Plant Circular RNA Database

Detail information of Zm00001d037982_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d037982_circ_g.3
					
						ID in PlantcircBase
						zma_circ_009090
					
						Alias
						zma_circ_0002359, GRMZM2G416667_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr6: 144225224-144227575  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d037982						
					
						Parent gene annotation
						
							AMP deaminase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d037982_circ_g.1 Zm00001d037982_circ_g.2 Zm00001d037982_circ_g.4 Zm00001d037982_circ_g.5 						
					
						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
						Zm00001d037982_T002:7
Zm00001d037982_T006:7
Zm00001d037982_T008:8
Zm00001d037982_T003:7
Zm00001d037982_T001:8
Zm00001d037982_T005:8
Zm00001d037982_T004:7
Zm00001d037982_T007:8

General Information
CircRNA Name	Zm00001d037982_circ_g.3
ID in PlantcircBase	zma_circ_009090
Alias	zma_circ_0002359, GRMZM2G416667_C1
Organism	Zea mays
Position	chr6: 144225224-144227575 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d037982
Parent gene annotation	AMP deaminase
Parent gene strand	-
Alternative splicing	Zm00001d037982_circ_g.1 Zm00001d037982_circ_g.2 Zm00001d037982_circ_g.4 Zm00001d037982_circ_g.5
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	Zm00001d037982_T002:7 Zm00001d037982_T006:7 Zm00001d037982_T008:8 Zm00001d037982_T003:7 Zm00001d037982_T001:8 Zm00001d037982_T005:8 Zm00001d037982_T004:7 Zm00001d037982_T007:8

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F:GGAAGGTTGACACTCATGTTCATC
 R:AGCAGGAGACTTGGGTGACTTAG
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	Yes 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	F:GGAAGGTTGACACTCATGTTCATC R:AGCAGGAGACTTGGGTGACTTAG 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  
						
							CAATAGTAACCTCAAAAAGAGGAACGAAAATGTTGTCAAGAAGATTTTGGAATGATGTAACGAT
ACCCATTTCCTTGTACACATTATATAAGCGTGGAATcaaaacatgaagtataattcccatagca
gctacaacgcaactcgtctggtatacacgaggctggacatcttacaggtccagctcgtctggta
ttaagatc

									
								

					

						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: 954
Transcript exons: 144225224-144225364,144225448-144225546,144225866-144225
946,144226118-144226291,144226681-144226791,144226862-14
4226915,144226991-144227143,144227435-144227575
CAAAACATGAAGTATAATTCCCATAGCAGCTACAACGCAACTCGTCTGGTATACACGAGGCTGG
ACATCTTACAGGTCCAGCTCGTCTGGTATTAAGATCTCATTGTCAGAGTACACTAGTTTCATTT
CATTTCTCCAGATCATCTCTCTAAATTGAACCCTGATGTGCGGTACATTGGTTCTGTGAATATC
ATTTCCAGCAGGTCCTCTTTTGAAGTAGTTCTTACCAATCCAGTGCGCCTTGAGAGCATGTGAA
AACCCAGATTGGTAAACAGAGTTCCTCGCAATTTCGCATAAATCACAAGAACTGAGCTTCCACA
GCGAAGCAGCAATGCTGTATTCTTCCACCAATGGTTCTTTTGTCAGGTGAATTTGCAAAGGGTC
ATCCGTAGATAATGAGACATTCAGACCTCGTTGGAAGAACGTTGGAAAAGGGTTGCGATGATAG
TCAAGAAATAAGGAGTTGTTGCTCAATGGGGACATCGCCAGACCAATCTGACCAAGATAGTACA
AGTACTGAAGCACAGGAGACTTCCTTAGATTAATTCCATGTGATATGTTGTGACAGAGAAGAAA
TGTCGCTGCCAAGTGATCAACATCTCCAGCCTCTCCAGCATGTGGACGGAATTTGATAGTGGTC
ATTCCCTTTGACTCACGCAGCTTGTTTAGGGTGAATAAGTTAGCATAGCAGTAGTACGCATAAT
ATGAAAATGCAGGGTTGAACACATTGGTCCACTGTTCAGGTGTGGGCATGTGCTTTGTTGGACG
CCTTTCTGGTTTACTTTCATCATCAACCAGGTCCAACCCTACAACCTGCTTCAGGAAGACATGG
AGCTGTGGGTGTGAAGCTGGATCAATAGTAACCTCAAAAAGAGGAACGAAAATGTTGTCAAGAA
GATTTTGGAATGATGTAACGATACCCATTTCCTTGTACACATTATATAAGCGTGGAAT
						
