Plant Circular RNA Database

Detail information of Zm00001d030266_circ_g.4

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d030266_circ_g.4
					

						ID in PlantcircBase
						zma_circ_006601
					

						Alias
						zma_circ_0000232
					

						Organism
						
							Zea mays						
					

						Position
						
							chr1: 117653460-117654227  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						find_circ
					

						Parent gene
						
							Zm00001d030266						
					

						Parent gene annotation
						
							Callose synthase 10
							
					

						Parent gene strand
						+
					

						Alternative splicing
						
							Zm00001d030266_circ_g.2 Zm00001d030266_circ_g.3 Zm00001d030266_circ_g.5 Zm00001d030266_circ_g.6 Zm00001d030266_circ_g.7 Zm00001d030266_circ_g.8 Zm00001d030266_circ_g.9 Zm00001d030266_circ_g.10 Zm00001d030266_circ_g.11 Zm00001d030266_circ_g.12 Zm00001d030266_circ_g.13 						
					

						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  
						
							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
						Zm00001d030266_T035:4
Zm00001d030266_T014:4
Zm00001d030266_T025:4
Zm00001d030266_T005:4
Zm00001d030266_T011:4
Zm00001d030266_T004:4
Zm00001d030266_T083:4
Zm00001d030266_T023:4
Zm00001d030266_T073:4
Zm00001d030266_T032:4
Zm00001d030266_T085:4
Zm00001d030266_T074:4
Zm00001d030266_T031:4
Zm00001d030266_T087:3
Zm00001d030266_T028:4
Zm00001d030266_T079:4
Zm00001d030266_T007:4
Zm00001d030266_T050:4
Zm00001d030266_T088:2
Zm00001d030266_T054:4
Zm00001d030266_T033:4
Zm00001d030266_T001:4
Zm00001d030266_T027:4
Zm00001d030266_T061:4
Zm00001d030266_T066:4
Zm00001d030266_T089:1
Zm00001d030266_T047:4
Zm00001d030266_T081:4
Zm00001d030266_T039:4
Zm00001d030266_T059:4
Zm00001d030266_T080:4
Zm00001d030266_T069:4
Zm00001d030266_T056:4
Zm00001d030266_T019:4
Zm00001d030266_T077:4
Zm00001d030266_T016:4
Zm00001d030266_T013:4
Zm00001d030266_T041:4
Zm00001d030266_T052:4
Zm00001d030266_T036:4
Zm00001d030266_T068:4
Zm00001d030266_T057:4
Zm00001d030266_T018:4
Zm00001d030266_T063:4
Zm00001d030266_T021:4
Zm00001d030266_T048:4
Zm00001d030266_T090:1
Zm00001d030266_T072:4
Zm00001d030266_T045:4
Zm00001d030266_T086:4
Zm00001d030266_T064:4
Zm00001d030266_T008:4

					

			
		

General Information
CircRNA Name	Zm00001d030266_circ_g.4
ID in PlantcircBase	zma_circ_006601
Alias	zma_circ_0000232
Organism	Zea mays
Position	chr1: 117653460-117654227 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d030266
Parent gene annotation	Callose synthase 10
Parent gene strand	+
Alternative splicing	Zm00001d030266_circ_g.2 Zm00001d030266_circ_g.3 Zm00001d030266_circ_g.5 Zm00001d030266_circ_g.6 Zm00001d030266_circ_g.7 Zm00001d030266_circ_g.8 Zm00001d030266_circ_g.9 Zm00001d030266_circ_g.10 Zm00001d030266_circ_g.11 Zm00001d030266_circ_g.12 Zm00001d030266_circ_g.13
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	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	Zm00001d030266_T035:4 Zm00001d030266_T014:4 Zm00001d030266_T025:4 Zm00001d030266_T005:4 Zm00001d030266_T011:4 Zm00001d030266_T004:4 Zm00001d030266_T083:4 Zm00001d030266_T023:4 Zm00001d030266_T073:4 Zm00001d030266_T032:4 Zm00001d030266_T085:4 Zm00001d030266_T074:4 Zm00001d030266_T031:4 Zm00001d030266_T087:3 Zm00001d030266_T028:4 Zm00001d030266_T079:4 Zm00001d030266_T007:4 Zm00001d030266_T050:4 Zm00001d030266_T088:2 Zm00001d030266_T054:4 Zm00001d030266_T033:4 Zm00001d030266_T001:4 Zm00001d030266_T027:4 Zm00001d030266_T061:4 Zm00001d030266_T066:4 Zm00001d030266_T089:1 Zm00001d030266_T047:4 Zm00001d030266_T081:4 Zm00001d030266_T039:4 Zm00001d030266_T059:4 Zm00001d030266_T080:4 Zm00001d030266_T069:4 Zm00001d030266_T056:4 Zm00001d030266_T019:4 Zm00001d030266_T077:4 Zm00001d030266_T016:4 Zm00001d030266_T013:4 Zm00001d030266_T041:4 Zm00001d030266_T052:4 Zm00001d030266_T036:4 Zm00001d030266_T068:4 Zm00001d030266_T057:4 Zm00001d030266_T018:4 Zm00001d030266_T063:4 Zm00001d030266_T021:4 Zm00001d030266_T048:4 Zm00001d030266_T090:1 Zm00001d030266_T072:4 Zm00001d030266_T045:4 Zm00001d030266_T086:4 Zm00001d030266_T064:4 Zm00001d030266_T008:4

