Plant Circular RNA Database

Detail information of Zm00001d001978_circ_g.4

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d001978_circ_g.4
					

						ID in PlantcircBase
						zma_circ_007021
					

						Alias
						zma_circ_0001041, GRMZM2G017654_C3
					

						Organism
						
							Zea mays						
					

						Position
						
							chr2: 3817610-3819097  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						find_circ, CIRI2
					

						Parent gene
						
							Zm00001d001978						
					

						Parent gene annotation
						
							MAP3K epsilon protein kinase 1
							
					

						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
						Zm00001d001978_T090:5
Zm00001d001978_T088:5
Zm00001d001978_T004:2
Zm00001d001978_T137:1
Zm00001d001978_T121:5
Zm00001d001978_T089:5
Zm00001d001978_T014:5
Zm00001d001978_T006:5
Zm00001d001978_T003:5
Zm00001d001978_T079:3
Zm00001d001978_T039:4
Zm00001d001978_T117:5
Zm00001d001978_T103:5
Zm00001d001978_T084:5
Zm00001d001978_T122:5
Zm00001d001978_T015:5
Zm00001d001978_T055:5
Zm00001d001978_T005:4
Zm00001d001978_T011:5
Zm00001d001978_T007:5
Zm00001d001978_T017:5
Zm00001d001978_T018:5
Zm00001d001978_T026:5
Zm00001d001978_T073:5
Zm00001d001978_T058:5
Zm00001d001978_T028:5
Zm00001d001978_T081:5
Zm00001d001978_T109:5
Zm00001d001978_T076:5
Zm00001d001978_T077:5
Zm00001d001978_T008:4
Zm00001d001978_T115:5
Zm00001d001978_T080:5
Zm00001d001978_T013:5
Zm00001d001978_T131:5
Zm00001d001978_T111:5
Zm00001d001978_T120:5
Zm00001d001978_T104:5
Zm00001d001978_T010:5
Zm00001d001978_T134:5
Zm00001d001978_T037:5
Zm00001d001978_T091:5
Zm00001d001978_T002:5
Zm00001d001978_T022:5
Zm00001d001978_T118:5
Zm00001d001978_T096:5
Zm00001d001978_T130:5
Zm00001d001978_T074:5
Zm00001d001978_T016:5
Zm00001d001978_T033:4
Zm00001d001978_T012:5
Zm00001d001978_T124:5
Zm00001d001978_T031:5
Zm00001d001978_T071:5
Zm00001d001978_T133:4
Zm00001d001978_T107:5
Zm00001d001978_T101:5
Zm00001d001978_T042:5
Zm00001d001978_T114:5
Zm00001d001978_T009:5
Zm00001d001978_T030:5
Zm00001d001978_T075:5
Zm00001d001978_T087:5
Zm00001d001978_T125:5
Zm00001d001978_T049:5
Zm00001d001978_T060:5

					

			
		

