Plant Circular RNA Database

Detail information of Zm00001d029608_circ_g.6

			
						 General Information
					
						CircRNA Name
						Zm00001d029608_circ_g.6
					
						ID in PlantcircBase
						zma_circ_006565
					
						Alias
						Zm01circ00078, zma_circ_0000217
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 79104922-79113874  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d029608						
					
						Parent gene annotation
						
							Mechanosensitive ion channel protein 3 chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d029608_circ_g.1 Zm00001d029608_circ_g.2 Zm00001d029608_circ_g.3 Zm00001d029608_circ_g.4 Zm00001d029608_circ_g.5 Zm00001d029608_circ_g.7 Zm00001d029608_circ_g.8 Zm00001d029608_circ_g.9 Zm00001d029608_circ_g.10 Zm00001d029608_circ_g.11 						
					
						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
						Zm00001d029608_T001:10
Zm00001d029608_T004:9
Zm00001d029608_T006:5
Zm00001d029608_T005:10
Zm00001d029608_T011:11
Zm00001d029608_T002:10
Zm00001d029608_T008:11
Zm00001d029608_T007:11
Zm00001d029608_T014:11
Zm00001d029608_T009:10
Zm00001d029608_T013:11
Zm00001d029608_T015:10
Zm00001d029608_T003:10

General Information
CircRNA Name	Zm00001d029608_circ_g.6
ID in PlantcircBase	zma_circ_006565
Alias	Zm01circ00078, zma_circ_0000217
Organism	Zea mays
Position	chr1: 79104922-79113874 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d029608
Parent gene annotation	Mechanosensitive ion channel protein 3 chloroplastic
Parent gene strand	-
Alternative splicing	Zm00001d029608_circ_g.1 Zm00001d029608_circ_g.2 Zm00001d029608_circ_g.3 Zm00001d029608_circ_g.4 Zm00001d029608_circ_g.5 Zm00001d029608_circ_g.7 Zm00001d029608_circ_g.8 Zm00001d029608_circ_g.9 Zm00001d029608_circ_g.10 Zm00001d029608_circ_g.11
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	Zm00001d029608_T001:10 Zm00001d029608_T004:9 Zm00001d029608_T006:5 Zm00001d029608_T005:10 Zm00001d029608_T011:11 Zm00001d029608_T002:10 Zm00001d029608_T008:11 Zm00001d029608_T007:11 Zm00001d029608_T014:11 Zm00001d029608_T009:10 Zm00001d029608_T013:11 Zm00001d029608_T015:10 Zm00001d029608_T003:10

			
						 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  
						
							AACTGCCATCTCAACCAAAACTCAAATCCAATGAAATTTACATCCACTGGATGCAGTTTCTTAT
CAGCCACTGATGTGTAATATGTGCTAGATTGCAACCcataagtgcttgattttttggatcaatt
ttctcaaagaatactctcctgtgcagcttttgttgttctatatgcggattttttgccaaaactt
tcctcatg

									
								

					

