Plant Circular RNA Database

Detail information of Zm00001d002089_circ_g.1

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d002089_circ_g.1
					

						ID in PlantcircBase
						zma_circ_007028
					

						Alias
						zma_circ_0001072, ZmciR121
					

						Organism
						
							Zea mays						
					

						Position
						
							chr2: 5790531-5792259  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						find_circ, CIRI2
					

						Parent gene
						
							Zm00001d002089						
					

						Parent gene annotation
						
							Tetratricopeptide repeat (TPR)-like superfamily protein
							
					

						Parent gene strand
						-
					

						Alternative splicing
						
							NA						
					

						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  
						
							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
						Zm00001d002089_T045:5
Zm00001d002089_T053:5
Zm00001d002089_T001:5
Zm00001d002089_T064:5
Zm00001d002089_T059:5
Zm00001d002089_T033:5
Zm00001d002089_T009:5
Zm00001d002089_T049:5
Zm00001d002089_T076:5
Zm00001d002089_T011:5
Zm00001d002089_T023:5
Zm00001d002089_T029:5
Zm00001d002089_T062:5
Zm00001d002089_T069:5
Zm00001d002089_T088:5
Zm00001d002089_T068:4
Zm00001d002089_T089:5
Zm00001d002089_T085:4
Zm00001d002089_T071:5
Zm00001d002089_T039:4
Zm00001d002089_T026:5
Zm00001d002089_T016:5
Zm00001d002089_T002:5
Zm00001d002089_T038:5
Zm00001d002089_T054:4
Zm00001d002089_T003:5
Zm00001d002089_T032:5
Zm00001d002089_T057:5
Zm00001d002089_T036:2
Zm00001d002089_T090:4
Zm00001d002089_T014:5
Zm00001d002089_T030:5
Zm00001d002089_T075:5
Zm00001d002089_T086:4
Zm00001d002089_T082:5
Zm00001d002089_T087:5
Zm00001d002089_T079:5
Zm00001d002089_T020:5
Zm00001d002089_T084:5
Zm00001d002089_T035:5
Zm00001d002089_T048:5
Zm00001d002089_T073:5
Zm00001d002089_T047:5
Zm00001d002089_T013:5
Zm00001d002089_T067:5
Zm00001d002089_T055:5
Zm00001d002089_T004:5
Zm00001d002089_T061:5
Zm00001d002089_T031:5
Zm00001d002089_T043:5
Zm00001d002089_T051:5
Zm00001d002089_T018:5
Zm00001d002089_T042:4
Zm00001d002089_T080:5
Zm00001d002089_T022:5

					

			
		

General Information
CircRNA Name	Zm00001d002089_circ_g.1
ID in PlantcircBase	zma_circ_007028
Alias	zma_circ_0001072, ZmciR121
Organism	Zea mays
Position	chr2: 5790531-5792259 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d002089
Parent gene annotation	Tetratricopeptide repeat (TPR)-like superfamily protein
Parent gene strand	-
Alternative splicing	NA
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	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	Zm00001d002089_T045:5 Zm00001d002089_T053:5 Zm00001d002089_T001:5 Zm00001d002089_T064:5 Zm00001d002089_T059:5 Zm00001d002089_T033:5 Zm00001d002089_T009:5 Zm00001d002089_T049:5 Zm00001d002089_T076:5 Zm00001d002089_T011:5 Zm00001d002089_T023:5 Zm00001d002089_T029:5 Zm00001d002089_T062:5 Zm00001d002089_T069:5 Zm00001d002089_T088:5 Zm00001d002089_T068:4 Zm00001d002089_T089:5 Zm00001d002089_T085:4 Zm00001d002089_T071:5 Zm00001d002089_T039:4 Zm00001d002089_T026:5 Zm00001d002089_T016:5 Zm00001d002089_T002:5 Zm00001d002089_T038:5 Zm00001d002089_T054:4 Zm00001d002089_T003:5 Zm00001d002089_T032:5 Zm00001d002089_T057:5 Zm00001d002089_T036:2 Zm00001d002089_T090:4 Zm00001d002089_T014:5 Zm00001d002089_T030:5 Zm00001d002089_T075:5 Zm00001d002089_T086:4 Zm00001d002089_T082:5 Zm00001d002089_T087:5 Zm00001d002089_T079:5 Zm00001d002089_T020:5 Zm00001d002089_T084:5 Zm00001d002089_T035:5 Zm00001d002089_T048:5 Zm00001d002089_T073:5 Zm00001d002089_T047:5 Zm00001d002089_T013:5 Zm00001d002089_T067:5 Zm00001d002089_T055:5 Zm00001d002089_T004:5 Zm00001d002089_T061:5 Zm00001d002089_T031:5 Zm00001d002089_T043:5 Zm00001d002089_T051:5 Zm00001d002089_T018:5 Zm00001d002089_T042:4 Zm00001d002089_T080:5 Zm00001d002089_T022:5

