Plant Circular RNA Database

Detail information of Zm00001d027340_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d027340_circ_g.3
					
						ID in PlantcircBase
						zma_circ_006350
					
						Alias
						Zm01circ00005, zma_circ_0000006
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 3277787-3280364  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d027340						
					
						Parent gene annotation
						
							Protein kinase superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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  
						
							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
						Zm00001d027340_T010:2
Zm00001d027340_T008:5
Zm00001d027340_T007:5
Zm00001d027340_T003:5
Zm00001d027340_T002:5
Zm00001d027340_T006:5
Zm00001d027340_T004:5
Zm00001d027340_T009:2
Zm00001d027340_T001:5
Zm00001d027340_T005:5

General Information
CircRNA Name	Zm00001d027340_circ_g.3
ID in PlantcircBase	zma_circ_006350
Alias	Zm01circ00005, zma_circ_0000006
Organism	Zea mays
Position	chr1: 3277787-3280364 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d027340
Parent gene annotation	Protein kinase superfamily protein
Parent gene strand	+
Alternative splicing	NA
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	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	Zm00001d027340_T010:2 Zm00001d027340_T008:5 Zm00001d027340_T007:5 Zm00001d027340_T003:5 Zm00001d027340_T002:5 Zm00001d027340_T006:5 Zm00001d027340_T004:5 Zm00001d027340_T009:2 Zm00001d027340_T001:5 Zm00001d027340_T005:5

			
						 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  
						
							GCAAATAGTCTTTCAAGAGCCAATAATCTTAGTGGCCCTCTGTCACTTCCAACTCGTGCTTCTG
CAAATAGTCTTTCTGCTCCTATTCGATCTTCTGCAGagtgagtaccaacgaggtgtcagtgcat
ggaacttcgatattgaggatctaaaggctcaggcatcactggtaaaggaatatgttttcttatc
ttttattc

									
								

					

						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: 673
Transcript exons: 3277787-3277855,3277968-3278036,3279402-3279460,3279639-
3279917,3280168-3280364
AGTGAGTACCAACGAGGTGTCAGTGCATGGAACTTCGATATTGAGGATCTAAAGGCTCAGGCAT
CACTGATATGTGATGATGATCCACCTGAAATAAAAGAAGACGATGACACTGGTAGAATAACTGA
CATTGATAAGGATACATCTTCTGACGATTATTTTGGAAAGACAGCACCATCGAATGGAAATAAC
TGCAGTGATCGTTCTTCTGTGCCAGCAAATCCTGGTCAAAATGGTCCCGAAATAAATGAAATAT
TGTCTTCCAACAATGGGAATGCCTACAGTGAAAGGAAGCCTGATGGACGTAAAAACCCAGAATC
AGAAAATGATTCATTGCCCTCGACGTCGAAGCATGATGCTGATGGGAAAGATTATAGATGTGAT
TTCAGGCAAAAACAGAGGACATACTCAGGTCCAGTTCTGCAATCTGGTCCGAATAATAGTTCGA
TGACTGAAAGGGGCCACATTATTGAAAGGGATGCAGGAGTTCAATCTGTATCTGATAAACAAAA
GAATGGTACAAGAAGAGCCAATAATCTTAGTGGTCCTTTGTCACTTCCAACTCGTGCTTCTGCA
AATAGTCTTTCAAGAGCCAATAATCTTAGTGGCCCTCTGTCACTTCCAACTCGTGCTTCTGCAA
ATAGTCTTTCTGCTCCTATTCGATCTTCTGCAG
						
					