						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: 3563
Transcript exons: 79104922-79105035,79105152-79105319,79105479-79105589,79
105661-79105810,79108386-79110802,79111177-79111271,7911
1397-79111517,79112628-79112785,79113563-79113622,791137
06-79113874
CATAAGTGCTTGATTTTTTGGATCAATTTTCTCAAAGAATACTCTCCTGTGCAGCTTTTGTTGT
TCTATATGCGGATTTTTTGCCAAAACTTTCCTCATGTCAGCAACTATAGTCCCAATTTTTCCAG
CATCCATGTGGCTAATAGCAAGATAGGTCTTAATACGCCAATGGGTCCTCTGAGTGTTATTCCT
TAATATAGAAACTGTAAACTTATGGTTAGGAATGTATATCGCTTCTCGATCAACACCTCTAATG
AGTGTTGGAGACCACAAACCAACATGCTCAACAATGCCAGAGACATCAACACCATCTATCTTTG
CATCGATCCATTCATTGACTACAAATGGGCGTGTTGCATTGATCATGACACTTGAGAGGAAGTT
AGTAAAAATCTCTCGACCAGCAAGTGTAAGCAACACTGTCCCAAACCCTCCAGCAGTTATCCAC
TTCTGGGTATTGAAACCCAGCAACTCCATAAAGAGAGAAACAGAAGCAATCCAAACACCAGTAT
AAAGAGCTTTCATGGTAAAATCAAACCCCATATTTCTTGTATCATTGGGATTGCGCATGTCCAT
AAGAAACTTTTGTACCTGCTGAATCAAGCTAAAAAGAACAAAAACTATCTTAGTGTTAACAAAA
CTTAATAAAACAGAACATAATGAAACCAAATCAATCATACAAGAGGACAACATAGATATAGACA
CATTAAAATTCATACAAATCAAGACAGCAAGGATTACGTGCATGTTTGAGAGTGAAGTATTTTT
GCAGCTTCTAGACGATACCATGGTTTTTGGAAATATCGTAGTATTTTATGTCATAAGATGTTTG
GTTGCATTTCTGAAAACTATGTTTTCAAAATCATGGTATCCCAGATACCATAGTATTTTTGGAG
TATTGGAAACTCCACTCTAACCCAAAGTTTTCATGGCAACTGGCTAGCTTTTGCCTAATACCAT
GGTTTACAATGTTGTATCCAAACAATACGGCCTTGTTTGGAAGTGTAGTATTTTTGCGGTTTCG
AAACAATACTATGGTATTTGATGATAGTGTAGTATTGGTCTATTGGAACTCAAAAGGTGTTTGG
TTTGTACAGGCAAAACACAGTTTCAAATACCATGGTTTCCCCAAAACCGTGGTATATTTGGAGT
TTTCGAAACTCCACTCAGGACCTCAGTTTTCTTCTCTTTTCTCTACATATACTTTGTTTTTCCA
ATAGAACCAAACAGATCTCGGTTTTGAGCAATACTGTGGTTTTACTGTGGTAAAGTAATACCGT
AGTATTTGTGTCATGTACAATTGTAAACTATGATATCTCAAAACTACAGTATTTCAAAACTGCA
TTCCCAAACAGGCCCTACTTCTCATAACCATGGTACTTTTGGAGCTGCCAAAACTACGGTATTG
TCACGACAATTGCAAAGTATAGTATTGTAAAACCATAGCTTTGAGAAACATTGTTACCAAACAG
GCCCTAACACATATCTGCACATCTTCCCATTGTAATACATGAAACACCATTGTACCTTAACTAA
GATGGTGTTTGGTTCCCCTAACTAAAGTTTAGTACGTGTCACATTGGATGTTTGAACACCAATT
ACGAGTATTAAATATAGTCTAATTACGAAATTGATTATATAGATGAAGACTAAACGACAAGACG
AATTTATTAAGCTTAATAATTCATGATTAGTAAATGTTTACTGTAGCATCATATGAGCGAACCA
TGGACTAATTAGGTTTAATGGATTTGTCTTACCGTTTAGTCCTTATTTGTGTAATTAGTTTTGT
AATTAGACTATATTTAATACTTCTAACTAGTGTTCAAAGATCCGATGTGACGGAACTAAAATTT
AGTCCTTTTAATCCAAATAGACCTTAATAATTCATCTGGATATATTCAACAAAACAAAAAATAA
TAGTATCACAAATATCACATCCATGATTCCTAGATATACAATGTTGAAATTAACTTAAAATAGA
TCACAATGCGATACATAATGTTAGCACGGAATGGCACTCACATCTCGGAATACCTTTTGTATGC
TTTAAAATTATATAAGTTTTAGCATTCCCCATATCTAAGTAGAAAAAAGTTCCAATACATTACT
CATCTATTTGTATTTGTATACCACAAACTGAAGCTAATCTTTGTTTATTCTTGTAATCTCACCA
GCTGTATTTCTTTGATATATGCAAAAGAGCCTCTACCGATGGTTAGGTGGTTTGAGTAGCATTC
TTCCGGTCCTGGTTCGACTTTCCATCAGATCGAAATTCAGGCTAGGGTTAAAAAATTCTCTCAT
TTATCCCATGCCAAAGCACAAGACTAAGGCACATCCCTAGTCATGGTCGTTCTCACATGGGCTA