			
						 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  
						
							TCTTAATGACAGTATAGCACAGGGTTCACTTTTAGTGACTATAAATCTGAAGAAGTTGCAGTTA
GTCCAGTCTAGATTGACGGGCTTGACCGGTCTTCTGgaatcagaaattacaactaagacgtatg
cctcaatattttccccattttggaatgaaattatcaagagcttgcgtgaagaggactatatcag
caacaggt

						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: 462
Transcript exons: 117653460-117653557,117653642-117653723,117653833-117653
993,117654107-117654227
GAATCAGAAATTACAACTAAGACGTATGCCTCAATATTTTCCCCATTTTGGAATGAAATTATCA
AGAGCTTGCGTGAAGAGGACTATATCAGCAACAGGGAAATGGATCTGCTTATGATGCCAAGTAA
CTGTGGAAATTTAATGCTTGTACAGTGGCCACTGTTTCTATTGACTAGCAAGATCATGTTGGCA
AATGACTATGCTTCTGACTGTAAAGACTCGCAGTATGAGCTATGGGATAGAATATCAAAAGATG
AATACATGGCTTATGCCGTCAAAGAATGTTACTACAGCACTGAAAAAATTCTTCACTCTTTAGT
TGATGCTGAAGGGCAGCACTGGGTTGTAAGGCTTTTCCGAGATCTTAATGACAGTATAGCACAG
GGTTCACTTTTAGTGACTATAAATCTGAAGAAGTTGCAGTTAGTCCAGTCTAGATTGACGGGCT
TGACCGGTCTTCTG
						
						Genomic sequence
						
							GAATCAGAAATTACAACTAAGACGTATGCCTCAATATTTTCCCCATTTTGGAATGAAATTATCA
AGAGCTTGCGTGAAGAGGACTATATCAGCAACAGGTGTGGCAGAAAATAATAATACATTATACA
GTATTATCTTATATGTGACTTCTTTGCTTCAGTATTGGGTGAATTTCTTTCCAGGGAAATGGAT
CTGCTTATGATGCCAAGTAACTGTGGAAATTTAATGCTTGTACAGTGGCCACTGTTTCTATTGA
CTAGCAAGGTATGAGATATCCTAGTTGAAATCAATGTTTTCTTTGGATGAATGAATCTTTTGCA
TATCGAAACCTTTAATTTGGATGATATCAATCTGTTGGTTGCTTCTTCTGTAGATCATGTTGGC
AAATGACTATGCTTCTGACTGTAAAGACTCGCAGTATGAGCTATGGGATAGAATATCAAAAGAT
GAATACATGGCTTATGCCGTCAAAGAATGTTACTACAGCACTGAAAAAATTCTTCACTCTTTAG
TTGATGCTGAAGGGCAGCACTGGTATGCTTCCTCACTGAAAAACCATGAATCTGATACTGAAAC
CAAGCCTTCTAACTGTTGTGCTAAACTTTGTCACTACTTACCTCTAATACATGCTGCTGTTACA
TATACAGGGTTGTAAGGCTTTTCCGAGATCTTAATGACAGTATAGCACAGGGTTCACTTTTAGT
GACTATAAATCTGAAGAAGTTGCAGTTAGTCCAGTCTAGATTGACGGGCTTGACCGGTCTTCTG

