Plant Circular RNA Database

Detail information of Zm00001d008429_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d008429_circ_g.3
					
						ID in PlantcircBase
						zma_circ_009540
					
						Alias
						Zm08circ00004, zma_circ_0002639, GRMZM2G334457_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr8: 8462416-8463479  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d008429						
					
						Parent gene annotation
						
							Paired amphipathic helix protein Sin3-like 3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d008429_circ_g.2 Zm00001d008429_circ_g.4 Zm00001d008429_circ_g.5 						
					
						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  
						
							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
						Zm00001d008429_T042:5
Zm00001d008429_T022:5
Zm00001d008429_T015:5
Zm00001d008429_T030:5
Zm00001d008429_T019:5
Zm00001d008429_T041:2
Zm00001d008429_T028:5
Zm00001d008429_T014:4
Zm00001d008429_T025:5
Zm00001d008429_T008:5
Zm00001d008429_T012:5
Zm00001d008429_T021:5
Zm00001d008429_T033:5
Zm00001d008429_T020:5
Zm00001d008429_T006:5
Zm00001d008429_T018:2
Zm00001d008429_T026:5
Zm00001d008429_T034:5
Zm00001d008429_T038:5
Zm00001d008429_T029:5
Zm00001d008429_T043:4
Zm00001d008429_T002:5
Zm00001d008429_T027:5
Zm00001d008429_T032:5
Zm00001d008429_T017:4
Zm00001d008429_T003:5
Zm00001d008429_T035:5
Zm00001d008429_T040:4
Zm00001d008429_T013:5
Zm00001d008429_T010:5
Zm00001d008429_T036:5
Zm00001d008429_T007:5
Zm00001d008429_T024:5
Zm00001d008429_T004:5

General Information
CircRNA Name	Zm00001d008429_circ_g.3
ID in PlantcircBase	zma_circ_009540
Alias	Zm08circ00004, zma_circ_0002639, GRMZM2G334457_C1
Organism	Zea mays
Position	chr8: 8462416-8463479 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d008429
Parent gene annotation	Paired amphipathic helix protein Sin3-like 3
Parent gene strand	-
Alternative splicing	Zm00001d008429_circ_g.2 Zm00001d008429_circ_g.4 Zm00001d008429_circ_g.5
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	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	Zm00001d008429_T042:5 Zm00001d008429_T022:5 Zm00001d008429_T015:5 Zm00001d008429_T030:5 Zm00001d008429_T019:5 Zm00001d008429_T041:2 Zm00001d008429_T028:5 Zm00001d008429_T014:4 Zm00001d008429_T025:5 Zm00001d008429_T008:5 Zm00001d008429_T012:5 Zm00001d008429_T021:5 Zm00001d008429_T033:5 Zm00001d008429_T020:5 Zm00001d008429_T006:5 Zm00001d008429_T018:2 Zm00001d008429_T026:5 Zm00001d008429_T034:5 Zm00001d008429_T038:5 Zm00001d008429_T029:5 Zm00001d008429_T043:4 Zm00001d008429_T002:5 Zm00001d008429_T027:5 Zm00001d008429_T032:5 Zm00001d008429_T017:4 Zm00001d008429_T003:5 Zm00001d008429_T035:5 Zm00001d008429_T040:4 Zm00001d008429_T013:5 Zm00001d008429_T010:5 Zm00001d008429_T036:5 Zm00001d008429_T007:5 Zm00001d008429_T024:5 Zm00001d008429_T004:5

			
						 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  
						
							TGGCTGTAGATGTGTAGACATTTCAAAAACTCCTGGTAAGCTTCATGCTCCAGTTTTTCCTTCA
CCTTCTCACAGAAATGGAACTCGTGCGTGTATACACctgtcatcctcgcatctaaataagcttt
cctcatactgattcttccgcatgtgcttaaatgaataatcttcacttccggatgtcactgatac
ccagtgat

									
								

					

						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: 664
Transcript exons: 8462416-8462570,8462644-8462912,8462988-8463017,8463112-
8463187,8463346-8463479
CTGTCATCCTCGCATCTAAATAAGCTTTCCTCATACTGATTCTTCCGCATGTGCTTAAATGAAT
AATCTTCACTTCCGGATGTCACTGATACCCAGTGATCATTAAGAACAGAGGCTCCAAGATCAGT
CCTGTTGCTGGCAGGGGGCATGGGATAATTTTTAGGTAGAAGCCGGTAACTCGGAGTGCAACGT
TGACAGTTTGAGAGATCAAGCTCTGATATTGGTTTGGATAGGTTGTACTTCTCTTTGCCAGAAA
ACATAGGAGGTTTGTGACAAGAACCGTCCTTTGAATTGAATGTTGACCCTTTATCGAGTCTTTC
TCGTTCCTTCTCTCTTTCCTTTTCCCGATCTCTATCCCTGTCCTCCCTGTCCCGATCTCTATCC
TTTTCTTTATCCTCAGTTTTAACAATCCTTGTTGTTGGGCGTTTGTTGAAGACACCAGCAAGAA
ATCCATCTATATTTTCACAATGTTCCAAGAATTCATTAAACCCTTCCATAAGATCTGGATAATG
CTGGAGTATATCATTCACCAAGTTCTTCAGTTCACTTCTCGTGATAATCTCTTGGCTGTAGATG
TGTAGACATTTCAAAAACTCCTGGTAAGCTTCATGCTCCAGTTTTTCCTTCACCTTCTCACAGA
AATGGAACTCGTGCGTGTATACAC
						
