Plant Circular RNA Database

Detail information of Zm00001d027333_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d027333_circ_g.3
					
						ID in PlantcircBase
						zma_circ_006345
					
						Alias
						Zm01circ00004
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 3107011-3116066  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d027333						
					
						Parent gene annotation
						
							AP-2 complex subunit alpha-2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d027333_circ_g.1 Zm00001d027333_circ_g.2 						
					
						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
						Zm00001d027333_T011:11
Zm00001d027333_T009:12
Zm00001d027333_T010:11
Zm00001d027333_T026:11
Zm00001d027333_T016:11
Zm00001d027333_T027:9
Zm00001d027333_T002:11
Zm00001d027333_T004:11
Zm00001d027333_T017:11
Zm00001d027333_T015:11
Zm00001d027333_T038:4
Zm00001d027333_T028:11
Zm00001d027333_T029:10
Zm00001d027333_T014:11
Zm00001d027333_T022:11
Zm00001d027333_T030:10
Zm00001d027333_T006:11
Zm00001d027333_T035:7
Zm00001d027333_T037:7
Zm00001d027333_T019:12
Zm00001d027333_T025:10
Zm00001d027333_T008:11
Zm00001d027333_T005:11
Zm00001d027333_T013:10
Zm00001d027333_T032:11
Zm00001d027333_T021:11
Zm00001d027333_T020:11
Zm00001d027333_T012:10
Zm00001d027333_T018:11
Zm00001d027333_T024:11
Zm00001d027333_T007:11
Zm00001d027333_T001:13
Zm00001d027333_T003:10
Zm00001d027333_T023:11

General Information
CircRNA Name	Zm00001d027333_circ_g.3
ID in PlantcircBase	zma_circ_006345
Alias	Zm01circ00004
Organism	Zea mays
Position	chr1: 3107011-3116066 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2
Parent gene	Zm00001d027333
Parent gene annotation	AP-2 complex subunit alpha-2
Parent gene strand	+
Alternative splicing	Zm00001d027333_circ_g.1 Zm00001d027333_circ_g.2
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	Zm00001d027333_T011:11 Zm00001d027333_T009:12 Zm00001d027333_T010:11 Zm00001d027333_T026:11 Zm00001d027333_T016:11 Zm00001d027333_T027:9 Zm00001d027333_T002:11 Zm00001d027333_T004:11 Zm00001d027333_T017:11 Zm00001d027333_T015:11 Zm00001d027333_T038:4 Zm00001d027333_T028:11 Zm00001d027333_T029:10 Zm00001d027333_T014:11 Zm00001d027333_T022:11 Zm00001d027333_T030:10 Zm00001d027333_T006:11 Zm00001d027333_T035:7 Zm00001d027333_T037:7 Zm00001d027333_T019:12 Zm00001d027333_T025:10 Zm00001d027333_T008:11 Zm00001d027333_T005:11 Zm00001d027333_T013:10 Zm00001d027333_T032:11 Zm00001d027333_T021:11 Zm00001d027333_T020:11 Zm00001d027333_T012:10 Zm00001d027333_T018:11 Zm00001d027333_T024:11 Zm00001d027333_T007:11 Zm00001d027333_T001:13 Zm00001d027333_T003:10 Zm00001d027333_T023:11

			
						 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  
						
							TTACCTCACAGTACCTTGATACAGCAGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGC
TATTCTTGCAGAAAAATTTGCTCCGCAACTATTGTGggcttatcaccatacgagaagaaaaaat
atgtatggaaaatgctttacatttatatgctgggttatgatgttgattttgggcatatggaaac
tgtctcgt

									
								

					