			
						 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  
						
							AGAAGACAGATAAATCCCCATAACTCTTCATAGTTTCCGGATGATCAAGACCCAGCTCCCTTTC
ATTGATATCAAGTGCCTTCTGTTGATATATAGTTGCctttgcacgccgacacttcctttgcaca
ttgctttcttttctttcctggactgggcttatgaagtcaagaagatctgatacactggaaaggt
agatgttt

									
								

					

						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: 645
Transcript exons: 5790531-5790612,5790689-5790801,5790881-5791012,5791645-
5791828,5792126-5792259
CTTTGCACGCCGACACTTCCTTTGCACATTGCTTTCTTTTCTTTCCTGGACTGGGCTTATGAAG
TCAAGAAGATCTGATACACTAAGATGTCCTTTACTTGCAATAGATGAATCAGGTTTTGGCATGC
CTCTTCGGGCAGCCTCTTGTTGTTCTAATGCTTTTGACTCAAAATATTCTAGCCATGCAGCAGC
ATCCTGAGTTCGGAGGTCATCTTCCCCTAGTTTCTCCTGAAGTATCTGCATGGTTGTTTGTTCA
TGTTGCACACTTAGGGAGTACGCATCCATCATTGAAAGGGCTATGGCTATAGCATGGTAGCTTG
CAGCAGTCTGGATGTGATCAGCTCCTAGCAACCTCTTATTGCACTTCAGGGCTTCATGCAAGTA
TCGAAGAGCAACATGAACATTTCCCATGCCTTCTTCCATCATAGCTACGTTTATGTAGGTGGCA
GCTGAATTTGGGTGTGAAAGCCCACATGAAAACTGAAGCAGATATAGCGCACGGTTGACATACT
TTAGAGCCATTTCAATGTGTTGAAGGCGGTAGTAGAAGACAGATAAATCCCCATAACTCTTCAT
AGTTTCCGGATGATCAAGACCCAGCTCCCTTTCATTGATATCAAGTGCCTTCTGTTGATATATA
GTTGC
						
					