						Genomic sequence
						
							AGTGAGTACCAACGAGGTGTCAGTGCATGGAACTTCGATATTGAGGATCTAAAGGCTCAGGCAT
CACTGGTAAAGGAATATGTTTTCTTATCTTTTATTCCTGTGATACCTTAGTTTTATGTTCTAAA
GTTGGCAGTATTTTTTGCCTTACAAGTTACAAGTAAGCTATATAACTTTGCAGATATGTGATGA
TGATCCACCTGAAATAAAAGAAGACGATGACACTGGTAGAATAACTGACATTGATAAGGTTTGC
TTGACTCTTTTTTCTTTATGTGTATATTCATATGTATATTCACTATGGAAAATGTTACCATGTG
TCTTTGAAAAAAGAAGAGAAATTAGATCATCATATGTTGGATTCAGACAGTAAGACATGTTTAA
GCGCGGCTGAAATGCTGTGTAGAGCGAAAGGGCCTCTAGCCGAGTTGGTTAGGTGGTCTGAGTA
ACACTCCTCAGGTCCTGGGTTCGACTCCTTATGGGAGCGAATTTTGAAGCTGTGATTAAAAAAA
TCCCCTCGTCTGTCCCATGCCAAAGCACAGGTCTAAGGCCCGCCCCTGGTCGCGGTCGTTCTCA
CATGTGCTACGGTGCCGTTGTCTATGGGTAGGGATGGCAGTTGAACCCGTGGGTATGGATATCC
GCGGGTTTCGTACCCGACGGATATGGATATGGGTAGAAAAACTCACCCGCGGGTTCTATCGGGT
CGGATACCCGAAATACATCGGGTAAGGTATGGGTAAAATACTTTACCCATGGATATCCAGTGGA
TACCCGAAATATCAATATACATCTTTAAAGGTGTCTACATCCACTAAAAATGTGCTACATTCAC
TAGAAAAACTCACCCGCATGTGTTGTTGATTAATGAATATTAATTTGTGTTGTGTTAATAGTCA
ATTGTAATGTAATCGAGACCAATGAGACATTGACAATGTTATGACTGTCAACTATCATGAACTC
ATTAATCTTTTATTCTCTGTACTCAAATTTAAATTTATTGGATGTGATAATTATGAGTTAAGAT
ATTGTATTGACATGTAGCCAAATATAGTCATTCTCGTGTTGCATTGGTGCTTAGATAGAAACTA
AAATATTTTAAGCATTTATTATAACACTAACCGAATGTTATTTAGTCTACAATAACATATCCAC
TGGATACCCGATACCCGGTGGATACCCGATGGGCACGGGTACGGGTACAGTTTCTCGCCCGATT
GACTTGGTGGGTATGAATATTTGTAGATGACTCGGGTTCAATTTCGGGTCGGGTATTATTATAC
CCGAACAAAATCCGACCCGCTGCCATCCCTATCTATGGGAGGGGCAGGGGTTGGGGGGTTTTCT
CGACCTGCGTGAGAATGTCTTCTTAATATAGACGGTCTTACCCCCGCAGGCTGAGTTTTTTTTT
GAAATGCTGTGTAGATCTGTGGATGCATTTCTGGATTCACTCCATTGGATACAAAAATAAAAGA
TATGCAATCCTTTTGTTTTATGTTTCACAGTTTTTCATTATTTGAAATTTGAAATTACAAAAGG
CATCTGCTTGCTCTGTGTGTTTAGCAAGAGAGAAGTGTATGGTTTATGTGCAAGTCATTTCTGA
ATGTGCTATTACCAGGATACATCTTCTGACGATTATTTTGGAAAGACAGCACCATCGAATGGAA
ATAACTGCAGGTTGAGTGAATCTACAACGTTTTAGCATCCTTCGATTCTCAATATTAACTTTGT
TCCCAATAGTTTTCTGTTTTTTATTTTCCATATTGATTTATCCGAATACAGAGGAACCTGTGGG
CTTCATGCATATTTCAGTTGCTGTAGGGTAGTTCATTTATAGTTTTCTGTTATGTTTCAGTGAT
CGTTCTTCTGTGCCAGCAAATCCTGGTCAAAATGGTCCCGAAATAAATGAAATATTGTCTTCCA
ACAATGGGAATGCCTACAGTGAAAGGAAGCCTGATGGACGTAAAAACCCAGAATCAGAAAATGA
TTCATTGCCCTCGACGTCGAAGCATGATGCTGATGGGAAAGATTATAGATGTGATTTCAGGCAA
AAACAGAGGACATACTCAGGTCCAGTTCTGCAATCTGGTCCGAATAATAGTTCGATGACTGAAA
GGGGCCACATTATTGAAAGGTGTGCCTAACAATATTTACTGAACATGTTCCATTTTAATTACCA
GATACTTTAATCTGACTTACTTTCTGTAAAAAAAACCTCGAAAAATTCTTGGCTTCGGACGAGG
CATTACATAATTTGGATACATGTGTCCAAAGGCACCAAACATCATTTTGATTTCTGAGTTCTTG
AATGAAAAATATTAGTTAATATTAGCTTATGCATTGTATATTCCAAGATTCTTTATCATCACTA
TTACTCATGGCAGGGATGCAGGAGTTCAATCTGTATCTGATAAACAAAAGAATGGTACAAGAAG
AGCCAATAATCTTAGTGGTCCTTTGTCACTTCCAACTCGTGCTTCTGCAAATAGTCTTTCAAGA
GCCAATAATCTTAGTGGCCCTCTGTCACTTCCAACTCGTGCTTCTGCAAATAGTCTTTCTGCTC
CTATTCGATCTTCTGCAG
						
					

			
		