General Information
CircRNA Name	Zm00001d001978_circ_g.4
ID in PlantcircBase	zma_circ_007021
Alias	zma_circ_0001041, GRMZM2G017654_C3
Organism	Zea mays
Position	chr2: 3817610-3819097 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d001978
Parent gene annotation	MAP3K epsilon protein kinase 1
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	Zm00001d001978_T090:5 Zm00001d001978_T088:5 Zm00001d001978_T004:2 Zm00001d001978_T137:1 Zm00001d001978_T121:5 Zm00001d001978_T089:5 Zm00001d001978_T014:5 Zm00001d001978_T006:5 Zm00001d001978_T003:5 Zm00001d001978_T079:3 Zm00001d001978_T039:4 Zm00001d001978_T117:5 Zm00001d001978_T103:5 Zm00001d001978_T084:5 Zm00001d001978_T122:5 Zm00001d001978_T015:5 Zm00001d001978_T055:5 Zm00001d001978_T005:4 Zm00001d001978_T011:5 Zm00001d001978_T007:5 Zm00001d001978_T017:5 Zm00001d001978_T018:5 Zm00001d001978_T026:5 Zm00001d001978_T073:5 Zm00001d001978_T058:5 Zm00001d001978_T028:5 Zm00001d001978_T081:5 Zm00001d001978_T109:5 Zm00001d001978_T076:5 Zm00001d001978_T077:5 Zm00001d001978_T008:4 Zm00001d001978_T115:5 Zm00001d001978_T080:5 Zm00001d001978_T013:5 Zm00001d001978_T131:5 Zm00001d001978_T111:5 Zm00001d001978_T120:5 Zm00001d001978_T104:5 Zm00001d001978_T010:5 Zm00001d001978_T134:5 Zm00001d001978_T037:5 Zm00001d001978_T091:5 Zm00001d001978_T002:5 Zm00001d001978_T022:5 Zm00001d001978_T118:5 Zm00001d001978_T096:5 Zm00001d001978_T130:5 Zm00001d001978_T074:5 Zm00001d001978_T016:5 Zm00001d001978_T033:4 Zm00001d001978_T012:5 Zm00001d001978_T124:5 Zm00001d001978_T031:5 Zm00001d001978_T071:5 Zm00001d001978_T133:4 Zm00001d001978_T107:5 Zm00001d001978_T101:5 Zm00001d001978_T042:5 Zm00001d001978_T114:5 Zm00001d001978_T009:5 Zm00001d001978_T030:5 Zm00001d001978_T075:5 Zm00001d001978_T087:5 Zm00001d001978_T125:5 Zm00001d001978_T049:5 Zm00001d001978_T060:5

			
						 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  
						
							ATATCTGGTTTGGAAAGGCATGAAACCATTCTGCCACTATTACATACATCGACAGAGAGGAAAA
CGAATGGTGAACTTGACTTAATGATGGATTTTGCTGtctgtggagtacagcaaaatagtagcac
aactgaaaccaggggaaagtgaagatgtaatactgttggcgtgccaaaagcttctatcaatctt
cagtcacc

									
								

					

						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: 1129
Transcript exons: 3817610-3817789,3817882-3817965,3818052-3818143,3818249-
3818332,3818409-3819097
TCTGTGGAGTACAGCAAAATAGTAGCACAACTGAAACCAGGGGAAAGTGAAGATGTAATACTGT
TGGCGTGCCAAAAGCTTCTATCAATCTTCAGTCACCGGCCTGAGCAAAAACAGATCTATATGGC
ACAGAATGGTTTCCTCCCGCTGATGGAACTCCTTGAAATTCCTAAAAATCGTATTTTATGCTCA
GTTCTGCAGCTTATCAACAACATTGTAAAAGATAGTACAGGCTTCCTGGAAAATGCTTGCCTTG
TTGGCCTTATTCCAGTGGTGATGAATTTTGCAGAACCAAATCGCCCAAAGGATGTTCGGGTGCA
AGCATCCTTGTTTCTTCAGCAGCTTTGTCAAGCCAGCACCTTGACATTGCAAATGTTCATTGCA
TGTCAAGGGATCCCTGTTTTGGTAAGCTTTATGGAGCCTGACTATGCAAAATACAGGGATATGG
TTCATCTTGCAATTGACGGCATTTGGCAGGTCTTTAAGCTCCAGCACTCAACTCCAAGAAATGA
CTTCTGCCGTATAGCAGCAAAAAATGGGATGCTTCCTAGGCTGGTGAATACACTATATAGCTTG
AACGAAGCAACACGATTTGCCTCAGTCTCAGGGTCAGGTGCTTCAGTAACACAGAATGGCTCAA
CCCCCCGACGAAGATCTGGCCAATTAGACCCTTCAGTTCTTGAAAGTTGCAAGGCGAGGCTGGA
TCATCATCATTCATCTGGTTCTTTGCAATCTCTACAAGCAGATGCAGATAAGCACCACATATTA
ATGGACTCCTCGTCATCTCCTAGGTTCAGCGACAAAACAAGCAGTAACTTGGAGAGGAATGAGA
ACGACTTGGTTATTCGGCCACAGAGGCTTAGTGTTTCTGCCGGAAGGACATCTACAGACAGATC
ACCGAAGCACATAGAACTAGTTTCAAATGGTCATAATAACAGTCAAAATGACCAGGTCCGACCT
CTACTGAGTTTATTGGAGAAAGAACCACCTTCTCGACATGTATCTGGACAACTTGATTATGTTC
GCCATATATCTGGTTTGGAAAGGCATGAAACCATTCTGCCACTATTACATACATCGACAGAGAG
GAAAACGAATGGTGAACTTGACTTAATGATGGATTTTGCTG
						
