Plant Circular RNA Database

Detail information of Zm00001d044570_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d044570_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007923
					
						Alias
						Zm03circ00141
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 231999902-232001072  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d044570						
					
						Parent gene annotation
						
							Pre-mRNA-processing protein 40A
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d044570_circ_ag.1 Zm00001d044570_circ_g.1 Zm00001d044570_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
						Zm00001d044570_T028:2
Zm00001d044570_T007:2
Zm00001d044570_T061:2
Zm00001d044570_T002:1
Zm00001d044570_T018:2
Zm00001d044570_T034:1
Zm00001d044570_T066:2
Zm00001d044570_T006:2
Zm00001d044570_T067:2
Zm00001d044570_T050:2
Zm00001d044570_T064:2
Zm00001d044570_T020:2
Zm00001d044570_T046:2
Zm00001d044570_T052:2
Zm00001d044570_T043:2
Zm00001d044570_T013:1
Zm00001d044570_T051:2
Zm00001d044570_T048:2
Zm00001d044570_T027:2
Zm00001d044570_T022:2
Zm00001d044570_T063:1
Zm00001d044570_T036:2
Zm00001d044570_T032:2
Zm00001d044570_T049:2
Zm00001d044570_T041:2
Zm00001d044570_T015:1
Zm00001d044570_T065:2
Zm00001d044570_T014:1
Zm00001d044570_T019:2
Zm00001d044570_T040:2
Zm00001d044570_T039:1
Zm00001d044570_T037:2
Zm00001d044570_T008:2
Zm00001d044570_T025:2
Zm00001d044570_T031:2
Zm00001d044570_T012:1
Zm00001d044570_T068:1
Zm00001d044570_T023:2
Zm00001d044570_T005:1
Zm00001d044570_T003:2
Zm00001d044570_T026:1
Zm00001d044570_T044:2
Zm00001d044570_T069:1
Zm00001d044570_T045:2
Zm00001d044570_T001:1

General Information
CircRNA Name	Zm00001d044570_circ_g.3
ID in PlantcircBase	zma_circ_007923
Alias	Zm03circ00141
Organism	Zea mays
Position	chr3: 231999902-232001072 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d044570
Parent gene annotation	Pre-mRNA-processing protein 40A
Parent gene strand	+
Alternative splicing	Zm00001d044570_circ_ag.1 Zm00001d044570_circ_g.1 Zm00001d044570_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	Zm00001d044570_T028:2 Zm00001d044570_T007:2 Zm00001d044570_T061:2 Zm00001d044570_T002:1 Zm00001d044570_T018:2 Zm00001d044570_T034:1 Zm00001d044570_T066:2 Zm00001d044570_T006:2 Zm00001d044570_T067:2 Zm00001d044570_T050:2 Zm00001d044570_T064:2 Zm00001d044570_T020:2 Zm00001d044570_T046:2 Zm00001d044570_T052:2 Zm00001d044570_T043:2 Zm00001d044570_T013:1 Zm00001d044570_T051:2 Zm00001d044570_T048:2 Zm00001d044570_T027:2 Zm00001d044570_T022:2 Zm00001d044570_T063:1 Zm00001d044570_T036:2 Zm00001d044570_T032:2 Zm00001d044570_T049:2 Zm00001d044570_T041:2 Zm00001d044570_T015:1 Zm00001d044570_T065:2 Zm00001d044570_T014:1 Zm00001d044570_T019:2 Zm00001d044570_T040:2 Zm00001d044570_T039:1 Zm00001d044570_T037:2 Zm00001d044570_T008:2 Zm00001d044570_T025:2 Zm00001d044570_T031:2 Zm00001d044570_T012:1 Zm00001d044570_T068:1 Zm00001d044570_T023:2 Zm00001d044570_T005:1 Zm00001d044570_T003:2 Zm00001d044570_T026:1 Zm00001d044570_T044:2 Zm00001d044570_T069:1 Zm00001d044570_T045:2 Zm00001d044570_T001:1

			
						 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  
						
							TCACCATGACACAGATGATGTAAGCTCTGAGAGGGATGATAAAGACGATGCTAAGAAGTCTCGG
AGGCATAGCAGCAGTGATCGCAAGAAATCTAGGAAGggccttggacagtgagacttatgctaga
gagctttttgaagagtgcgttgtccacctgaaagaaaggttaaaagagaaagaacgtttgaggg
aggaagaa

									
								

					