Sequences
Splice junction sequence	GCAAATAGTCTTTCAAGAGCCAATAATCTTAGTGGCCCTCTGTCACTTCCAACTCGTGCTTCTG CAAATAGTCTTTCTGCTCCTATTCGATCTTCTGCAGagtgagtaccaacgaggtgtcagtgcat ggaacttcgatattgaggatctaaaggctcaggcatcactggtaaaggaatatgttttcttatc ttttattc
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: 673 Transcript exons: 3277787-3277855,3277968-3278036,3279402-3279460,3279639- 3279917,3280168-3280364 AGTGAGTACCAACGAGGTGTCAGTGCATGGAACTTCGATATTGAGGATCTAAAGGCTCAGGCAT CACTGATATGTGATGATGATCCACCTGAAATAAAAGAAGACGATGACACTGGTAGAATAACTGA CATTGATAAGGATACATCTTCTGACGATTATTTTGGAAAGACAGCACCATCGAATGGAAATAAC TGCAGTGATCGTTCTTCTGTGCCAGCAAATCCTGGTCAAAATGGTCCCGAAATAAATGAAATAT TGTCTTCCAACAATGGGAATGCCTACAGTGAAAGGAAGCCTGATGGACGTAAAAACCCAGAATC AGAAAATGATTCATTGCCCTCGACGTCGAAGCATGATGCTGATGGGAAAGATTATAGATGTGAT TTCAGGCAAAAACAGAGGACATACTCAGGTCCAGTTCTGCAATCTGGTCCGAATAATAGTTCGA TGACTGAAAGGGGCCACATTATTGAAAGGGATGCAGGAGTTCAATCTGTATCTGATAAACAAAA GAATGGTACAAGAAGAGCCAATAATCTTAGTGGTCCTTTGTCACTTCCAACTCGTGCTTCTGCA AATAGTCTTTCAAGAGCCAATAATCTTAGTGGCCCTCTGTCACTTCCAACTCGTGCTTCTGCAA ATAGTCTTTCTGCTCCTATTCGATCTTCTGCAG
Genomic sequence	AGTGAGTACCAACGAGGTGTCAGTGCATGGAACTTCGATATTGAGGATCTAAAGGCTCAGGCAT CACTGGTAAAGGAATATGTTTTCTTATCTTTTATTCCTGTGATACCTTAGTTTTATGTTCTAAA GTTGGCAGTATTTTTTGCCTTACAAGTTACAAGTAAGCTATATAACTTTGCAGATATGTGATGA TGATCCACCTGAAATAAAAGAAGACGATGACACTGGTAGAATAACTGACATTGATAAGGTTTGC TTGACTCTTTTTTCTTTATGTGTATATTCATATGTATATTCACTATGGAAAATGTTACCATGTG TCTTTGAAAAAAGAAGAGAAATTAGATCATCATATGTTGGATTCAGACAGTAAGACATGTTTAA GCGCGGCTGAAATGCTGTGTAGAGCGAAAGGGCCTCTAGCCGAGTTGGTTAGGTGGTCTGAGTA ACACTCCTCAGGTCCTGGGTTCGACTCCTTATGGGAGCGAATTTTGAAGCTGTGATTAAAAAAA TCCCCTCGTCTGTCCCATGCCAAAGCACAGGTCTAAGGCCCGCCCCTGGTCGCGGTCGTTCTCA CATGTGCTACGGTGCCGTTGTCTATGGGTAGGGATGGCAGTTGAACCCGTGGGTATGGATATCC GCGGGTTTCGTACCCGACGGATATGGATATGGGTAGAAAAACTCACCCGCGGGTTCTATCGGGT CGGATACCCGAAATACATCGGGTAAGGTATGGGTAAAATACTTTACCCATGGATATCCAGTGGA TACCCGAAATATCAATATACATCTTTAAAGGTGTCTACATCCACTAAAAATGTGCTACATTCAC TAGAAAAACTCACCCGCATGTGTTGTTGATTAATGAATATTAATTTGTGTTGTGTTAATAGTCA ATTGTAATGTAATCGAGACCAATGAGACATTGACAATGTTATGACTGTCAACTATCATGAACTC ATTAATCTTTTATTCTCTGTACTCAAATTTAAATTTATTGGATGTGATAATTATGAGTTAAGAT ATTGTATTGACATGTAGCCAAATATAGTCATTCTCGTGTTGCATTGGTGCTTAGATAGAAACTA AAATATTTTAAGCATTTATTATAACACTAACCGAATGTTATTTAGTCTACAATAACATATCCAC TGGATACCCGATACCCGGTGGATACCCGATGGGCACGGGTACGGGTACAGTTTCTCGCCCGATT GACTTGGTGGGTATGAATATTTGTAGATGACTCGGGTTCAATTTCGGGTCGGGTATTATTATAC CCGAACAAAATCCGACCCGCTGCCATCCCTATCTATGGGAGGGGCAGGGGTTGGGGGGTTTTCT CGACCTGCGTGAGAATGTCTTCTTAATATAGACGGTCTTACCCCCGCAGGCTGAGTTTTTTTTT GAAATGCTGTGTAGATCTGTGGATGCATTTCTGGATTCACTCCATTGGATACAAAAATAAAAGA TATGCAATCCTTTTGTTTTATGTTTCACAGTTTTTCATTATTTGAAATTTGAAATTACAAAAGG CATCTGCTTGCTCTGTGTGTTTAGCAAGAGAGAAGTGTATGGTTTATGTGCAAGTCATTTCTGA ATGTGCTATTACCAGGATACATCTTCTGACGATTATTTTGGAAAGACAGCACCATCGAATGGAA ATAACTGCAGGTTGAGTGAATCTACAACGTTTTAGCATCCTTCGATTCTCAATATTAACTTTGT TCCCAATAGTTTTCTGTTTTTTATTTTCCATATTGATTTATCCGAATACAGAGGAACCTGTGGG CTTCATGCATATTTCAGTTGCTGTAGGGTAGTTCATTTATAGTTTTCTGTTATGTTTCAGTGAT CGTTCTTCTGTGCCAGCAAATCCTGGTCAAAATGGTCCCGAAATAAATGAAATATTGTCTTCCA ACAATGGGAATGCCTACAGTGAAAGGAAGCCTGATGGACGTAAAAACCCAGAATCAGAAAATGA TTCATTGCCCTCGACGTCGAAGCATGATGCTGATGGGAAAGATTATAGATGTGATTTCAGGCAA AAACAGAGGACATACTCAGGTCCAGTTCTGCAATCTGGTCCGAATAATAGTTCGATGACTGAAA GGGGCCACATTATTGAAAGGTGTGCCTAACAATATTTACTGAACATGTTCCATTTTAATTACCA GATACTTTAATCTGACTTACTTTCTGTAAAAAAAACCTCGAAAAATTCTTGGCTTCGGACGAGG CATTACATAATTTGGATACATGTGTCCAAAGGCACCAAACATCATTTTGATTTCTGAGTTCTTG AATGAAAAATATTAGTTAATATTAGCTTATGCATTGTATATTCCAAGATTCTTTATCATCACTA TTACTCATGGCAGGGATGCAGGAGTTCAATCTGTATCTGATAAACAAAAGAATGGTACAAGAAG AGCCAATAATCTTAGTGGTCCTTTGTCACTTCCAACTCGTGCTTCTGCAAATAGTCTTTCAAGA GCCAATAATCTTAGTGGCCCTCTGTCACTTCCAACTCGTGCTTCTGCAAATAGTCTTTCTGCTC CTATTCGATCTTCTGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.075004432