						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: 1665
Transcript exons: 3107011-3107142,3107273-3107398,3107555-3107587,3107634-
3107980,3108293-3108477,3108560-3108657,3108737-3108944,
3109597-3109668,3109746-3109838,3109925-3110026,3110149-
3110246,3115792-3115873,3115978-3116066
GGCTTATCACCATACGAGAAGAAAAAATATGTATGGAAAATGCTTTACATTTATATGCTGGGTT
ATGATGTTGATTTTGGGCATATGGAAACTGTCTCGTTGATATCTGCACCAAAGTATCCTGAGAA
GCAGGTTGGGTATATTGTGACATCTTGCTTACTGAATGAGAATAATGATTTCTTAAGAATGGTA
ATAAATACAGTAAGGAATGACATAATCGGACGAAATGAGACCTTCCAGTGCTTAGCATTGACAA
TGGCTGTGTCGAACATAAGGCCTTTGGCTCAGTGGAACTATCACATAAATTTGATTTAGAAAAG
GCACTTTTGTCGTATTAAAACTATCTTGTGGTGCAATAAGTTGTTATGGACATCTAATTAGTAC
AAACATCATAAAAGAAAATAAACAACTCAAACTTGAAAGCAATGTCTTCAAAATTGCAGAGCAT
GTGTTAAGATCTTCACTAGATTTTAGGCATATTCTTGTTATTTAATGGTTTTTTATTGCTATAC
CTTATATTGACTTTTATTGTTATTTTTTTTGTTGTAATAATTTTTTTTGTTTCTACGTCTTGAG
CTTCATAATAATTATTTTATGAGATATCATATTGCACACCTCCTACATCTACCACACTAAGGAA
TTTAGTCCATTTCATCTGCTCTAAGACTTGATAGTCTAGCTCTTATATTATCCCCCCTGCAATT
ACACTTTTTTCCTGTCTCCTGTGTCCTGTGTCATCTTTTCTTGAAATATTTTTCAGGTAGGTAA
CATTGGTGGTAAAGAATTTTCTGAGTCACTAGCCCCAGATGTCCAGAAACTTCTTATTTCAAGC
AGTTGCCGTCCTGTTGTCAGAAAGAAGGCTGCTCTATGCCTTCTGCGGCTTTATAGGAAGAATC
CTGATGTTGTGAATATTGATGGCTGGGCTGACCGAATGGCACAACTTCTAGATGAGCGTGATTT
AGGTGTGCTGACATCTGTCACGAGTCTTTTTGTTTCACTAGTATCCAACAATGTTGAAGCATAT
TGGAATTGTCTTCCTAAATGTGTGAGAATATTGGAGAGGTTAGCAAGAAATCAAGATATTCCAC
AAGAGTACACTTACTATGGAATTCCATCTCCTTGGCTTCAGGTTAAGACAATGAGAGCTCTTCA
GTACTTCCCTACCATTGAAGATCCCAACGCAAGACGAGCTTTGTTTGAGGTTTTACAGCGCATT
TTGATGGGTACTGATGTTGTTAAAAACGTTAACAAGAACAATGCCTCACATGCTGTTCTCTTTG
AAGCTCTTGCTCTGGTCATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCT
TCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGGAAAACATGACT
AGGATGCTGTTAGTAACAGATGTGCAGGATATCATTAAAAGGCACCAGGCTCAGATCATCACAT
CTTTGAAGGATCCAGATATCAGCATTAGGAGAAGGGCTCTTGATTTATTATATGGCATGTGTGA
TGTTACAAACGCGAAGGAAATTGTGGAGGAGTTGTTGCAGTACCTTGATACAGCAGAATTTGCA
ATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCGCAACTATTGT
G
						
					

						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	TTACCTCACAGTACCTTGATACAGCAGAATTTGCAATGCGTGAAGAGTTGTCTCTGAAGGCAGC TATTCTTGCAGAAAAATTTGCTCCGCAACTATTGTGggcttatcaccatacgagaagaaaaaat atgtatggaaaatgctttacatttatatgctgggttatgatgttgattttgggcatatggaaac tgtctcgt
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: 1665 Transcript exons: 3107011-3107142,3107273-3107398,3107555-3107587,3107634- 3107980,3108293-3108477,3108560-3108657,3108737-3108944, 3109597-3109668,3109746-3109838,3109925-3110026,3110149- 3110246,3115792-3115873,3115978-3116066 GGCTTATCACCATACGAGAAGAAAAAATATGTATGGAAAATGCTTTACATTTATATGCTGGGTT ATGATGTTGATTTTGGGCATATGGAAACTGTCTCGTTGATATCTGCACCAAAGTATCCTGAGAA GCAGGTTGGGTATATTGTGACATCTTGCTTACTGAATGAGAATAATGATTTCTTAAGAATGGTA ATAAATACAGTAAGGAATGACATAATCGGACGAAATGAGACCTTCCAGTGCTTAGCATTGACAA TGGCTGTGTCGAACATAAGGCCTTTGGCTCAGTGGAACTATCACATAAATTTGATTTAGAAAAG GCACTTTTGTCGTATTAAAACTATCTTGTGGTGCAATAAGTTGTTATGGACATCTAATTAGTAC AAACATCATAAAAGAAAATAAACAACTCAAACTTGAAAGCAATGTCTTCAAAATTGCAGAGCAT GTGTTAAGATCTTCACTAGATTTTAGGCATATTCTTGTTATTTAATGGTTTTTTATTGCTATAC CTTATATTGACTTTTATTGTTATTTTTTTTGTTGTAATAATTTTTTTTGTTTCTACGTCTTGAG CTTCATAATAATTATTTTATGAGATATCATATTGCACACCTCCTACATCTACCACACTAAGGAA TTTAGTCCATTTCATCTGCTCTAAGACTTGATAGTCTAGCTCTTATATTATCCCCCCTGCAATT ACACTTTTTTCCTGTCTCCTGTGTCCTGTGTCATCTTTTCTTGAAATATTTTTCAGGTAGGTAA CATTGGTGGTAAAGAATTTTCTGAGTCACTAGCCCCAGATGTCCAGAAACTTCTTATTTCAAGC AGTTGCCGTCCTGTTGTCAGAAAGAAGGCTGCTCTATGCCTTCTGCGGCTTTATAGGAAGAATC CTGATGTTGTGAATATTGATGGCTGGGCTGACCGAATGGCACAACTTCTAGATGAGCGTGATTT AGGTGTGCTGACATCTGTCACGAGTCTTTTTGTTTCACTAGTATCCAACAATGTTGAAGCATAT TGGAATTGTCTTCCTAAATGTGTGAGAATATTGGAGAGGTTAGCAAGAAATCAAGATATTCCAC AAGAGTACACTTACTATGGAATTCCATCTCCTTGGCTTCAGGTTAAGACAATGAGAGCTCTTCA GTACTTCCCTACCATTGAAGATCCCAACGCAAGACGAGCTTTGTTTGAGGTTTTACAGCGCATT TTGATGGGTACTGATGTTGTTAAAAACGTTAACAAGAACAATGCCTCACATGCTGTTCTCTTTG AAGCTCTTGCTCTGGTCATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCT TCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTCTGGAAAACATGACT AGGATGCTGTTAGTAACAGATGTGCAGGATATCATTAAAAGGCACCAGGCTCAGATCATCACAT CTTTGAAGGATCCAGATATCAGCATTAGGAGAAGGGCTCTTGATTTATTATATGGCATGTGTGA TGTTACAAACGCGAAGGAAATTGTGGAGGAGTTGTTGCAGTACCTTGATACAGCAGAATTTGCA ATGCGTGAAGAGTTGTCTCTGAAGGCAGCTATTCTTGCAGAAAAATTTGCTCCGCAACTATTGT G
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
						0.104454845

