Plant Circular RNA Database

Detail information of Zm00001d033155_circ_g.5

			
						 General Information
					
						CircRNA Name
						Zm00001d033155_circ_g.5
					
						ID in PlantcircBase
						zma_circ_006856
					
						Alias
						Zm01circ00156, zma_circ_0000478, GRMZM2G153928_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 252356629-252357238  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d033155						
					
						Parent gene annotation
						
							DUF21 domain-containing protein  chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d033155_circ_g.1 Zm00001d033155_circ_g.2 Zm00001d033155_circ_g.3 Zm00001d033155_circ_g.4 Zm00001d033155_circ_g.6 Zm00001d033155_circ_g.7 Zm00001d033155_circ_g.8 						
					
						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  
						
							CT-AC							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
						Zm00001d033155_T001:2
Zm00001d033155_T002:2
Zm00001d033155_T003:2

General Information
CircRNA Name	Zm00001d033155_circ_g.5
ID in PlantcircBase	zma_circ_006856
Alias	Zm01circ00156, zma_circ_0000478, GRMZM2G153928_C1
Organism	Zea mays
Position	chr1: 252356629-252357238 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d033155
Parent gene annotation	DUF21 domain-containing protein chloroplastic
Parent gene strand	-
Alternative splicing	Zm00001d033155_circ_g.1 Zm00001d033155_circ_g.2 Zm00001d033155_circ_g.3 Zm00001d033155_circ_g.4 Zm00001d033155_circ_g.6 Zm00001d033155_circ_g.7 Zm00001d033155_circ_g.8
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	CT-AC 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	Zm00001d033155_T001:2 Zm00001d033155_T002:2 Zm00001d033155_T003:2

			
						 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  
						
							CAAGCTCTTCAGATAGGTGATCTATCGATGTGTTTGCATCAACATCAAATGTTCCATCCCCCCG
CCTTACTATATAGCCTGTTTTCTTCTGGATTTCCTCctcgagttcataagcttgagttttttct
ctatcatcttggcgatcaggaccttcctcctgatattcaccgttttcttctctgaaattctttt
caagaatc

						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: 297
Transcript exons: 252356629-252356808,252357122-252357238
CTCGAGTTCATAAGCTTGAGTTTTTTCTCTATCATCTTGGCGATCAGGACCTTCCTCCTGATAT
TCACCGTTTTCTTCTCTGAAATTCTTTTCAAGAATCACAAGCATTTTCCCACCTTCTTCTGGAA
TATAGCCAAAAGATGCACAGACAAAACCAGACACCGTCTCATACTGATGTCCCTCTGGTATTTT
GATACCAAGCTCTTCAGATAGGTGATCTATCGATGTGTTTGCATCAACATCAAATGTTCCATCC
CCCCGCCTTACTATATAGCCTGTTTTCTTCTGGATTTCCTC
						
						Genomic sequence
						
							CTCGAGTTCATAAGCTTGAGTTTTTTCTCTATCATCTTGGCGATCAGGACCTTCCTCCTGATAT
TCACCGTTTTCTTCTCTGAAATTCTTTTCAAGAATCACAAGCATTTTCCCACCTTCTTCTGGAA
TATAGCCAAAAGATGCACAGACAAAACCAGACACCGTCTCATACTGATGTCCCTGCAAAAAAAT
GGTGTCCAAGTGTCTCAAGATATAAGCCAATCTATGAAAAAATGACAGAAATACACAGCACCAC
ATAATGATGACTGCCAAGGGAATACTTTACAATTAGAACATTTGTGAATATTTGGGTGACCTAA
ATAGTAAATGTCCAGTTTCCACAAAAAATCTGTATAGGTTCTGCAAACCAGGCATCTCTAATTT
GATGATGGAAGTCAACTTTTGATGATCATACAGTGTACAACAGGCACACATGTCCAAGGGAATC
CATAGCAACTGTAGAGAAAGCTAAATATCTAATGAGAAACAACACCTCTGGTATTTTGATACCA
AGCTCTTCAGATAGGTGATCTATCGATGTGTTTGCATCAACATCAAATGTTCCATCCCCCCGCC
TTACTATATAGCCTGTTTTCTTCTGGATTTCCTC