TGGTGTTGCTGTGTATGTGGGGCAGGGCCGCAGGGGTTTCTCCAGCTCTCCACCAACGTGAAAA
GGACAAAAGGTACTCTCCTTAATGCAATGCCTGACCCCCCCCCCCACCAGCGCAGTTCGAGGTT
TTTTATTATTTTTTACATACTATCACTAATATTTCAATCACCAATATGTAATTAGTTTATCTAG
TTGTGCCAGAACTATGCATTGTCATTCAAGCTACGTAGCCAGCAAACCAACCATTTGTATTTCA
AGATGATAGACAAAACTAAAGTTGGGGAGAAAAGAACCGTCCATGGCCAAAATTGTAATTTGTA
ATCTCCAACATGTGCTTTTGCAGTTACAGTTATCTTGAGTACTACTTGACTGCATAAATGTTGT
CATTACCTGTACATAACTTAGATGGGCATGATCGAATTAAAGCTACAACTTACAAAAAACAACT
GCAGTTTTTCTGAGGATGTAGCATGTGCACCTTGTGAGAATATATGCAACAGCCAGGACAGTTG
ATAATGATCTCACAAAAGTTATCAGACGTGTTTTCACAGCTTGACTTGCTGCTGAAGGCAAGAC
AACTGGATCCAAACCCCTGCAGATTAGTGTTGCTCCTGTCCAGAGAAGTAGAGGTTGAAGGTAC
GACGAAGAAATCAAATATGTAGGACTCTTCTTCCAGTTGCCTCCATGATCAAAACGGTTTCTAA
TATCCCGCATTAGAGGCAAAAAACCCCACAGAGCAAACACAATAATCCCGATTGCAGGGACCAC
AAGTGAGGTAGCAGGATTTGCAAGTAAAGCATCACATGACCTAGTTAGTGCTAATGATGTGTTC
TTGACAAGAGGAATTTCCTTCAAAGGAATTGGCAAGGCAAAAGATCTAAAGCCCAAAGATCTAT
ATCTGCGAGGTGTATAAAGCATGGGCATGCAGCTACTCTCTAACACATTGCGACCCCAACAGTC
TCGCCTATCAGCAACTGAAGGAAACGAGGTGGATGGCAAGGGAAGAGAACTCCTCATCTCAGAA
CTCCTAAATTTGTTCCTTTGGCAAAAGATGTCAGTAGCAGTTACTCTTTGGAACAGCTGAGATG
TCAATCCAACTGCCATCTCAACCAAAACTCAAATCCAATGAAATTTACATCCACTGGATGCAGT
TTCTTATCAGCCACTGATGTGTAATATGTGCTAGATTGCAACC
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	AACTGCCATCTCAACCAAAACTCAAATCCAATGAAATTTACATCCACTGGATGCAGTTTCTTAT CAGCCACTGATGTGTAATATGTGCTAGATTGCAACCcataagtgcttgattttttggatcaatt ttctcaaagaatactctcctgtgcagcttttgttgttctatatgcggattttttgccaaaactt tcctcatg
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: 3563 Transcript exons: 79104922-79105035,79105152-79105319,79105479-79105589,79 105661-79105810,79108386-79110802,79111177-79111271,7911 1397-79111517,79112628-79112785,79113563-79113622,791137 06-79113874 CATAAGTGCTTGATTTTTTGGATCAATTTTCTCAAAGAATACTCTCCTGTGCAGCTTTTGTTGT TCTATATGCGGATTTTTTGCCAAAACTTTCCTCATGTCAGCAACTATAGTCCCAATTTTTCCAG CATCCATGTGGCTAATAGCAAGATAGGTCTTAATACGCCAATGGGTCCTCTGAGTGTTATTCCT TAATATAGAAACTGTAAACTTATGGTTAGGAATGTATATCGCTTCTCGATCAACACCTCTAATG AGTGTTGGAGACCACAAACCAACATGCTCAACAATGCCAGAGACATCAACACCATCTATCTTTG CATCGATCCATTCATTGACTACAAATGGGCGTGTTGCATTGATCATGACACTTGAGAGGAAGTT AGTAAAAATCTCTCGACCAGCAAGTGTAAGCAACACTGTCCCAAACCCTCCAGCAGTTATCCAC TTCTGGGTATTGAAACCCAGCAACTCCATAAAGAGAGAAACAGAAGCAATCCAAACACCAGTAT AAAGAGCTTTCATGGTAAAATCAAACCCCATATTTCTTGTATCATTGGGATTGCGCATGTCCAT AAGAAACTTTTGTACCTGCTGAATCAAGCTAAAAAGAACAAAAACTATCTTAGTGTTAACAAAA CTTAATAAAACAGAACATAATGAAACCAAATCAATCATACAAGAGGACAACATAGATATAGACA CATTAAAATTCATACAAATCAAGACAGCAAGGATTACGTGCATGTTTGAGAGTGAAGTATTTTT GCAGCTTCTAGACGATACCATGGTTTTTGGAAATATCGTAGTATTTTATGTCATAAGATGTTTG GTTGCATTTCTGAAAACTATGTTTTCAAAATCATGGTATCCCAGATACCATAGTATTTTTGGAG TATTGGAAACTCCACTCTAACCCAAAGTTTTCATGGCAACTGGCTAGCTTTTGCCTAATACCAT