Conservation Information
Conserved circRNAs	NA
PMCS	0.104454845

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3107051-3107110(+)
3107392-3116061(-)
						
						Potential amino acid sequence
						
							MLYIYMLGYDVDFGHMETVSLISAPKYPEKQVGYIVTSCLLNENNDFLRMVINTVRNDIIGRNE
TFQCLALTMVGNIGGKEFSESLAPDVQKLLISSSCRPVVRKKAALCLLRLYRKNPDVVNIDGWA
DRMAQLLDERDLGVLTSVTSLFVSLVSNNVEAYWNCLPKCVRILERLARNQDIPQEYTYYGIPS
PWLQVKTMRALQYFPTIEDPNARRALFEVLQRILMGTDVVKNVNKNNASHAVLFEALALVMHLD
AEKEMMSQCVALLGKFIAVREPNIRYLGLENMTRMLLVTDVQDIIKRHQAQIITSLKDPDISIR
RRALDLLYGMCDVTNAKEIVEELLQYLDTAEFAMREELSLKAAILAEKFAPQLLWAYHHTRRKN
MYGKCFTFICWVMMLILGIWKLSR*(+)
MLSTGRSHFVRLCHSLLYLLPFLRNHYSHSVSKMSQYTQPASQDTLVQISTRQFPYAQNQHHNP
AYKCKAFSIHIFSSRMVISPQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3107051-3107110(+) 3107392-3116061(-)
Potential amino acid sequence	MLYIYMLGYDVDFGHMETVSLISAPKYPEKQVGYIVTSCLLNENNDFLRMVINTVRNDIIGRNE TFQCLALTMVGNIGGKEFSESLAPDVQKLLISSSCRPVVRKKAALCLLRLYRKNPDVVNIDGWA DRMAQLLDERDLGVLTSVTSLFVSLVSNNVEAYWNCLPKCVRILERLARNQDIPQEYTYYGIPS PWLQVKTMRALQYFPTIEDPNARRALFEVLQRILMGTDVVKNVNKNNASHAVLFEALALVMHLD AEKEMMSQCVALLGKFIAVREPNIRYLGLENMTRMLLVTDVQDIIKRHQAQIITSLKDPDISIR RRALDLLYGMCDVTNAKEIVEELLQYLDTAEFAMREELSLKAAILAEKFAPQLLWAYHHTRRKN MYGKCFTFICWVMMLILGIWKLSR(+) MLSTGRSHFVRLCHSLLYLLPFLRNHYSHSVSKMSQYTQPASQDTLVQISTRQFPYAQNQHHNP AYKCKAFSIHIFSSRMVISPQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d027333_circ_g.3

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