Sequences
Splice junction sequence	TCTTAATGACAGTATAGCACAGGGTTCACTTTTAGTGACTATAAATCTGAAGAAGTTGCAGTTA GTCCAGTCTAGATTGACGGGCTTGACCGGTCTTCTGgaatcagaaattacaactaagacgtatg cctcaatattttccccattttggaatgaaattatcaagagcttgcgtgaagaggactatatcag caacaggt
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: 462 Transcript exons: 117653460-117653557,117653642-117653723,117653833-117653 993,117654107-117654227 GAATCAGAAATTACAACTAAGACGTATGCCTCAATATTTTCCCCATTTTGGAATGAAATTATCA AGAGCTTGCGTGAAGAGGACTATATCAGCAACAGGGAAATGGATCTGCTTATGATGCCAAGTAA CTGTGGAAATTTAATGCTTGTACAGTGGCCACTGTTTCTATTGACTAGCAAGATCATGTTGGCA AATGACTATGCTTCTGACTGTAAAGACTCGCAGTATGAGCTATGGGATAGAATATCAAAAGATG AATACATGGCTTATGCCGTCAAAGAATGTTACTACAGCACTGAAAAAATTCTTCACTCTTTAGT TGATGCTGAAGGGCAGCACTGGGTTGTAAGGCTTTTCCGAGATCTTAATGACAGTATAGCACAG GGTTCACTTTTAGTGACTATAAATCTGAAGAAGTTGCAGTTAGTCCAGTCTAGATTGACGGGCT TGACCGGTCTTCTG
Genomic sequence	GAATCAGAAATTACAACTAAGACGTATGCCTCAATATTTTCCCCATTTTGGAATGAAATTATCA AGAGCTTGCGTGAAGAGGACTATATCAGCAACAGGTGTGGCAGAAAATAATAATACATTATACA GTATTATCTTATATGTGACTTCTTTGCTTCAGTATTGGGTGAATTTCTTTCCAGGGAAATGGAT CTGCTTATGATGCCAAGTAACTGTGGAAATTTAATGCTTGTACAGTGGCCACTGTTTCTATTGA CTAGCAAGGTATGAGATATCCTAGTTGAAATCAATGTTTTCTTTGGATGAATGAATCTTTTGCA TATCGAAACCTTTAATTTGGATGATATCAATCTGTTGGTTGCTTCTTCTGTAGATCATGTTGGC AAATGACTATGCTTCTGACTGTAAAGACTCGCAGTATGAGCTATGGGATAGAATATCAAAAGAT GAATACATGGCTTATGCCGTCAAAGAATGTTACTACAGCACTGAAAAAATTCTTCACTCTTTAG TTGATGCTGAAGGGCAGCACTGGTATGCTTCCTCACTGAAAAACCATGAATCTGATACTGAAAC CAAGCCTTCTAACTGTTGTGCTAAACTTTGTCACTACTTACCTCTAATACATGCTGCTGTTACA TATACAGGGTTGTAAGGCTTTTCCGAGATCTTAATGACAGTATAGCACAGGGTTCACTTTTAGT GACTATAAATCTGAAGAAGTTGCAGTTAGTCCAGTCTAGATTGACGGGCTTGACCGGTCTTCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.293708046

Conservation Information
Conserved circRNAs	NA
PMCS	0.293708046

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							117653647-117654224(+)
						
						Potential amino acid sequence
						
							MDLLMMPSNCGNLMLVQWPLFLLTSKIMLANDYASDCKDSQYELWDRISKDEYMAYAVKECYYS
TEKILHSLVDAEGQHWVVRLFRDLNDSIAQGSLLVTINLKKLQLVQSRLTGLTGLLESEITTKT
YASIFSPFWNEIIKSLREEDYISNREMDLLMMPSNCGNLMLVQWPLFLLTSKIMLANDYASDCK
DSQYELWDRISKDEYMAYAVKECYYSTEKILHSLVDAEGQHWVVRLFRDLNDSIAQGSLLVTIN
LKKLQLVQSRLTGLTGLLESEITTKTYASIFSPFWNEIIKSLREEDYISNREMDLLMMPSNCGN
LMLVQWPLFLLTSKIMLANDYASDCKDSQYELWDRISKDEYMAYAVKECYYSTEKILHSLVDAE
GQHWVVRLFRDLNDSIAQGSLLVTINLKKLQLVQSRLTGLTGLLESEITTKTYASIFSPFWNEI
IKSLREEDYISNREMDLLMMPSNCGNLMLVQWPLFLLTSKIMLANDYASDCKDSQYELWDRISK
DEYMAYAVKECYYSTEKILHSLVDAEGQHWVVRLFRDLNDSIAQGSLLVTINLKKLQLVQSRLT
GLTGLL(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	117653647-117654224(+)
Potential amino acid sequence	MDLLMMPSNCGNLMLVQWPLFLLTSKIMLANDYASDCKDSQYELWDRISKDEYMAYAVKECYYS TEKILHSLVDAEGQHWVVRLFRDLNDSIAQGSLLVTINLKKLQLVQSRLTGLTGLLESEITTKT YASIFSPFWNEIIKSLREEDYISNREMDLLMMPSNCGNLMLVQWPLFLLTSKIMLANDYASDCK DSQYELWDRISKDEYMAYAVKECYYSTEKILHSLVDAEGQHWVVRLFRDLNDSIAQGSLLVTIN LKKLQLVQSRLTGLTGLLESEITTKTYASIFSPFWNEIIKSLREEDYISNREMDLLMMPSNCGN LMLVQWPLFLLTSKIMLANDYASDCKDSQYELWDRISKDEYMAYAVKECYYSTEKILHSLVDAE GQHWVVRLFRDLNDSIAQGSLLVTINLKKLQLVQSRLTGLTGLLESEITTKTYASIFSPFWNEI IKSLREEDYISNREMDLLMMPSNCGNLMLVQWPLFLLTSKIMLANDYASDCKDSQYELWDRISK DEYMAYAVKECYYSTEKILHSLVDAEGQHWVVRLFRDLNDSIAQGSLLVTINLKKLQLVQSRLT GLTGLL(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d030266_circ_g.4

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