Plant Circular RNA Database

Detail information of Zm00001d027324_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d027324_circ_g.2
					
						ID in PlantcircBase
						zma_circ_006344
					
						Alias
						Zm01circ00003, GRMZM2G006673_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 2960401-2961596  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d027324						
					
						Parent gene annotation
						
							THO complex subunit 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d027324_circ_g.1 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d027324_T003:5
Zm00001d027324_T002:5
Zm00001d027324_T001:5

General Information
CircRNA Name	Zm00001d027324_circ_g.2
ID in PlantcircBase	zma_circ_006344
Alias	Zm01circ00003, GRMZM2G006673_C1
Organism	Zea mays
Position	chr1: 2960401-2961596 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d027324
Parent gene annotation	THO complex subunit 1
Parent gene strand	+
Alternative splicing	Zm00001d027324_circ_g.1
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d027324_T003:5 Zm00001d027324_T002:5 Zm00001d027324_T001:5

			
						 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  
						
							ACTGATTATCGTTTTGGGTTGTTTGTAGCAAGAACTTTTTGGACGTGGCAAACTAGTTATGCTA
AGGACTTGCAACCAACTTCTTCGCAGACTATCGAAGggagttttcaggagcgcgttgtctagga
acgaacccccggaaacattttcccttcagacggttcaggaagcaattaaacctcaggtatgtac
gttgaatc

									
								

					

						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: 468
Transcript exons: 2960401-2960484,2960662-2960736,2961052-2961142,2961280-
2961425,2961525-2961596
GGAGTTTTCAGGAGCGCGTTGTCTAGGAACGAACCCCCGGAAACATTTTCCCTTCAGACGGTTC
AGGAAGCAATTAAACCTCAGAAGGAAACCGTGTTGGTTCTAGAGGAGAATCAGTCCTTGGAAAA
TGCTCTTCGAACTTTGCTGCAGGAGCTTGTGTCATCTGCGGTCCAATCGGATAAAAAGATTATG
CAGTACGGGAATTCTTTGGATAGCGGAGAAAGTAACTGCCTGATAACTCGCCTTCTTGATATTG
TGCTTTACCTTTGCGAAAGAGGGCATGTTGAAGGTGGTATGGTATTCCAGCTGTTAGAAGACCT
AACTGAAATGTCAACAATCAAAGACTGCAAAGATATCTTTGGGTATATTGAGAGCCAGCAAGAT
GTATTGGGGAAGCAAGAACTTTTTGGACGTGGCAAACTAGTTATGCTAAGGACTTGCAACCAAC
TTCTTCGCAGACTATCGAAG
						
					

						Genomic sequence
						
							GGAGTTTTCAGGAGCGCGTTGTCTAGGAACGAACCCCCGGAAACATTTTCCCTTCAGACGGTTC
AGGAAGCAATTAAACCTCAGGTATGTACGTTGAATCTGGCATGCTTGTGAGTCTTGATTTGATG
ATGAACCGTCAGTGGTTCATGTTATTATTTTCCTCTATTTTATTTGCTTGTGTTTTGGGTAATA
CCTATCTGATTCGACTTGTCTTTTAGTTCAGTTAATCATCTGATTTGACACACATATCTCATTT
CACAGAAGGAAACCGTGTTGGTTCTAGAGGAGAATCAGTCCTTGGAAAATGCTCTTCGAACTTT
GCTGCAGGAGCTTGTGGTAACTTTCCATGTGGCTACACTGTTCTTTGATCTCACTTGATGATAA
GGTGGTTAGGGAGTGTTGTTGGCGCGTGCATTGTTCTGGTCACTGCATCGTTAGGAATACTATG
TTTCAGAGTAGCAGAGTTTTAATGACGATTTCTAAAATAAAACGGAAGACGTGGCTGTATTTTT
TTTATTTCAGTCCTAGAAAATTACATTGATTGCTGATTCTGTTTTATATGAAAAGTGCAGGTCA
GCAGGTGTATAGTTCATTTGCCATCTTAGGAACCAAAATTGATTGCTGATTCTGTTTTATATTT
TTTATTCTTAGTCATCTGCGGTCCAATCGGATAAAAAGATTATGCAGTACGGGAATTCTTTGGA
TAGCGGAGAAAGTAACTGCCTGATAACTCGCCTTCTTGGTCAGTTACACTTCTTCCAACATTCT
ATGTTCGAATCTGTTCCTATCTAAGGACTTATGCCATCACCTTCTGAGCACTATTTGGTGCATG
TGTAGTATTATTTTCTGTTCTGAGAAACCAATGCTCTTCCATGATAGATATTGTGCTTTACCTT
TGCGAAAGAGGGCATGTTGAAGGTGGTATGGTATTCCAGCTGTTAGAAGACCTAACTGAAATGT
CAACAATCAAAGACTGCAAAGATATCTTTGGGTATATTGAGAGCCAGCAAGATGTATTGGGGAA
GGTAATTTTGATCCCTATTTCGTTTGGTTAGTTCTGGTTAAATAGAGAAGATGCATGCTTGTAA
CGTTGTTGACTGATTATCGTTTTGGGTTGTTTGTAGCAAGAACTTTTTGGACGTGGCAAACTAG
TTATGCTAAGGACTTGCAACCAACTTCTTCGCAGACTATCGAAG
						