						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: 436
Transcript exons: 231999902-232000004,232000740-232001072
GGCCTTGGACAGTGAGACTTATGCTAGAGAGCTTTTTGAAGAGTGCGTTGTCCACCTGAAAGAA
AGGTTAAAAGAGAAAGAACGTTTGAGGGAGGAAGAAAAGGCAAAAAGAGAGAAAGAGCGTGAGG
AGAAAGAGAAGAAGAAAGAGAAAGAGAAAGAAAGGAAGGAGAAAGAACGCAAAGAAAAAGAAAG
AGACCACCGGGAGGAGAGAGAAAAGGAGAAAGGGAAGGATCGATCAAGGAGAGATGAAATGGAG
TTTGATGGTGCTGATTTGAACACCCATGGTACAAAAGATAAGAAAAGAGATAAAGAAAAAGAAA
AGAAACATAAGAGACGTCACCATGACACAGATGATGTAAGCTCTGAGAGGGATGATAAAGACGA
TGCTAAGAAGTCTCGGAGGCATAGCAGCAGTGATCGCAAGAAATCTAGGAAG
						
					

						Genomic sequence
						
							GGCCTTGGACAGTGAGACTTATGCTAGAGAGCTTTTTGAAGAGTGCGTTGTCCACCTGAAAGAA
AGGTTAAAAGAGAAAGAACGTTTGAGGGAGGAAGAAAAGGTAAATGGTTGTATTGTTGTCTCCT
ATCATCTATCTGCAGTCGTCATAGCTTGTTCACTTATGTTGCTTATCAGAGGTGGAAAAAAAGT
GTGATCCAAGCTACCTGAGTGAAAATAGCTGATTTCTTTGCTGATTGGCTCTTTTGGTTCAGTT
TTGTCTCAACTTTGGAGACCTGTATGACTGATGTGCTGAAAAGCTAGATTATCTTGGCTTATAA
GCCTTTTAACCTATACTCAATTTGTTCGTAACTATCATGTACATCCATTCCTTGATAATATTTG
AATTCAAAAGCACTAGTATTTTAAGCTACTTCCTTTATTTTATCTAATAAGTTGTGATTCACAT
CTATACGGCCCTCACTCCCTCTGTTCCGAATTATAAGTTGTGTTGGCTTTTCTAGGTGCATAGC
TTTATCTATGGACCTAGATATATACTATATCTAGATACATAATAAACCCTATTTATCTGGAAAA
ACCAGAATGACTTATAATTTGTAATAGAGGAAATATGATTTGTATGTGTTAAGATTAAGCCAAA
CTAAGCATTTGTGCTTGGATTTGATCTGAGACAGACAATGCCAAGATTTCAAATATGGTTAATG
TTTTTATGGGAACCAACTGAATTAATTATCACTTTATCTTCAACACTACCTTCATTGTTTGCCG
CATACTATAGTTTTTATGAGATGTTTCTTTTCATTTTTCTTTTCCACCCCTGAACTTTTACTCT
TATTAGGCAAAAAGAGAGAAAGAGCGTGAGGAGAAAGAGAAGAAGAAAGAGAAAGAGAAAGAAA
GGAAGGAGAAAGAACGCAAAGAAAAAGAAAGAGACCACCGGGAGGAGAGAGAAAAGGAGAAAGG
GAAGGATCGATCAAGGAGAGATGAAATGGAGTTTGATGGTGCTGATTTGAACACCCATGGTACA
AAAGATAAGAAAAGAGATAAAGAAAAAGAAAAGAAACATAAGAGACGTCACCATGACACAGATG
ATGTAAGCTCTGAGAGGGATGATAAAGACGATGCTAAGAAGTCTCGGAGGCATAGCAGCAGTGA
TCGCAAGAAATCTAGGAAG
						
					

			
		

