLSHIF(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d010716_circ_g.2

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