					

						Genomic sequence
						
							CAAAACATGAAGTATAATTCCCATAGCAGCTACAACGCAACTCGTCTGGTATACACGAGGCTGG
ACATCTTACAGGTCCAGCTCGTCTGGTATTAAGATCTCATTGTCAGAGTACACTAGTTTCATTT
CATTTCTCCAGATCTGATAAAGGGGAACAGTTTAAGAGTCAGATTTCACCAAAATACCACTTGC
CAAGACAATAAAGGGAGAACAGAATTTTATACCATCTCTCTAAATTGAACCCTGATGTGCGGTA
CATTGGTTCTGTGAATATCATTTCCAGCAGGTCCTCTTTTGAAGTAGTTCTTACCAATCCAGTG
CGCCTGCCAAAGATCGTATGATTATTTGATGTGTGTTCTACACACATTTATACTAAGCAGGTAA
CGACCTTCTCTAATATATTTCCAGTGTCTCAAGAGAGGGCTTCAATGCATGCTGAAGGCTACAT
TTCATACCATCACTCTGTAACTAAAGTGAAGGTAAGGCTTGGAACACACCGAGGGCTTGTTTTG
GAGCAAGGGGATTGAGGGAGGCTAAAATCTCATTTCTATTTAAATAGAAATGAGATTTTAGCCC
CGTCAATTCCCTTTCTCCCAAACAAGCCCTAAAGTGTTTCCAGAGAAGTAGCAAAAGATCGCTC
ACCTTGAGAGCATGTGAAAACCCAGATTGGTAAACAGAGTTCCTCGCAATTTCGCATAAATCAC
AAGAACTGAGCTTCCACAGCTGAAACAATCAAAATGGAGTAATGGACATTAGTCACTCGTCCCT
TTTGGCGTGGGTACAATAGTATCTATGCGTAAAGGTGTGTGCTGCATACACGTGCACACAAAGC
TCGTGCTGCATGTGTGAAAGAACAATCAAAAGGCGCAAAAAAGCGAGGGAAGTAGCGAGTACCG
AAGCAGCAATGCTGTATTCTTCCACCAATGGTTCTTTTGTCAGGTGAATTTGCAAAGGGTCATC
CGTAGATAATGAGACATTCAGACCTCGTTGGAAGAACGTTGGAAAAGGGTTGCGATGATAGTCA
AGAAATAAGGAGTTGTTGCTCAATGGGGACATCGCCAGACCAATCTGACAAGATTTAAAGTAAC
AGGTTGAAAGAGGAACATCATCTTTCAAAATAAAGAAACTGAAGTGCAAAAGGTTATGCCATTT
GCTGGTGGTGTTGCCTCCGGCCACTAAACATGTGAAGTTTTAAGCATTATAGTCCCCAAAACAC
ATCATCGACCAGTAAGTTCTATTCATGAATGTACTACCCAACACGCCAAAGATGTATTTTTCAC
AAGTTAAATATTCATTTAATATCTGTTGCCAAAAACTAGAAAAAATTGCATTCATCATAAAACA
TCACTTAATTTAACTGGAATGGAAGATACAAGTACTGGAGAAAGTAAACACCATCGAAGAATAT
CAGAAGAGACCAAAATCATGCTGGGTTATGGAACTTGGTAACATATTACCTGACCAAGATAGTA
CAAGTACTGAAGCACAGGAGACTTCCTTAGATTAATTCCATGTGATATGTTGTGACAGAGAAGA
AATGTCGCTGCCAAGTGATCAACATCTCCAGCCTGTACGAGCATAACCATTAGTGCAAACAGGA
TACTGTACTTTCAGAGAGGAACCTGGAATAGATTTTACCTCTCCAGCATGTGGACGGAATTTGA
TAGTGGTCATTCCCTTTGACTCACGCAGCTGAAAATTGAACAGAATCATTACCACTCTGAGAAA
CGTGGAGAAAATTGAGGAAGGGGAGGAAGATATGATCACCTTGTTTAGGGTGAATAAGTTAGCA
TAGCAGTAGTACGCATAATATGAAAATGCAGGGTTGAACACATTGGTCCACTGTTCAGGTGTGG
GCATGTGCTTTGTTGGACGCCTTTCTGGTTTACTTTCATCATCAACCAGGTCCAACCCTACAAC
CTGCAAGGCCCAGAAAGAGTCAATTGAAGTTGTGATATCATGTATCTGAGATAAATACATGCGA
ACGTATTTCTCAATTATCATTACTGAAAAAACTAATGTTGAAATTTAGCATTAGTTCTCCATGT
CACACACACTTGCAGGCTGGCATGTGAGACACACGAAACACACACACTGGGATGTGAGACACAC
ACAATAGCGAGTTATGGTTGATGTCTGAAATGTTGATGCATGACACAAGGCAGAAATACAGTCG
ATATGCATATTCCTTGTAACCAATGTTTTCTCAACCTGCTTCAGGAAGACATGGAGCTGTGGGT
GTGAAGCTGGATCAATAGTAACCTCAAAAAGAGGAACGAAAATGTTGTCAAGAAGATTTTGGAA
TGATGTAACGATACCCATTTCCTTGTACACATTATATAAGCGTGGAAT
						