						Genomic sequence
						
							CTTTGCACGCCGACACTTCCTTTGCACATTGCTTTCTTTTCTTTCCTGGACTGGGCTTATGAAG
TCAAGAAGATCTGATACACTGGAAAGGTAGATGTTTCAATCTAAATTTAAATATTTTATAAATG
AAACTGCTCAGATTATTTGTAGTTTCATACCTAAGATGTCCTTTACTTGCAATAGATGAATCAG
GTTTTGGCATGCCTCTTCGGGCAGCCTCTTGTTGTTCTAATGCTTTTGACTCAAAATATTCTAG
CCATGCAGCAGCATCCTGCATCGAAAAGTAATGTGTTAATTCAAGAGAACATCGGAGTATATAT
CCTATGTTTTTGTACGCTGAGAAAAAGAACCTGAGTTCGGAGGTCATCTTCCCCTAGTTTCTCC
TGAAGTATCTGCATGGTTGTTTGTTCATGTTGCACACTTAGGGAGTACGCATCCATCATTGAAA
GGGCTATGGCTATAGCATGGTAGCTTGCAGCAGTCTGATTGATTGAAAAAAAATTGCTTGTTAG
TTCATAGTAAGTAATTAAATCACAGGACCCAATTATTCATCATATTATTCAATGAATTATAAAT
CAGGTGTGTACATGCTCTACGACAAGAATCATATGCTTATAGTATATTTCACTGAATCATACAT
TATTAACATTAATAACTTGCAAAAAAACTTATACAACAATTACAATACATTACTTCATTAAAAG
AAATAGCAACCAGATCAATAGGATTATAGGATATCTCAATATACCAGAGGTGTCTTTATTATGT
ATTGTTATATAAGACATGCATTCCAGCACTATTATGCAGTTCTGGAGAAAGGGAAATATTGATG
TGATAGATTCCTTCGAGTAATGTATTTTAGACACATTAGTATATATATCAAATAGTTGTTTGAG
TCAAGATTGGATTTTGATACACATTGACCGTTTCCATGAGAAACCCTGGCCACTATTTTACGTG
AAAACCTTTTGACGGGTTCATGGAAATCCGTAAGCATGGAATGCCCAAACTTACACCTTTACAC
CTTAGAAGTTCTTTAGTTTGCAAAGATAATTCAATGGCTACAATCATACGACACTTTGGAAAAT
AAAGGATATAATTTAGCTTCTTTCACCTGGATGTGATCAGCTCCTAGCAACCTCTTATTGCACT
TCAGGGCTTCATGCAAGTATCGAAGAGCAACATGAACATTTCCCATGCCTTCTTCCATCATAGC
TACGTTTATGTAGGTGGCAGCTGAATTTGGGTGTGAAAGCCCACATGAAAACTGAAGCAGATAT
AGCGCACGGTTGACATACCTTCAAGGGTAAGACAAAATTAGGTATAGAAGAAATCTATATTGAA
CACAAATGGTAGAAGTTGGATTACAAGTGTGATTGAAACTTGGAAGTTATATAGCAAACAGTCT
CCACGGTATCTATTTTTACATGTGGACACAAGTAGTCAAGCACCAGTCACATGCCAAAGGATGA
AGCTGCAAGGCCCATTTCAGTATGTATGACTGTTTAATGCACATGATGATTATAAACTAGCACC
ATGGTAGACTGGTTCAATTGATGCCACCAATTTCATGCTTCAGCAAAGACCATACTTACTTTAG
AGCCATTTCAATGTGTTGAAGGCGGTAGTAGAAGACAGATAAATCCCCATAACTCTTCATAGTT
TCCGGATGATCAAGACCCAGCTCCCTTTCATTGATATCAAGTGCCTTCTGTTGATATATAGTTG
C
						
					

			
		