Sequences
Splice junction sequence	TCACCATGACACAGATGATGTAAGCTCTGAGAGGGATGATAAAGACGATGCTAAGAAGTCTCGG AGGCATAGCAGCAGTGATCGCAAGAAATCTAGGAAGggccttggacagtgagacttatgctaga gagctttttgaagagtgcgttgtccacctgaaagaaaggttaaaagagaaagaacgtttgaggg aggaagaa
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: 436 Transcript exons: 231999902-232000004,232000740-232001072 GGCCTTGGACAGTGAGACTTATGCTAGAGAGCTTTTTGAAGAGTGCGTTGTCCACCTGAAAGAA AGGTTAAAAGAGAAAGAACGTTTGAGGGAGGAAGAAAAGGCAAAAAGAGAGAAAGAGCGTGAGG AGAAAGAGAAGAAGAAAGAGAAAGAGAAAGAAAGGAAGGAGAAAGAACGCAAAGAAAAAGAAAG AGACCACCGGGAGGAGAGAGAAAAGGAGAAAGGGAAGGATCGATCAAGGAGAGATGAAATGGAG TTTGATGGTGCTGATTTGAACACCCATGGTACAAAAGATAAGAAAAGAGATAAAGAAAAAGAAA AGAAACATAAGAGACGTCACCATGACACAGATGATGTAAGCTCTGAGAGGGATGATAAAGACGA TGCTAAGAAGTCTCGGAGGCATAGCAGCAGTGATCGCAAGAAATCTAGGAAG
Genomic sequence	GGCCTTGGACAGTGAGACTTATGCTAGAGAGCTTTTTGAAGAGTGCGTTGTCCACCTGAAAGAA AGGTTAAAAGAGAAAGAACGTTTGAGGGAGGAAGAAAAGGTAAATGGTTGTATTGTTGTCTCCT ATCATCTATCTGCAGTCGTCATAGCTTGTTCACTTATGTTGCTTATCAGAGGTGGAAAAAAAGT GTGATCCAAGCTACCTGAGTGAAAATAGCTGATTTCTTTGCTGATTGGCTCTTTTGGTTCAGTT TTGTCTCAACTTTGGAGACCTGTATGACTGATGTGCTGAAAAGCTAGATTATCTTGGCTTATAA GCCTTTTAACCTATACTCAATTTGTTCGTAACTATCATGTACATCCATTCCTTGATAATATTTG AATTCAAAAGCACTAGTATTTTAAGCTACTTCCTTTATTTTATCTAATAAGTTGTGATTCACAT CTATACGGCCCTCACTCCCTCTGTTCCGAATTATAAGTTGTGTTGGCTTTTCTAGGTGCATAGC TTTATCTATGGACCTAGATATATACTATATCTAGATACATAATAAACCCTATTTATCTGGAAAA ACCAGAATGACTTATAATTTGTAATAGAGGAAATATGATTTGTATGTGTTAAGATTAAGCCAAA CTAAGCATTTGTGCTTGGATTTGATCTGAGACAGACAATGCCAAGATTTCAAATATGGTTAATG TTTTTATGGGAACCAACTGAATTAATTATCACTTTATCTTCAACACTACCTTCATTGTTTGCCG CATACTATAGTTTTTATGAGATGTTTCTTTTCATTTTTCTTTTCCACCCCTGAACTTTTACTCT TATTAGGCAAAAAGAGAGAAAGAGCGTGAGGAGAAAGAGAAGAAGAAAGAGAAAGAGAAAGAAA GGAAGGAGAAAGAACGCAAAGAAAAAGAAAGAGACCACCGGGAGGAGAGAGAAAAGGAGAAAGG GAAGGATCGATCAAGGAGAGATGAAATGGAGTTTGATGGTGCTGATTTGAACACCCATGGTACA AAAGATAAGAAAAGAGATAAAGAAAAAGAAAAGAAACATAAGAGACGTCACCATGACACAGATG ATGTAAGCTCTGAGAGGGATGATAAAGACGATGCTAAGAAGTCTCGGAGGCATAGCAGCAGTGA TCGCAAGAAATCTAGGAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.134624803

Conservation Information
Conserved circRNAs	NA
PMCS	0.134624803

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							232000888-231999913(+)
232001009-231999913(+)
						
						Potential amino acid sequence
						
							MEFDGADLNTHGTKDKKRDKEKEKKHKRRHHDTDDVSSERDDKDDAKKSRRHSSSDRKKSRKGL
GQ*(+)
MIKTMLRSLGGIAAVIARNLGRALDSETYARELFEECVVHLKERLKEKERLREEEKAKREKERE
EKEKKKEKEKERKEKERKEKERDHREEREKEKGKDRSRRDEMEFDGADLNTHGTKDKKRDKEKE
KKHKRRHHDTDDVSSERDDKDDAKKSRRHSSSDRKKSRKGLGQ*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	232000888-231999913(+) 232001009-231999913(+)
Potential amino acid sequence	MEFDGADLNTHGTKDKKRDKEKEKKHKRRHHDTDDVSSERDDKDDAKKSRRHSSSDRKKSRKGL GQ(+) MIKTMLRSLGGIAAVIARNLGRALDSETYARELFEECVVHLKERLKEKERLREEEKAKREKERE EKEKKKEKEKERKEKERKEKERDHREEREKEKGKDRSRRDEMEFDGADLNTHGTKDKKRDKEKE KKHKRRHHDTDDVSSERDDKDDAKKSRRHSSSDRKKSRKGLGQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d044570_circ_g.3

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