					

						Genomic sequence
						
							TCTGTGGAGTACAGCAAAATAGTAGCACAACTGAAACCAGGGGAAAGTGAAGATGTAATACTGT
TGGCGTGCCAAAAGCTTCTATCAATCTTCAGTCACCGGCCTGAGCAAAAACAGATCTATATGGC
ACAGAATGGTTTCCTCCCGCTGATGGAACTCCTTGAAATTCCTAAAAATCGTGTATGATATTTC
ACTGTGGTTTACAAACATTTTTTCCTGGCCCTTTACACCATAAAGTTGTTTTGTTTTTTATTTT
ATTTTATTTTTGGCAGATTTTATGCTCAGTTCTGCAGCTTATCAACAACATTGTAAAAGATAGT
ACAGGCTTCCTGGAAAATGCTTGCCTTGTTGGCCTTGTAAGTCTAATGTTCCAGAGCAATTCAT
GACCTTATGCTCTGTTGACTCTAGTGAAAGGTACTTGATATTTAAAATTTATCTGCAGATTCCA
GTGGTGATGAATTTTGCAGAACCAAATCGCCCAAAGGATGTTCGGGTGCAAGCATCCTTGTTTC
TTCAGCAGCTTTGTCAAGCCAGGTCTTTTTCTTTGCTTTGACACAGTTGATAGTTTCTGACATT
TTTTAGTAAAAGAGTGGAAGGGACAAATGCTTTGGCGTACTAATTTTCAGTTTCCATCTCCAGC
ACCTTGACATTGCAAATGTTCATTGCATGTCAAGGGATCCCTGTTTTGGTAAGCTTTATGGAGC
CTGACTATGCAAAATACAGGCAAGTCTGCTTGTTGTTGATATAATTATTCCTCCATATTTTTCT
TCTGTATTAATTATTTAAATGCTTGTAGCAGGGATATGGTTCATCTTGCAATTGACGGCATTTG
GCAGGTCTTTAAGCTCCAGCACTCAACTCCAAGAAATGACTTCTGCCGTATAGCAGCAAAAAAT
GGGATGCTTCCTAGGCTGGTGAATACACTATATAGCTTGAACGAAGCAACACGATTTGCCTCAG
TCTCAGGGTCAGGTGCTTCAGTAACACAGAATGGCTCAACCCCCCGACGAAGATCTGGCCAATT
AGACCCTTCAGTTCTTGAAAGTTGCAAGGCGAGGCTGGATCATCATCATTCATCTGGTTCTTTG
CAATCTCTACAAGCAGATGCAGATAAGCACCACATATTAATGGACTCCTCGTCATCTCCTAGGT
TCAGCGACAAAACAAGCAGTAACTTGGAGAGGAATGAGAACGACTTGGTTATTCGGCCACAGAG
GCTTAGTGTTTCTGCCGGAAGGACATCTACAGACAGATCACCGAAGCACATAGAACTAGTTTCA
AATGGTCATAATAACAGTCAAAATGACCAGGTCCGACCTCTACTGAGTTTATTGGAGAAAGAAC
CACCTTCTCGACATGTATCTGGACAACTTGATTATGTTCGCCATATATCTGGTTTGGAAAGGCA
TGAAACCATTCTGCCACTATTACATACATCGACAGAGAGGAAAACGAATGGTGAACTTGACTTA
ATGATGGATTTTGCTG
						
					

			
		