Sequences
Splice junction sequence	AGAAGACAGATAAATCCCCATAACTCTTCATAGTTTCCGGATGATCAAGACCCAGCTCCCTTTC ATTGATATCAAGTGCCTTCTGTTGATATATAGTTGCctttgcacgccgacacttcctttgcaca ttgctttcttttctttcctggactgggcttatgaagtcaagaagatctgatacactggaaaggt agatgttt
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: 645 Transcript exons: 5790531-5790612,5790689-5790801,5790881-5791012,5791645- 5791828,5792126-5792259 CTTTGCACGCCGACACTTCCTTTGCACATTGCTTTCTTTTCTTTCCTGGACTGGGCTTATGAAG TCAAGAAGATCTGATACACTAAGATGTCCTTTACTTGCAATAGATGAATCAGGTTTTGGCATGC CTCTTCGGGCAGCCTCTTGTTGTTCTAATGCTTTTGACTCAAAATATTCTAGCCATGCAGCAGC ATCCTGAGTTCGGAGGTCATCTTCCCCTAGTTTCTCCTGAAGTATCTGCATGGTTGTTTGTTCA TGTTGCACACTTAGGGAGTACGCATCCATCATTGAAAGGGCTATGGCTATAGCATGGTAGCTTG CAGCAGTCTGGATGTGATCAGCTCCTAGCAACCTCTTATTGCACTTCAGGGCTTCATGCAAGTA TCGAAGAGCAACATGAACATTTCCCATGCCTTCTTCCATCATAGCTACGTTTATGTAGGTGGCA GCTGAATTTGGGTGTGAAAGCCCACATGAAAACTGAAGCAGATATAGCGCACGGTTGACATACT TTAGAGCCATTTCAATGTGTTGAAGGCGGTAGTAGAAGACAGATAAATCCCCATAACTCTTCAT AGTTTCCGGATGATCAAGACCCAGCTCCCTTTCATTGATATCAAGTGCCTTCTGTTGATATATA GTTGC
Genomic sequence	CTTTGCACGCCGACACTTCCTTTGCACATTGCTTTCTTTTCTTTCCTGGACTGGGCTTATGAAG TCAAGAAGATCTGATACACTGGAAAGGTAGATGTTTCAATCTAAATTTAAATATTTTATAAATG AAACTGCTCAGATTATTTGTAGTTTCATACCTAAGATGTCCTTTACTTGCAATAGATGAATCAG GTTTTGGCATGCCTCTTCGGGCAGCCTCTTGTTGTTCTAATGCTTTTGACTCAAAATATTCTAG CCATGCAGCAGCATCCTGCATCGAAAAGTAATGTGTTAATTCAAGAGAACATCGGAGTATATAT CCTATGTTTTTGTACGCTGAGAAAAAGAACCTGAGTTCGGAGGTCATCTTCCCCTAGTTTCTCC TGAAGTATCTGCATGGTTGTTTGTTCATGTTGCACACTTAGGGAGTACGCATCCATCATTGAAA GGGCTATGGCTATAGCATGGTAGCTTGCAGCAGTCTGATTGATTGAAAAAAAATTGCTTGTTAG TTCATAGTAAGTAATTAAATCACAGGACCCAATTATTCATCATATTATTCAATGAATTATAAAT CAGGTGTGTACATGCTCTACGACAAGAATCATATGCTTATAGTATATTTCACTGAATCATACAT TATTAACATTAATAACTTGCAAAAAAACTTATACAACAATTACAATACATTACTTCATTAAAAG AAATAGCAACCAGATCAATAGGATTATAGGATATCTCAATATACCAGAGGTGTCTTTATTATGT ATTGTTATATAAGACATGCATTCCAGCACTATTATGCAGTTCTGGAGAAAGGGAAATATTGATG TGATAGATTCCTTCGAGTAATGTATTTTAGACACATTAGTATATATATCAAATAGTTGTTTGAG TCAAGATTGGATTTTGATACACATTGACCGTTTCCATGAGAAACCCTGGCCACTATTTTACGTG AAAACCTTTTGACGGGTTCATGGAAATCCGTAAGCATGGAATGCCCAAACTTACACCTTTACAC CTTAGAAGTTCTTTAGTTTGCAAAGATAATTCAATGGCTACAATCATACGACACTTTGGAAAAT AAAGGATATAATTTAGCTTCTTTCACCTGGATGTGATCAGCTCCTAGCAACCTCTTATTGCACT TCAGGGCTTCATGCAAGTATCGAAGAGCAACATGAACATTTCCCATGCCTTCTTCCATCATAGC TACGTTTATGTAGGTGGCAGCTGAATTTGGGTGTGAAAGCCCACATGAAAACTGAAGCAGATAT AGCGCACGGTTGACATACCTTCAAGGGTAAGACAAAATTAGGTATAGAAGAAATCTATATTGAA CACAAATGGTAGAAGTTGGATTACAAGTGTGATTGAAACTTGGAAGTTATATAGCAAACAGTCT CCACGGTATCTATTTTTACATGTGGACACAAGTAGTCAAGCACCAGTCACATGCCAAAGGATGA AGCTGCAAGGCCCATTTCAGTATGTATGACTGTTTAATGCACATGATGATTATAAACTAGCACC ATGGTAGACTGGTTCAATTGATGCCACCAATTTCATGCTTCAGCAAAGACCATACTTACTTTAG AGCCATTTCAATGTGTTGAAGGCGGTAGTAGAAGACAGATAAATCCCCATAACTCTTCATAGTT TCCGGATGATCAAGACCCAGCTCCCTTTCATTGATATCAAGTGCCTTCTGTTGATATATAGTTG C

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.169254711

Conservation Information
Conserved circRNAs	NA
PMCS	0.169254711

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5792201-5790605(+)
5792192-5790533(-)
5790561-5792189(-)
						