					

						Genomic sequence
						
							CTGTCATCCTCGCATCTAAATAAGCTTTCCTCATACTGATTCTTCCGCATGTGCTTAAATGAAT
AATCTTCACTTCCGGATGTCACTGATACCCAGTGATCATTAAGAACAGAGGCTCCAAGATCAGT
CCTGTTGCTGGCAGGGGGCATGGGATACTGAAAACATGATTGAACCAAAAGTTATATGAAACAC
AGTACAGAAAGAACTATATGATATGAATCAGCTTACATTTTTAGGTAGAAGCCGGTAACTCGGA
GTGCAACGTTGACAGTTTGAGAGATCAAGCTCTGATATTGGTTTGGATAGGTTGTACTTCTCTT
TGCCAGAAAACATAGGAGGTTTGTGACAAGAACCGTCCTTTGAATTGAATGTTGACCCTTTATC
GAGTCTTTCTCGTTCCTTCTCTCTTTCCTTTTCCCGATCTCTATCCCTGTCCTCCCTGTCCCGA
TCTCTATCCTTTTCTTTATCCTCAGTTTTAACAATCCTTGTTGTTGGGCCTTCATATTAGATAA
TCAATGTGAATGTGATATTTTGGAAGCATTAAGGAAAGGTTAAATCTAGTAACCACGTACGTTT
GTTGAAGACACCAGCAAGAAATCCATCTGCAACAAGGGGCCAAACTAGGTAAAACCATGAAACT
TGGACAATTGAAATGTTACAATATGATCATACAAATGTATAAAGTTTGTAAATTACCTATATTT
TCACAATGTTCCAAGAATTCATTAAACCCTTCCATAAGATCTGGATAATGCTGGAGTATATCAT
TCACCTGCAAATCAATAAAATTTATCAATGCTTCACCTTGTGGTAAGTAAACATGCACATATAC
TTAAGAGTTAAGACATATTATAACTGAAGTTAGTGATAACTTGAGAAATTCAAGCATTAAGCAT
GAATCATAAAATAAAATAAAAATAAGAAACCAACCAAGTTCTTCAGTTCACTTCTCGTGATAAT
CTCTTGGCTGTAGATGTGTAGACATTTCAAAAACTCCTGGTAAGCTTCATGCTCCAGTTTTTCC
TTCACCTTCTCACAGAAATGGAACTCGTGCGTGTATACAC
						
					

			
		