Sequences
Splice junction sequence	ATATCTGGTTTGGAAAGGCATGAAACCATTCTGCCACTATTACATACATCGACAGAGAGGAAAA CGAATGGTGAACTTGACTTAATGATGGATTTTGCTGtctgtggagtacagcaaaatagtagcac aactgaaaccaggggaaagtgaagatgtaatactgttggcgtgccaaaagcttctatcaatctt cagtcacc
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: 1129 Transcript exons: 3817610-3817789,3817882-3817965,3818052-3818143,3818249- 3818332,3818409-3819097 TCTGTGGAGTACAGCAAAATAGTAGCACAACTGAAACCAGGGGAAAGTGAAGATGTAATACTGT TGGCGTGCCAAAAGCTTCTATCAATCTTCAGTCACCGGCCTGAGCAAAAACAGATCTATATGGC ACAGAATGGTTTCCTCCCGCTGATGGAACTCCTTGAAATTCCTAAAAATCGTATTTTATGCTCA GTTCTGCAGCTTATCAACAACATTGTAAAAGATAGTACAGGCTTCCTGGAAAATGCTTGCCTTG TTGGCCTTATTCCAGTGGTGATGAATTTTGCAGAACCAAATCGCCCAAAGGATGTTCGGGTGCA AGCATCCTTGTTTCTTCAGCAGCTTTGTCAAGCCAGCACCTTGACATTGCAAATGTTCATTGCA TGTCAAGGGATCCCTGTTTTGGTAAGCTTTATGGAGCCTGACTATGCAAAATACAGGGATATGG TTCATCTTGCAATTGACGGCATTTGGCAGGTCTTTAAGCTCCAGCACTCAACTCCAAGAAATGA CTTCTGCCGTATAGCAGCAAAAAATGGGATGCTTCCTAGGCTGGTGAATACACTATATAGCTTG AACGAAGCAACACGATTTGCCTCAGTCTCAGGGTCAGGTGCTTCAGTAACACAGAATGGCTCAA CCCCCCGACGAAGATCTGGCCAATTAGACCCTTCAGTTCTTGAAAGTTGCAAGGCGAGGCTGGA TCATCATCATTCATCTGGTTCTTTGCAATCTCTACAAGCAGATGCAGATAAGCACCACATATTA ATGGACTCCTCGTCATCTCCTAGGTTCAGCGACAAAACAAGCAGTAACTTGGAGAGGAATGAGA ACGACTTGGTTATTCGGCCACAGAGGCTTAGTGTTTCTGCCGGAAGGACATCTACAGACAGATC ACCGAAGCACATAGAACTAGTTTCAAATGGTCATAATAACAGTCAAAATGACCAGGTCCGACCT CTACTGAGTTTATTGGAGAAAGAACCACCTTCTCGACATGTATCTGGACAACTTGATTATGTTC GCCATATATCTGGTTTGGAAAGGCATGAAACCATTCTGCCACTATTACATACATCGACAGAGAG GAAAACGAATGGTGAACTTGACTTAATGATGGATTTTGCTG
Genomic sequence	TCTGTGGAGTACAGCAAAATAGTAGCACAACTGAAACCAGGGGAAAGTGAAGATGTAATACTGT TGGCGTGCCAAAAGCTTCTATCAATCTTCAGTCACCGGCCTGAGCAAAAACAGATCTATATGGC ACAGAATGGTTTCCTCCCGCTGATGGAACTCCTTGAAATTCCTAAAAATCGTGTATGATATTTC ACTGTGGTTTACAAACATTTTTTCCTGGCCCTTTACACCATAAAGTTGTTTTGTTTTTTATTTT ATTTTATTTTTGGCAGATTTTATGCTCAGTTCTGCAGCTTATCAACAACATTGTAAAAGATAGT ACAGGCTTCCTGGAAAATGCTTGCCTTGTTGGCCTTGTAAGTCTAATGTTCCAGAGCAATTCAT GACCTTATGCTCTGTTGACTCTAGTGAAAGGTACTTGATATTTAAAATTTATCTGCAGATTCCA GTGGTGATGAATTTTGCAGAACCAAATCGCCCAAAGGATGTTCGGGTGCAAGCATCCTTGTTTC TTCAGCAGCTTTGTCAAGCCAGGTCTTTTTCTTTGCTTTGACACAGTTGATAGTTTCTGACATT TTTTAGTAAAAGAGTGGAAGGGACAAATGCTTTGGCGTACTAATTTTCAGTTTCCATCTCCAGC ACCTTGACATTGCAAATGTTCATTGCATGTCAAGGGATCCCTGTTTTGGTAAGCTTTATGGAGC CTGACTATGCAAAATACAGGCAAGTCTGCTTGTTGTTGATATAATTATTCCTCCATATTTTTCT TCTGTATTAATTATTTAAATGCTTGTAGCAGGGATATGGTTCATCTTGCAATTGACGGCATTTG GCAGGTCTTTAAGCTCCAGCACTCAACTCCAAGAAATGACTTCTGCCGTATAGCAGCAAAAAAT GGGATGCTTCCTAGGCTGGTGAATACACTATATAGCTTGAACGAAGCAACACGATTTGCCTCAG TCTCAGGGTCAGGTGCTTCAGTAACACAGAATGGCTCAACCCCCCGACGAAGATCTGGCCAATT AGACCCTTCAGTTCTTGAAAGTTGCAAGGCGAGGCTGGATCATCATCATTCATCTGGTTCTTTG CAATCTCTACAAGCAGATGCAGATAAGCACCACATATTAATGGACTCCTCGTCATCTCCTAGGT TCAGCGACAAAACAAGCAGTAACTTGGAGAGGAATGAGAACGACTTGGTTATTCGGCCACAGAG GCTTAGTGTTTCTGCCGGAAGGACATCTACAGACAGATCACCGAAGCACATAGAACTAGTTTCA AATGGTCATAATAACAGTCAAAATGACCAGGTCCGACCTCTACTGAGTTTATTGGAGAAAGAAC CACCTTCTCGACATGTATCTGGACAACTTGATTATGTTCGCCATATATCTGGTTTGGAAAGGCA TGAAACCATTCTGCCACTATTACATACATCGACAGAGAGGAAAACGAATGGTGAACTTGACTTA ATGATGGATTTTGCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.279410076