					

			
		

Sequences
Splice junction sequence	ACTGATTATCGTTTTGGGTTGTTTGTAGCAAGAACTTTTTGGACGTGGCAAACTAGTTATGCTA AGGACTTGCAACCAACTTCTTCGCAGACTATCGAAGggagttttcaggagcgcgttgtctagga acgaacccccggaaacattttcccttcagacggttcaggaagcaattaaacctcaggtatgtac gttgaatc
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: 468 Transcript exons: 2960401-2960484,2960662-2960736,2961052-2961142,2961280- 2961425,2961525-2961596 GGAGTTTTCAGGAGCGCGTTGTCTAGGAACGAACCCCCGGAAACATTTTCCCTTCAGACGGTTC AGGAAGCAATTAAACCTCAGAAGGAAACCGTGTTGGTTCTAGAGGAGAATCAGTCCTTGGAAAA TGCTCTTCGAACTTTGCTGCAGGAGCTTGTGTCATCTGCGGTCCAATCGGATAAAAAGATTATG CAGTACGGGAATTCTTTGGATAGCGGAGAAAGTAACTGCCTGATAACTCGCCTTCTTGATATTG TGCTTTACCTTTGCGAAAGAGGGCATGTTGAAGGTGGTATGGTATTCCAGCTGTTAGAAGACCT AACTGAAATGTCAACAATCAAAGACTGCAAAGATATCTTTGGGTATATTGAGAGCCAGCAAGAT GTATTGGGGAAGCAAGAACTTTTTGGACGTGGCAAACTAGTTATGCTAAGGACTTGCAACCAAC TTCTTCGCAGACTATCGAAG
Genomic sequence	GGAGTTTTCAGGAGCGCGTTGTCTAGGAACGAACCCCCGGAAACATTTTCCCTTCAGACGGTTC AGGAAGCAATTAAACCTCAGGTATGTACGTTGAATCTGGCATGCTTGTGAGTCTTGATTTGATG ATGAACCGTCAGTGGTTCATGTTATTATTTTCCTCTATTTTATTTGCTTGTGTTTTGGGTAATA CCTATCTGATTCGACTTGTCTTTTAGTTCAGTTAATCATCTGATTTGACACACATATCTCATTT CACAGAAGGAAACCGTGTTGGTTCTAGAGGAGAATCAGTCCTTGGAAAATGCTCTTCGAACTTT GCTGCAGGAGCTTGTGGTAACTTTCCATGTGGCTACACTGTTCTTTGATCTCACTTGATGATAA GGTGGTTAGGGAGTGTTGTTGGCGCGTGCATTGTTCTGGTCACTGCATCGTTAGGAATACTATG TTTCAGAGTAGCAGAGTTTTAATGACGATTTCTAAAATAAAACGGAAGACGTGGCTGTATTTTT TTTATTTCAGTCCTAGAAAATTACATTGATTGCTGATTCTGTTTTATATGAAAAGTGCAGGTCA GCAGGTGTATAGTTCATTTGCCATCTTAGGAACCAAAATTGATTGCTGATTCTGTTTTATATTT TTTATTCTTAGTCATCTGCGGTCCAATCGGATAAAAAGATTATGCAGTACGGGAATTCTTTGGA TAGCGGAGAAAGTAACTGCCTGATAACTCGCCTTCTTGGTCAGTTACACTTCTTCCAACATTCT ATGTTCGAATCTGTTCCTATCTAAGGACTTATGCCATCACCTTCTGAGCACTATTTGGTGCATG TGTAGTATTATTTTCTGTTCTGAGAAACCAATGCTCTTCCATGATAGATATTGTGCTTTACCTT TGCGAAAGAGGGCATGTTGAAGGTGGTATGGTATTCCAGCTGTTAGAAGACCTAACTGAAATGT CAACAATCAAAGACTGCAAAGATATCTTTGGGTATATTGAGAGCCAGCAAGATGTATTGGGGAA GGTAATTTTGATCCCTATTTCGTTTGGTTAGTTCTGGTTAAATAGAGAAGATGCATGCTTGTAA CGTTGTTGACTGATTATCGTTTTGGGTTGTTTGTAGCAAGAACTTTTTGGACGTGGCAAACTAG TTATGCTAAGGACTTGCAACCAACTTCTTCGCAGACTATCGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.093489293