Sequences
Splice junction sequence	CAAGCTCTTCAGATAGGTGATCTATCGATGTGTTTGCATCAACATCAAATGTTCCATCCCCCCG CCTTACTATATAGCCTGTTTTCTTCTGGATTTCCTCctcgagttcataagcttgagttttttct ctatcatcttggcgatcaggaccttcctcctgatattcaccgttttcttctctgaaattctttt caagaatc
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: 297 Transcript exons: 252356629-252356808,252357122-252357238 CTCGAGTTCATAAGCTTGAGTTTTTTCTCTATCATCTTGGCGATCAGGACCTTCCTCCTGATAT TCACCGTTTTCTTCTCTGAAATTCTTTTCAAGAATCACAAGCATTTTCCCACCTTCTTCTGGAA TATAGCCAAAAGATGCACAGACAAAACCAGACACCGTCTCATACTGATGTCCCTCTGGTATTTT GATACCAAGCTCTTCAGATAGGTGATCTATCGATGTGTTTGCATCAACATCAAATGTTCCATCC CCCCGCCTTACTATATAGCCTGTTTTCTTCTGGATTTCCTC
Genomic sequence	CTCGAGTTCATAAGCTTGAGTTTTTTCTCTATCATCTTGGCGATCAGGACCTTCCTCCTGATAT TCACCGTTTTCTTCTCTGAAATTCTTTTCAAGAATCACAAGCATTTTCCCACCTTCTTCTGGAA TATAGCCAAAAGATGCACAGACAAAACCAGACACCGTCTCATACTGATGTCCCTGCAAAAAAAT GGTGTCCAAGTGTCTCAAGATATAAGCCAATCTATGAAAAAATGACAGAAATACACAGCACCAC ATAATGATGACTGCCAAGGGAATACTTTACAATTAGAACATTTGTGAATATTTGGGTGACCTAA ATAGTAAATGTCCAGTTTCCACAAAAAATCTGTATAGGTTCTGCAAACCAGGCATCTCTAATTT GATGATGGAAGTCAACTTTTGATGATCATACAGTGTACAACAGGCACACATGTCCAAGGGAATC CATAGCAACTGTAGAGAAAGCTAAATATCTAATGAGAAACAACACCTCTGGTATTTTGATACCA AGCTCTTCAGATAGGTGATCTATCGATGTGTTTGCATCAACATCAAATGTTCCATCCCCCCGCC TTACTATATAGCCTGTTTTCTTCTGGATTTCCTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.131259356

Conservation Information
Conserved circRNAs	NA
PMCS	0.131259356

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							252357167-252356708(+)
252356738-252356631(-)
252356665-252357210(-)
						
						Potential amino acid sequence
						
							MCLHQHQMFHPPALLYSLFSSGFPPRVHKLEFFLYHLGDQDLPPDIHRFLL*(+)
MLVILEKNFREENGEYQEEGPDRQDDREKTQAYELEEEIQKKTGYIVRRGDGTFDVDANTSIDH
LSEELGIKIPEGHQYETVSGFVCASFGYIPEEGGKMLVILEKNFREENGEYQEEGPDRQDDREK
TQAYELEEEIQKKTGYIVRRGDGTFDVDANTSIDHLSEELGIKIPEGHQYETVSGFVCASFGYI
PEEGGKMLVILEKNFREENGEYQEEGPDRQDDREKTQAYELEEEIQKKTGYIVRRGDGTFDVDA
NTSIDHLSEELGIKIPEGHQYETVSGFVCASFGYIPEEGGKMLVILEKNFREENGEYQEEGPDR
QDDREKTQAYELE(-)
MIEKKLKLMNSRRKSRRKQAI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	252357167-252356708(+) 252356738-252356631(-) 252356665-252357210(-)
Potential amino acid sequence	MCLHQHQMFHPPALLYSLFSSGFPPRVHKLEFFLYHLGDQDLPPDIHRFLL(+) MLVILEKNFREENGEYQEEGPDRQDDREKTQAYELEEEIQKKTGYIVRRGDGTFDVDANTSIDH LSEELGIKIPEGHQYETVSGFVCASFGYIPEEGGKMLVILEKNFREENGEYQEEGPDRQDDREK TQAYELEEEIQKKTGYIVRRGDGTFDVDANTSIDHLSEELGIKIPEGHQYETVSGFVCASFGYI PEEGGKMLVILEKNFREENGEYQEEGPDRQDDREKTQAYELEEEIQKKTGYIVRRGDGTFDVDA NTSIDHLSEELGIKIPEGHQYETVSGFVCASFGYIPEEGGKMLVILEKNFREENGEYQEEGPDR QDDREKTQAYELE(-) MIEKKLKLMNSRRKSRRKQAI(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d033155_circ_g.5

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