					

			
		

Sequences
Splice junction sequence	CAATAGTAACCTCAAAAAGAGGAACGAAAATGTTGTCAAGAAGATTTTGGAATGATGTAACGAT ACCCATTTCCTTGTACACATTATATAAGCGTGGAATcaaaacatgaagtataattcccatagca gctacaacgcaactcgtctggtatacacgaggctggacatcttacaggtccagctcgtctggta ttaagatc
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: 954 Transcript exons: 144225224-144225364,144225448-144225546,144225866-144225 946,144226118-144226291,144226681-144226791,144226862-14 4226915,144226991-144227143,144227435-144227575 CAAAACATGAAGTATAATTCCCATAGCAGCTACAACGCAACTCGTCTGGTATACACGAGGCTGG ACATCTTACAGGTCCAGCTCGTCTGGTATTAAGATCTCATTGTCAGAGTACACTAGTTTCATTT CATTTCTCCAGATCATCTCTCTAAATTGAACCCTGATGTGCGGTACATTGGTTCTGTGAATATC ATTTCCAGCAGGTCCTCTTTTGAAGTAGTTCTTACCAATCCAGTGCGCCTTGAGAGCATGTGAA AACCCAGATTGGTAAACAGAGTTCCTCGCAATTTCGCATAAATCACAAGAACTGAGCTTCCACA GCGAAGCAGCAATGCTGTATTCTTCCACCAATGGTTCTTTTGTCAGGTGAATTTGCAAAGGGTC ATCCGTAGATAATGAGACATTCAGACCTCGTTGGAAGAACGTTGGAAAAGGGTTGCGATGATAG TCAAGAAATAAGGAGTTGTTGCTCAATGGGGACATCGCCAGACCAATCTGACCAAGATAGTACA AGTACTGAAGCACAGGAGACTTCCTTAGATTAATTCCATGTGATATGTTGTGACAGAGAAGAAA TGTCGCTGCCAAGTGATCAACATCTCCAGCCTCTCCAGCATGTGGACGGAATTTGATAGTGGTC ATTCCCTTTGACTCACGCAGCTTGTTTAGGGTGAATAAGTTAGCATAGCAGTAGTACGCATAAT ATGAAAATGCAGGGTTGAACACATTGGTCCACTGTTCAGGTGTGGGCATGTGCTTTGTTGGACG CCTTTCTGGTTTACTTTCATCATCAACCAGGTCCAACCCTACAACCTGCTTCAGGAAGACATGG AGCTGTGGGTGTGAAGCTGGATCAATAGTAACCTCAAAAAGAGGAACGAAAATGTTGTCAAGAA GATTTTGGAATGATGTAACGATACCCATTTCCTTGTACACATTATATAAGCGTGGAAT
Genomic sequence	CAAAACATGAAGTATAATTCCCATAGCAGCTACAACGCAACTCGTCTGGTATACACGAGGCTGG ACATCTTACAGGTCCAGCTCGTCTGGTATTAAGATCTCATTGTCAGAGTACACTAGTTTCATTT CATTTCTCCAGATCTGATAAAGGGGAACAGTTTAAGAGTCAGATTTCACCAAAATACCACTTGC CAAGACAATAAAGGGAGAACAGAATTTTATACCATCTCTCTAAATTGAACCCTGATGTGCGGTA CATTGGTTCTGTGAATATCATTTCCAGCAGGTCCTCTTTTGAAGTAGTTCTTACCAATCCAGTG CGCCTGCCAAAGATCGTATGATTATTTGATGTGTGTTCTACACACATTTATACTAAGCAGGTAA CGACCTTCTCTAATATATTTCCAGTGTCTCAAGAGAGGGCTTCAATGCATGCTGAAGGCTACAT