Conservation Information
Conserved circRNAs	NA
PMCS	0.093489293

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2961083-2961593(+)
						
						Potential amino acid sequence
						
							MQYGNSLDSGESNCLITRLLDIVLYLCERGHVEGGMVFQLLEDLTEMSTIKDCKDIFGYIESQQ
DVLGKQELFGRGKLVMLRTCNQLLRRLSKGVFRSALSRNEPPETFSLQTVQEAIKPQKETVLVL
EENQSLENALRTLLQELVSSAVQSDKKIMQYGNSLDSGESNCLITRLLDIVLYLCERGHVEGGM
VFQLLEDLTEMSTIKDCKDIFGYIESQQDVLGKQELFGRGKLVMLRTCNQLLRRLSKGVFRSAL
SRNEPPETFSLQTVQEAIKPQKETVLVLEENQSLENALRTLLQELVSSAVQSDKKIMQYGNSLD
SGESNCLITRLLDIVLYLCERGHVEGGMVFQLLEDLTEMSTIKDCKDIFGYIESQQDVLGKQEL
FGRGKLVMLRTCNQLLRRLSKGVFRSALSRNEPPETFSLQTVQEAIKPQKETVLVLEENQSLEN
ALRTLLQELVSSAVQSDKKIMQYGNSLDSGESNCLITRLLDIVLYLCERGHVEGGMVFQLLEDL
TEMSTIKDCKDIFGYIESQQDVLGKQELFGRGKLVMLRTCNQLLRRLSK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2961083-2961593(+)
Potential amino acid sequence	MQYGNSLDSGESNCLITRLLDIVLYLCERGHVEGGMVFQLLEDLTEMSTIKDCKDIFGYIESQQ DVLGKQELFGRGKLVMLRTCNQLLRRLSKGVFRSALSRNEPPETFSLQTVQEAIKPQKETVLVL EENQSLENALRTLLQELVSSAVQSDKKIMQYGNSLDSGESNCLITRLLDIVLYLCERGHVEGGM VFQLLEDLTEMSTIKDCKDIFGYIESQQDVLGKQELFGRGKLVMLRTCNQLLRRLSKGVFRSAL SRNEPPETFSLQTVQEAIKPQKETVLVLEENQSLENALRTLLQELVSSAVQSDKKIMQYGNSLD SGESNCLITRLLDIVLYLCERGHVEGGMVFQLLEDLTEMSTIKDCKDIFGYIESQQDVLGKQEL FGRGKLVMLRTCNQLLRRLSKGVFRSALSRNEPPETFSLQTVQEAIKPQKETVLVLEENQSLEN ALRTLLQELVSSAVQSDKKIMQYGNSLDSGESNCLITRLLDIVLYLCERGHVEGGMVFQLLEDL TEMSTIKDCKDIFGYIESQQDVLGKQELFGRGKLVMLRTCNQLLRRLSK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d027324_circ_g.2

Address

Any questions?

Supported by