Conservation Information
Conserved circRNAs	NA
PMCS	0.075004432

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3279890-3277788(+)
3280171-3277788(+)
						
						Potential amino acid sequence
						
							MTERGHIIERDAGVQSVSDKQKNGTRRANNLSGPLSLPTRASANSLSRANNLSGPLSLPTRASA
NSLSAPIRSSAE*(+)
MQEFNLYLINKRMVQEEPIILVVLCHFQLVLLQIVFQEPIILVALCHFQLVLLQIVFLLLFDLL
QSEYQRGVSAWNFDIEDLKAQASLICDDDPPEIKEDDDTGRITDIDKDTSSDDYFGKTAPSNGN
NCSDRSSVPANPGQNGPEINEILSSNNGNAYSERKPDGRKNPESENDSLPSTSKHDADGKDYRC
DFRQKQRTYSGPVLQSGPNNSSMTERGHIIERDAGVQSVSDKQKNGTRRANNLSGPLSLPTRAS
ANSLSRANNLSGPLSLPTRASANSLSAPIRSSAE*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3279890-3277788(+) 3280171-3277788(+)
Potential amino acid sequence	MTERGHIIERDAGVQSVSDKQKNGTRRANNLSGPLSLPTRASANSLSRANNLSGPLSLPTRASA NSLSAPIRSSAE(+) MQEFNLYLINKRMVQEEPIILVVLCHFQLVLLQIVFQEPIILVALCHFQLVLLQIVFLLLFDLL QSEYQRGVSAWNFDIEDLKAQASLICDDDPPEIKEDDDTGRITDIDKDTSSDDYFGKTAPSNGN NCSDRSSVPANPGQNGPEINEILSSNNGNAYSERKPDGRKNPESENDSLPSTSKHDADGKDYRC DFRQKQRTYSGPVLQSGPNNSSMTERGHIIERDAGVQSVSDKQKNGTRRANNLSGPLSLPTRAS ANSLSRANNLSGPLSLPTRASANSLSAPIRSSAE(+)
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 Zm00001d027340_circ_g.3

Address

Any questions?

Supported by