Plant Circular RNA Database

Detail information of Zm00001d049449_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d049449_circ_g.1
					
						ID in PlantcircBase
						zma_circ_001648
					
						Alias
						circ2228
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 30659129-30660655  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplor2
					
						Parent gene
						
							Zm00001d049449						
					
						Parent gene annotation
						
							 cold regulated protein homolog1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d049449_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						seedling leaves
					
						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-CA							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
						Zm00001d049449_T005:6
Zm00001d049449_T001:6
Zm00001d049449_T004:6
Zm00001d049449_T003:6
Zm00001d049449_T002:6

General Information
CircRNA Name	Zm00001d049449_circ_g.1
ID in PlantcircBase	zma_circ_001648
Alias	circ2228
Organism	Zea mays
Position	chr4: 30659129-30660655 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	CIRCexplor2
Parent gene	Zm00001d049449
Parent gene annotation	cold regulated protein homolog1
Parent gene strand	+
Alternative splicing	Zm00001d049449_circ_g.2
Support reads	2
Tissues	seedling leaves
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-CA 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	Zm00001d049449_T005:6 Zm00001d049449_T001:6 Zm00001d049449_T004:6 Zm00001d049449_T003:6 Zm00001d049449_T002:6

			
						 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  
						
							GGTGGGGCATCTAGCCGCTAATTGTGAAGGAAAGGCAAAGAGAAAAGCTGGGGAATACGATGAG
AAAGGTGAAGCTATTGTTCCAAAGAAACCATACCAGgccctctccaacaacatttgctgaggtt
ttccagtgcatgttcgattacatcgatagactcttcatcatggttcgccctaggaagcttatgt
acatggcc

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							GCCCTCTCCAACAACATTTGCTGAGGTTTTCCAGTGCATGTTCGATTACATCGATAGACTCTTC
ATCATGGTTCGCCCTAGGAAGCTTATGTACATGGCCATTGGTATGTTTTCCGTAAACCTTTATG
CAGATTACACTGTTCTTACTACTTTATTATAGTGTACTAGAAATTAGGGTTCATATGGTCATAT
ATATTAGCTACAATTAGGAACACACACGATAGTTATTCTTTTAAGGTGTTGTTAGAGTTTGTGC
CACCACATATATGCTGATTATACAGTGGCTTACAGATGGTGTGGCTCCACGTGCTAAAATGAAC
CAACAGCGTTCTAGACGATTCAGAGCTGCAAAAGATGCAGCTGATGCGGTCAGTATTCTAGTGG
AATTATCATCGTCTGTTCAGTTCATGATCATACGCTGTCATTTCAATATTGGTTTTGAAACAGT
ATAAACCATTTGTAGTTGCACTCATTGCTCAGTATTGTTCTATCAGGCTGCAGAGGAAGAACGG
TTGCGTGAAGAGTTTGAGAGGGAAGGAAGAAGGCTTCCTGCAAAACAACAATCACAAACTTGTG
ATTCTAATGTTATTACTCCAGGAACCGAGTTTATGGCTGTTCTTTCAGTTGCGTTACAGTACTA
CATTCATCAAAGACTGAATTATGATCCTGGATGGAAAAAAATCAAAGTAAGTGCTATATCTGTT
GCCAATTTGGACTTTGATACTTGTAACTCCCGATAGTTAATAATGAAGAAATGGTATGTTCTGA
CCAAATCATTTTGAAGGTTATTCTATCTGATGCCAATGTTCCTGGCGAAGGGGAGCATAAAATA
ATGTCGTATATTCGTGGTCAACGGAATCTCCCTGGATTTAATCCAAACACACGCCATTGCTTAT
ATGGCCTGGTACGTTTTGGAAACGAAGATATGCTTTCAGTTGAACTTCGTTTCTTCAGTGCTGC
TGATGCATAGGCTTGCATGTGTACATATGCAGGATGCAGACCTCATAATGTTAGCTTTAGCAAC
TCATGAAGTACACTTCTCTATATTGAGAGAGGTAAGCCTTGCTTAGCGAGTTTGAAATTAATTA
CTTTCTTTGTTAAAATATTTGGTCATCTAATTTCTGCTATCTTTGTCACTTTTTAAATCTGTTA
AGAAAACCATTAGTTTCACCTTGTAGTCTTCTAGTAGAGTTTGTTTTTGTTCAGACAATCTTGT
ACACTCTGTAACATTAGTGTGAGTGGGTGTGGATGTGTATCTGTAAGGATTTATTACATTTTTT
TCCTTAATACGATGATACACAACTCTCCTTCATATTCACTTCATTTTAACATTTTTCTTGTAAA
ATCTTCAGTTTAAGATTATGAGTTTTATGTTTGCAGGTAGTTTTTACACCTGGGCAGCAGGACA
AATGCTTCTTATGTGGTCAGGTGGGGCATCTAGCCGCTAATTGTGAAGGAAAGGCAAAGAGAAA
AGCTGGGGAATACGATGAGAAAGGTGAAGCTATTGTTCCAAAGAAACCATACCAG
						