GGTTTACAATGTTGTATCCAAACAATACGGCCTTGTTTGGAAGTGTAGTATTTTTGCGGTTTCG AAACAATACTATGGTATTTGATGATAGTGTAGTATTGGTCTATTGGAACTCAAAAGGTGTTTGG TTTGTACAGGCAAAACACAGTTTCAAATACCATGGTTTCCCCAAAACCGTGGTATATTTGGAGT TTTCGAAACTCCACTCAGGACCTCAGTTTTCTTCTCTTTTCTCTACATATACTTTGTTTTTCCA ATAGAACCAAACAGATCTCGGTTTTGAGCAATACTGTGGTTTTACTGTGGTAAAGTAATACCGT AGTATTTGTGTCATGTACAATTGTAAACTATGATATCTCAAAACTACAGTATTTCAAAACTGCA TTCCCAAACAGGCCCTACTTCTCATAACCATGGTACTTTTGGAGCTGCCAAAACTACGGTATTG TCACGACAATTGCAAAGTATAGTATTGTAAAACCATAGCTTTGAGAAACATTGTTACCAAACAG GCCCTAACACATATCTGCACATCTTCCCATTGTAATACATGAAACACCATTGTACCTTAACTAA GATGGTGTTTGGTTCCCCTAACTAAAGTTTAGTACGTGTCACATTGGATGTTTGAACACCAATT ACGAGTATTAAATATAGTCTAATTACGAAATTGATTATATAGATGAAGACTAAACGACAAGACG AATTTATTAAGCTTAATAATTCATGATTAGTAAATGTTTACTGTAGCATCATATGAGCGAACCA TGGACTAATTAGGTTTAATGGATTTGTCTTACCGTTTAGTCCTTATTTGTGTAATTAGTTTTGT AATTAGACTATATTTAATACTTCTAACTAGTGTTCAAAGATCCGATGTGACGGAACTAAAATTT AGTCCTTTTAATCCAAATAGACCTTAATAATTCATCTGGATATATTCAACAAAACAAAAAATAA TAGTATCACAAATATCACATCCATGATTCCTAGATATACAATGTTGAAATTAACTTAAAATAGA TCACAATGCGATACATAATGTTAGCACGGAATGGCACTCACATCTCGGAATACCTTTTGTATGC TTTAAAATTATATAAGTTTTAGCATTCCCCATATCTAAGTAGAAAAAAGTTCCAATACATTACT CATCTATTTGTATTTGTATACCACAAACTGAAGCTAATCTTTGTTTATTCTTGTAATCTCACCA GCTGTATTTCTTTGATATATGCAAAAGAGCCTCTACCGATGGTTAGGTGGTTTGAGTAGCATTC TTCCGGTCCTGGTTCGACTTTCCATCAGATCGAAATTCAGGCTAGGGTTAAAAAATTCTCTCAT TTATCCCATGCCAAAGCACAAGACTAAGGCACATCCCTAGTCATGGTCGTTCTCACATGGGCTA TGGTGTTGCTGTGTATGTGGGGCAGGGCCGCAGGGGTTTCTCCAGCTCTCCACCAACGTGAAAA GGACAAAAGGTACTCTCCTTAATGCAATGCCTGACCCCCCCCCCCACCAGCGCAGTTCGAGGTT TTTTATTATTTTTTACATACTATCACTAATATTTCAATCACCAATATGTAATTAGTTTATCTAG TTGTGCCAGAACTATGCATTGTCATTCAAGCTACGTAGCCAGCAAACCAACCATTTGTATTTCA AGATGATAGACAAAACTAAAGTTGGGGAGAAAAGAACCGTCCATGGCCAAAATTGTAATTTGTA ATCTCCAACATGTGCTTTTGCAGTTACAGTTATCTTGAGTACTACTTGACTGCATAAATGTTGT CATTACCTGTACATAACTTAGATGGGCATGATCGAATTAAAGCTACAACTTACAAAAAACAACT GCAGTTTTTCTGAGGATGTAGCATGTGCACCTTGTGAGAATATATGCAACAGCCAGGACAGTTG ATAATGATCTCACAAAAGTTATCAGACGTGTTTTCACAGCTTGACTTGCTGCTGAAGGCAAGAC AACTGGATCCAAACCCCTGCAGATTAGTGTTGCTCCTGTCCAGAGAAGTAGAGGTTGAAGGTAC GACGAAGAAATCAAATATGTAGGACTCTTCTTCCAGTTGCCTCCATGATCAAAACGGTTTCTAA TATCCCGCATTAGAGGCAAAAAACCCCACAGAGCAAACACAATAATCCCGATTGCAGGGACCAC AAGTGAGGTAGCAGGATTTGCAAGTAAAGCATCACATGACCTAGTTAGTGCTAATGATGTGTTC TTGACAAGAGGAATTTCCTTCAAAGGAATTGGCAAGGCAAAAGATCTAAAGCCCAAAGATCTAT ATCTGCGAGGTGTATAAAGCATGGGCATGCAGCTACTCTCTAACACATTGCGACCCCAACAGTC TCGCCTATCAGCAACTGAAGGAAACGAGGTGGATGGCAAGGGAAGAGAACTCCTCATCTCAGAA CTCCTAAATTTGTTCCTTTGGCAAAAGATGTCAGTAGCAGTTACTCTTTGGAACAGCTGAGATG TCAATCCAACTGCCATCTCAACCAAAACTCAAATCCAATGAAATTTACATCCACTGGATGCAGT TTCTTATCAGCCACTGATGTGTAATATGTGCTAGATTGCAACC
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.053586843