						Potential amino acid sequence
						
							MIKTQLPFIDIKCLLLIYSCLCTPTLPLHIAFFSFLDWAYEVKKI*(+)
MKSYGDLSVFYYRLQHIEMALKYVNRALYLLQFSCGLSHPNSAATYINVAMMEEGMGNVHVALR
YLHEALKCNKRLLGADHIQTAASYHAIAIALSMMDAYSLSVQHEQTTMQILQEKLGEDDLRTQD
AAAWLEYFESKALEQQEAARRGMPKPDSSIASKGHLSVSDLLDFISPVQERKESNVQRKCRRAK
ATIYQQKALDINERELGLDHPETMKSYGDLSVFYYRLQHIEMALKYVNRALYLLQFSCGLSHPN
SAATYINVAMMEEGMGNVHVALRYLHEALKCNKRLLGADHIQTAASYHAIAIALSMMDAYSLSV
QHEQTTMQILQEKLGEDDLRTQDAAAWLEYFESKALEQQEAARRGMPKPDSSIASKGHLSVSDL
LDFISPVQERKESNVQRKCRRAKATIYQQKALDINERELGLDHPETMKSYGDLSVFYYRLQHIE
MALKYVNRALYLLQFSCGLSHPNSAATYINVAMMEEGMGNVHVALRYLHEALKCNKRLLGADHI
QTAASYHAIAIALSMMDAYSLSVQHEQTTMQILQEKLGEDDLRTQDAAAWLEYFESKALEQQEA
ARRGMPKPDSSIASKGHLSVSDLLDFISPVQERKESNVQRKCRRAKATIYQQKALDINERELGL
DHPETMKSYGDLSVFYYRLQHIEMALKYVNRALYLLQFSCGLSHPNSAATYINVAMMEEGMGNV
HVALRYLHEALKCNKRLLGADHIQTAASYHAIAIALSMMDAYSLSVQHEQTTMQILQEKLGEDD
LRTQDAAAWLEYFESKALEQQEAARRGMPKPDSSIASKGHLSVSDLLDFISPVQERKESNVQRK
CRRAK(-)
MCKGSVGVQRQLYINRRHLISMKGSWVLIIRKL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	5792201-5790605(+) 5792192-5790533(-) 5790561-5792189(-)
Potential amino acid sequence	MIKTQLPFIDIKCLLLIYSCLCTPTLPLHIAFFSFLDWAYEVKKI(+) MKSYGDLSVFYYRLQHIEMALKYVNRALYLLQFSCGLSHPNSAATYINVAMMEEGMGNVHVALR YLHEALKCNKRLLGADHIQTAASYHAIAIALSMMDAYSLSVQHEQTTMQILQEKLGEDDLRTQD AAAWLEYFESKALEQQEAARRGMPKPDSSIASKGHLSVSDLLDFISPVQERKESNVQRKCRRAK ATIYQQKALDINERELGLDHPETMKSYGDLSVFYYRLQHIEMALKYVNRALYLLQFSCGLSHPN SAATYINVAMMEEGMGNVHVALRYLHEALKCNKRLLGADHIQTAASYHAIAIALSMMDAYSLSV QHEQTTMQILQEKLGEDDLRTQDAAAWLEYFESKALEQQEAARRGMPKPDSSIASKGHLSVSDL LDFISPVQERKESNVQRKCRRAKATIYQQKALDINERELGLDHPETMKSYGDLSVFYYRLQHIE MALKYVNRALYLLQFSCGLSHPNSAATYINVAMMEEGMGNVHVALRYLHEALKCNKRLLGADHI QTAASYHAIAIALSMMDAYSLSVQHEQTTMQILQEKLGEDDLRTQDAAAWLEYFESKALEQQEA ARRGMPKPDSSIASKGHLSVSDLLDFISPVQERKESNVQRKCRRAKATIYQQKALDINERELGL DHPETMKSYGDLSVFYYRLQHIEMALKYVNRALYLLQFSCGLSHPNSAATYINVAMMEEGMGNV HVALRYLHEALKCNKRLLGADHIQTAASYHAIAIALSMMDAYSLSVQHEQTTMQILQEKLGEDD LRTQDAAAWLEYFESKALEQQEAARRGMPKPDSSIASKGHLSVSDLLDFISPVQERKESNVQRK CRRAK(-) MCKGSVGVQRQLYINRRHLISMKGSWVLIIRKL(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d002089_circ_g.1

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