Sequences
Splice junction sequence	TGGCTGTAGATGTGTAGACATTTCAAAAACTCCTGGTAAGCTTCATGCTCCAGTTTTTCCTTCA CCTTCTCACAGAAATGGAACTCGTGCGTGTATACACctgtcatcctcgcatctaaataagcttt cctcatactgattcttccgcatgtgcttaaatgaataatcttcacttccggatgtcactgatac ccagtgat
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: 664 Transcript exons: 8462416-8462570,8462644-8462912,8462988-8463017,8463112- 8463187,8463346-8463479 CTGTCATCCTCGCATCTAAATAAGCTTTCCTCATACTGATTCTTCCGCATGTGCTTAAATGAAT AATCTTCACTTCCGGATGTCACTGATACCCAGTGATCATTAAGAACAGAGGCTCCAAGATCAGT CCTGTTGCTGGCAGGGGGCATGGGATAATTTTTAGGTAGAAGCCGGTAACTCGGAGTGCAACGT TGACAGTTTGAGAGATCAAGCTCTGATATTGGTTTGGATAGGTTGTACTTCTCTTTGCCAGAAA ACATAGGAGGTTTGTGACAAGAACCGTCCTTTGAATTGAATGTTGACCCTTTATCGAGTCTTTC TCGTTCCTTCTCTCTTTCCTTTTCCCGATCTCTATCCCTGTCCTCCCTGTCCCGATCTCTATCC TTTTCTTTATCCTCAGTTTTAACAATCCTTGTTGTTGGGCGTTTGTTGAAGACACCAGCAAGAA ATCCATCTATATTTTCACAATGTTCCAAGAATTCATTAAACCCTTCCATAAGATCTGGATAATG CTGGAGTATATCATTCACCAAGTTCTTCAGTTCACTTCTCGTGATAATCTCTTGGCTGTAGATG TGTAGACATTTCAAAAACTCCTGGTAAGCTTCATGCTCCAGTTTTTCCTTCACCTTCTCACAGA AATGGAACTCGTGCGTGTATACAC
Genomic sequence	CTGTCATCCTCGCATCTAAATAAGCTTTCCTCATACTGATTCTTCCGCATGTGCTTAAATGAAT AATCTTCACTTCCGGATGTCACTGATACCCAGTGATCATTAAGAACAGAGGCTCCAAGATCAGT CCTGTTGCTGGCAGGGGGCATGGGATACTGAAAACATGATTGAACCAAAAGTTATATGAAACAC AGTACAGAAAGAACTATATGATATGAATCAGCTTACATTTTTAGGTAGAAGCCGGTAACTCGGA GTGCAACGTTGACAGTTTGAGAGATCAAGCTCTGATATTGGTTTGGATAGGTTGTACTTCTCTT TGCCAGAAAACATAGGAGGTTTGTGACAAGAACCGTCCTTTGAATTGAATGTTGACCCTTTATC GAGTCTTTCTCGTTCCTTCTCTCTTTCCTTTTCCCGATCTCTATCCCTGTCCTCCCTGTCCCGA TCTCTATCCTTTTCTTTATCCTCAGTTTTAACAATCCTTGTTGTTGGGCCTTCATATTAGATAA TCAATGTGAATGTGATATTTTGGAAGCATTAAGGAAAGGTTAAATCTAGTAACCACGTACGTTT GTTGAAGACACCAGCAAGAAATCCATCTGCAACAAGGGGCCAAACTAGGTAAAACCATGAAACT TGGACAATTGAAATGTTACAATATGATCATACAAATGTATAAAGTTTGTAAATTACCTATATTT TCACAATGTTCCAAGAATTCATTAAACCCTTCCATAAGATCTGGATAATGCTGGAGTATATCAT TCACCTGCAAATCAATAAAATTTATCAATGCTTCACCTTGTGGTAAGTAAACATGCACATATAC TTAAGAGTTAAGACATATTATAACTGAAGTTAGTGATAACTTGAGAAATTCAAGCATTAAGCAT GAATCATAAAATAAAATAAAAATAAGAAACCAACCAAGTTCTTCAGTTCACTTCTCGTGATAAT CTCTTGGCTGTAGATGTGTAGACATTTCAAAAACTCCTGGTAAGCTTCATGCTCCAGTTTTTCC TTCACCTTCTCACAGAAATGGAACTCGTGCGTGTATACAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005881* 						
					
						PMCS
						0.211624797

Conservation Information
Conserved circRNAs	osi_circ_005881*
PMCS	0.211624797

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8463425-8462431(+)
8462451-8463451(-)
8463156-8463451(-)
						
						Potential amino acid sequence
						
							MLQFFLHLLTEMELVRVYTCHPRI*(+)
MRKAYLDARMTGVYTHEFHFCEKVKEKLEHEAYQEFLKCLHIYSQEIITRSELKNLVNDILQHY
PDLMEGFNEFLEHCENIDGFLAGVFNKRPTTRIVKTEDKEKDRDRDREDRDRDREKEREKERER
LDKGSTFNSKDGSCHKPPMFSGKEKYNLSKPISELDLSNCQRCTPSYRLLPKNYPMPPASNRTD
LGASVLNDHWVSVTSGSEDYSFKHMRKNQYEESLFRCEDDRCIHARVPFL*(-)
MEGFNEFLEHCENIDGFLAGVFNKRPTTRIVKTEDKEKDRDRDREDRDRDREKEREKERERLDK
GSTFNSKDGSCHKPPMFSGKEKYNLSKPISELDLSNCQRCTPSYRLLPKNYPMPPASNRTDLGA
SVLNDHWVSVTSGSEDYSFKHMRKNQYEESLFRCEDDRCIHARVPFL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	8463425-8462431(+) 8462451-8463451(-) 8463156-8463451(-)
Potential amino acid sequence	MLQFFLHLLTEMELVRVYTCHPRI(+) MRKAYLDARMTGVYTHEFHFCEKVKEKLEHEAYQEFLKCLHIYSQEIITRSELKNLVNDILQHY PDLMEGFNEFLEHCENIDGFLAGVFNKRPTTRIVKTEDKEKDRDRDREDRDRDREKEREKERER LDKGSTFNSKDGSCHKPPMFSGKEKYNLSKPISELDLSNCQRCTPSYRLLPKNYPMPPASNRTD LGASVLNDHWVSVTSGSEDYSFKHMRKNQYEESLFRCEDDRCIHARVPFL(-) MEGFNEFLEHCENIDGFLAGVFNKRPTTRIVKTEDKEKDRDRDREDRDRDREKEREKERERLDK GSTFNSKDGSCHKPPMFSGKEKYNLSKPISELDLSNCQRCTPSYRLLPKNYPMPPASNRTDLGA SVLNDHWVSVTSGSEDYSFKHMRKNQYEESLFRCEDDRCIHARVPFL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d008429_circ_g.3

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