					

			
		

Sequences
Splice junction sequence	GGTGGGGCATCTAGCCGCTAATTGTGAAGGAAAGGCAAAGAGAAAAGCTGGGGAATACGATGAG AAAGGTGAAGCTATTGTTCCAAAGAAACCATACCAGgccctctccaacaacatttgctgaggtt ttccagtgcatgttcgattacatcgatagactcttcatcatggttcgccctaggaagcttatgt acatggcc
Assembled circRNA sequence	NA 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	NA
Genomic sequence	GCCCTCTCCAACAACATTTGCTGAGGTTTTCCAGTGCATGTTCGATTACATCGATAGACTCTTC ATCATGGTTCGCCCTAGGAAGCTTATGTACATGGCCATTGGTATGTTTTCCGTAAACCTTTATG CAGATTACACTGTTCTTACTACTTTATTATAGTGTACTAGAAATTAGGGTTCATATGGTCATAT ATATTAGCTACAATTAGGAACACACACGATAGTTATTCTTTTAAGGTGTTGTTAGAGTTTGTGC CACCACATATATGCTGATTATACAGTGGCTTACAGATGGTGTGGCTCCACGTGCTAAAATGAAC CAACAGCGTTCTAGACGATTCAGAGCTGCAAAAGATGCAGCTGATGCGGTCAGTATTCTAGTGG AATTATCATCGTCTGTTCAGTTCATGATCATACGCTGTCATTTCAATATTGGTTTTGAAACAGT ATAAACCATTTGTAGTTGCACTCATTGCTCAGTATTGTTCTATCAGGCTGCAGAGGAAGAACGG TTGCGTGAAGAGTTTGAGAGGGAAGGAAGAAGGCTTCCTGCAAAACAACAATCACAAACTTGTG ATTCTAATGTTATTACTCCAGGAACCGAGTTTATGGCTGTTCTTTCAGTTGCGTTACAGTACTA CATTCATCAAAGACTGAATTATGATCCTGGATGGAAAAAAATCAAAGTAAGTGCTATATCTGTT GCCAATTTGGACTTTGATACTTGTAACTCCCGATAGTTAATAATGAAGAAATGGTATGTTCTGA CCAAATCATTTTGAAGGTTATTCTATCTGATGCCAATGTTCCTGGCGAAGGGGAGCATAAAATA ATGTCGTATATTCGTGGTCAACGGAATCTCCCTGGATTTAATCCAAACACACGCCATTGCTTAT ATGGCCTGGTACGTTTTGGAAACGAAGATATGCTTTCAGTTGAACTTCGTTTCTTCAGTGCTGC TGATGCATAGGCTTGCATGTGTACATATGCAGGATGCAGACCTCATAATGTTAGCTTTAGCAAC TCATGAAGTACACTTCTCTATATTGAGAGAGGTAAGCCTTGCTTAGCGAGTTTGAAATTAATTA CTTTCTTTGTTAAAATATTTGGTCATCTAATTTCTGCTATCTTTGTCACTTTTTAAATCTGTTA AGAAAACCATTAGTTTCACCTTGTAGTCTTCTAGTAGAGTTTGTTTTTGTTCAGACAATCTTGT ACACTCTGTAACATTAGTGTGAGTGGGTGTGGATGTGTATCTGTAAGGATTTATTACATTTTTT TCCTTAATACGATGATACACAACTCTCCTTCATATTCACTTCATTTTAACATTTTTCTTGTAAA ATCTTCAGTTTAAGATTATGAGTTTTATGTTTGCAGGTAGTTTTTACACCTGGGCAGCAGGACA AATGCTTCTTATGTGGTCAGGTGGGGCATCTAGCCGCTAATTGTGAAGGAAAGGCAAAGAGAAA AGCTGGGGAATACGATGAGAAAGGTGAAGCTATTGTTCCAAAGAAACCATACCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.081750349