Conservation Information
Conserved circRNAs	NA
PMCS	0.053586843

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							79108633-79113814(-)
						
						Potential amino acid sequence
						
							MVSSRSCKNTSLSNMHVILAVLICMNFNVSISMLSSCMIDLVSLCSVLLSFVNTKIVFVLFSLI
QQVQKFLMDMRNPNDTRNMGFDFTMKALYTGVWIASVSLFMELLGFNTQKWITAGGFGTVLLTL
AGREIFTNFLSSVMINATRPFVVNEWIDAKIDGVDVSGIVEHVGLWSPTLIRGVDREAIYIPNH
KFTVSILRNNTQRTHWRIKTYLAISHMDAGKIGTIVADMRKVLAKNPHIEQQKLHRRVFFEKID
PKNQALMGCNLAHITHQWLIRNCIQWM*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	79108633-79113814(-)
Potential amino acid sequence	MVSSRSCKNTSLSNMHVILAVLICMNFNVSISMLSSCMIDLVSLCSVLLSFVNTKIVFVLFSLI QQVQKFLMDMRNPNDTRNMGFDFTMKALYTGVWIASVSLFMELLGFNTQKWITAGGFGTVLLTL AGREIFTNFLSSVMINATRPFVVNEWIDAKIDGVDVSGIVEHVGLWSPTLIRGVDREAIYIPNH KFTVSILRNNTQRTHWRIKTYLAISHMDAGKIGTIVADMRKVLAKNPHIEQQKLHRRVFFEKID PKNQALMGCNLAHITHQWLIRNCIQWM*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d029608_circ_g.6

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