Conservation Information
Conserved circRNAs	NA
PMCS	0.279410076

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3817734-3817656(+)
						
						Potential amino acid sequence
						
							MAQNGFLPLMELLEIPKNRILCSVLQLINNIVKDSTGFLENACLVGLIPVVMNFAEPNRPKDVR
VQASLFLQQLCQASTLTLQMFIACQGIPVLVSFMEPDYAKYRDMVHLAIDGIWQVFKLQHSTPR
NDFCRIAAKNGMLPRLVNTLYSLNEATRFASVSGSGASVTQNGSTPRRRSGQLDPSVLESCKAR
LDHHHSSGSLQSLQADADKHHILMDSSSSPRFSDKTSSNLERNENDLVIRPQRLSVSAGRTSTD
RSPKHIELVSNGHNNSQNDQVRPLLSLLEKEPPSRHVSGQLDYVRHISGLERHETILPLLHTST
ERKTNGELDLMMDFAVCGVQQNSSTTETRGK*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	3817734-3817656(+)
Potential amino acid sequence	MAQNGFLPLMELLEIPKNRILCSVLQLINNIVKDSTGFLENACLVGLIPVVMNFAEPNRPKDVR VQASLFLQQLCQASTLTLQMFIACQGIPVLVSFMEPDYAKYRDMVHLAIDGIWQVFKLQHSTPR NDFCRIAAKNGMLPRLVNTLYSLNEATRFASVSGSGASVTQNGSTPRRRSGQLDPSVLESCKAR LDHHHSSGSLQSLQADADKHHILMDSSSSPRFSDKTSSNLERNENDLVIRPQRLSVSAGRTSTD RSPKHIELVSNGHNNSQNDQVRPLLSLLEKEPPSRHVSGQLDYVRHISGLERHETILPLLHTST ERKTNGELDLMMDFAVCGVQQNSSTTETRGK*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d001978_circ_g.4

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