TTCATACCATCACTCTGTAACTAAAGTGAAGGTAAGGCTTGGAACACACCGAGGGCTTGTTTTG GAGCAAGGGGATTGAGGGAGGCTAAAATCTCATTTCTATTTAAATAGAAATGAGATTTTAGCCC CGTCAATTCCCTTTCTCCCAAACAAGCCCTAAAGTGTTTCCAGAGAAGTAGCAAAAGATCGCTC ACCTTGAGAGCATGTGAAAACCCAGATTGGTAAACAGAGTTCCTCGCAATTTCGCATAAATCAC AAGAACTGAGCTTCCACAGCTGAAACAATCAAAATGGAGTAATGGACATTAGTCACTCGTCCCT TTTGGCGTGGGTACAATAGTATCTATGCGTAAAGGTGTGTGCTGCATACACGTGCACACAAAGC TCGTGCTGCATGTGTGAAAGAACAATCAAAAGGCGCAAAAAAGCGAGGGAAGTAGCGAGTACCG AAGCAGCAATGCTGTATTCTTCCACCAATGGTTCTTTTGTCAGGTGAATTTGCAAAGGGTCATC CGTAGATAATGAGACATTCAGACCTCGTTGGAAGAACGTTGGAAAAGGGTTGCGATGATAGTCA AGAAATAAGGAGTTGTTGCTCAATGGGGACATCGCCAGACCAATCTGACAAGATTTAAAGTAAC AGGTTGAAAGAGGAACATCATCTTTCAAAATAAAGAAACTGAAGTGCAAAAGGTTATGCCATTT GCTGGTGGTGTTGCCTCCGGCCACTAAACATGTGAAGTTTTAAGCATTATAGTCCCCAAAACAC ATCATCGACCAGTAAGTTCTATTCATGAATGTACTACCCAACACGCCAAAGATGTATTTTTCAC AAGTTAAATATTCATTTAATATCTGTTGCCAAAAACTAGAAAAAATTGCATTCATCATAAAACA TCACTTAATTTAACTGGAATGGAAGATACAAGTACTGGAGAAAGTAAACACCATCGAAGAATAT CAGAAGAGACCAAAATCATGCTGGGTTATGGAACTTGGTAACATATTACCTGACCAAGATAGTA CAAGTACTGAAGCACAGGAGACTTCCTTAGATTAATTCCATGTGATATGTTGTGACAGAGAAGA AATGTCGCTGCCAAGTGATCAACATCTCCAGCCTGTACGAGCATAACCATTAGTGCAAACAGGA TACTGTACTTTCAGAGAGGAACCTGGAATAGATTTTACCTCTCCAGCATGTGGACGGAATTTGA TAGTGGTCATTCCCTTTGACTCACGCAGCTGAAAATTGAACAGAATCATTACCACTCTGAGAAA CGTGGAGAAAATTGAGGAAGGGGAGGAAGATATGATCACCTTGTTTAGGGTGAATAAGTTAGCA TAGCAGTAGTACGCATAATATGAAAATGCAGGGTTGAACACATTGGTCCACTGTTCAGGTGTGG GCATGTGCTTTGTTGGACGCCTTTCTGGTTTACTTTCATCATCAACCAGGTCCAACCCTACAAC CTGCAAGGCCCAGAAAGAGTCAATTGAAGTTGTGATATCATGTATCTGAGATAAATACATGCGA ACGTATTTCTCAATTATCATTACTGAAAAAACTAATGTTGAAATTTAGCATTAGTTCTCCATGT CACACACACTTGCAGGCTGGCATGTGAGACACACGAAACACACACACTGGGATGTGAGACACAC ACAATAGCGAGTTATGGTTGATGTCTGAAATGTTGATGCATGACACAAGGCAGAAATACAGTCG ATATGCATATTCCTTGTAACCAATGTTTTCTCAACCTGCTTCAGGAAGACATGGAGCTGTGGGT GTGAAGCTGGATCAATAGTAACCTCAAAAAGAGGAACGAAAATGTTGTCAAGAAGATTTTGGAA TGATGTAACGATACCCATTTCCTTGTACACATTATATAAGCGTGGAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.193983445