Conservation Information
Conserved circRNAs	NA
PMCS	0.081750349

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30659167-30659149(+)
30660616-30659149(+)
30659169-30660568(-)
30659147-30660555(-)
						
						Potential amino acid sequence
						
							MFDYIDRLFIMVRPRKLMYMAIDGVAPRAKMNQQRSRRFRAAKDAADAAAEEERLREEFEREGR
RLPAKQQSQTCDSNVITPGTEFMAVLSVALQYYIHQRLNYDPGWKKIKVILSDANVPGEGEHKI
MSYIRGQRNLPGFNPNTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQVGH
LAANCEGKAKRKAGEYDEKGEAIVPKKPYQALSNNIC*(+)
MRKVKLLFQRNHTRPSPTTFAEVFQCMFDYIDRLFIMVRPRKLMYMAIDGVAPRAKMNQQRSRR
FRAAKDAADAAAEEERLREEFEREGRRLPAKQQSQTCDSNVITPGTEFMAVLSVALQYYIHQRL
NYDPGWKKIKVILSDANVPGEGEHKIMSYIRGQRNLPGFNPNTRHCLYGLDADLIMLALATHEV
HFSILREVVFTPGQQDKCFLCGQVGHLAANCEGKAKRKAGEYDEKGEAIVPKKPYQALSNNIC*
(+)
MHWKTSANVVGEGLVWFLWNNSFTFLIVFPSFSLCLSFTISG*(-)
MLLERAWYGFFGTIASPFSSYSPAFLFAFPSQLAARCPT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	30659167-30659149(+) 30660616-30659149(+) 30659169-30660568(-) 30659147-30660555(-)
Potential amino acid sequence	MFDYIDRLFIMVRPRKLMYMAIDGVAPRAKMNQQRSRRFRAAKDAADAAAEEERLREEFEREGR RLPAKQQSQTCDSNVITPGTEFMAVLSVALQYYIHQRLNYDPGWKKIKVILSDANVPGEGEHKI MSYIRGQRNLPGFNPNTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQVGH LAANCEGKAKRKAGEYDEKGEAIVPKKPYQALSNNIC(+) MRKVKLLFQRNHTRPSPTTFAEVFQCMFDYIDRLFIMVRPRKLMYMAIDGVAPRAKMNQQRSRR FRAAKDAADAAAEEERLREEFEREGRRLPAKQQSQTCDSNVITPGTEFMAVLSVALQYYIHQRL NYDPGWKKIKVILSDANVPGEGEHKIMSYIRGQRNLPGFNPNTRHCLYGLDADLIMLALATHEV HFSILREVVFTPGQQDKCFLCGQVGHLAANCEGKAKRKAGEYDEKGEAIVPKKPYQALSNNIC (+) MHWKTSANVVGEGLVWFLWNNSFTFLIVFPSFSLCLSFTISG(-) MLLERAWYGFFGTIASPFSSYSPAFLFAFPSQLAARCPT(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chen et al., 2017b

circRNA

Detail information of Zm00001d049449_circ_g.1

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