Conservation Information
Conserved circRNAs	NA
PMCS	0.193983445

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							144227083-144225230(+)
144225249-144225295(-)
						
						Potential amino acid sequence
						
							MCFVGRLSGLLSSSTRSNPTTCFRKTWSCGCEAGSIVTSKRGTKMLSRRFWNDVTIPISLYTLY
KRGIKT*(+)
MGIILHVLIPRLYNVYKEMGIVTSFQNLLDNIFVPLFEVTIDPASHPQLHVFLKQVVGLDLVDD
ESKPERRPTKHMPTPEQWTNVFNPAFSYYAYYCYANLFTLNKLRESKGMTTIKFRPHAGEAGDV
DHLAATFLLCHNISHGINLRKSPVLQYLYYLGQIGLAMSPLSNNSLFLDYHRNPFPTFFQRGLN
VSLSTDDPLQIHLTKEPLVEEYSIAASAHWIGKNYFKRGPAGNDIHRTNVPHIRVQFREMIWRN
EMKLVYSDNEILIPDELDL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	144227083-144225230(+) 144225249-144225295(-)
Potential amino acid sequence	MCFVGRLSGLLSSSTRSNPTTCFRKTWSCGCEAGSIVTSKRGTKMLSRRFWNDVTIPISLYTLY KRGIKT(+) MGIILHVLIPRLYNVYKEMGIVTSFQNLLDNIFVPLFEVTIDPASHPQLHVFLKQVVGLDLVDD ESKPERRPTKHMPTPEQWTNVFNPAFSYYAYYCYANLFTLNKLRESKGMTTIKFRPHAGEAGDV DHLAATFLLCHNISHGINLRKSPVLQYLYYLGQIGLAMSPLSNNSLFLDYHRNPFPTFFQRGLN VSLSTDDPLQIHLTKEPLVEEYSIAASAHWIGKNYFKRGPAGNDIHRTNVPHIRVQFREMIWRN EMKLVYSDNEILIPDELDL(-)
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 Zm00001d037982_circ_g.3

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