Plant Circular RNA Database

Detail information of Zm00001d031873_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d031873_circ_g.4
					
						ID in PlantcircBase
						zma_circ_006738
					
						Alias
						Zm01circ00127, zma_circ_0000394
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 204969766-204976072  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d031873						
					
						Parent gene annotation
						
							Ribonuclease E/G-like protein chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d031873_circ_g.3 						
					
						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
						Zm00001d031873_T001:3

General Information
CircRNA Name	Zm00001d031873_circ_g.4
ID in PlantcircBase	zma_circ_006738
Alias	Zm01circ00127, zma_circ_0000394
Organism	Zea mays
Position	chr1: 204969766-204976072 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d031873
Parent gene annotation	Ribonuclease E/G-like protein chloroplastic
Parent gene strand	-
Alternative splicing	Zm00001d031873_circ_g.3
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	Zm00001d031873_T001:3

			
						 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  
						
							AGCGGGTCTCCTGTTATGAATATTAAGCACCCATCTTGTAAATCTGCTTTCAGGTTCCATAATA
TTGTACAGAATCCTTTACAGGTTATGGCTGAATCATccaaaatcggcttcgcaggcatggaaat
ggactaagtgttggacctttcgtacccaatccttctttgacaacttgaaccattacttttgtgc
ccttgcga

									
								

					

						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: 1652
Transcript exons: 204969766-204970922,204971030-204971339,204975888-204976
072
CCAAAATCGGCTTCGCAGGCATGGAAATGGACTAAGTGTTGGACCTTTCGTACCCAATCCTTCT
TTGACAACTTGAACCATTACTTTTGTGCCCTTGCGAACTTGAGACCATCTGCTTCCATTTGTGT
CATCATTAGATTCTCTTAAAGCATGCTGAATTGAAGATAAAGTCTTGAGATCATTGGAAATTTC
TGATTGATATCCTTGCAGTATGCCCTCACTATATTCATCTTCCATGTGGTCATTTTCTTCATCT
TTGTCTACGTCATAAACAGAAATGCTGTCAACTTCATCATCATCGACATTGTTATCTGTAACAT
TCTCAACTGGAAATGATGAACCATCATGAGCTTCTTCATCTGCAAATTCGTCGTCACTCATATC
ATCATCGTTTTCATAAGCTGGAAGGTTCTCTTCATTACAATAATCACCAACATGATCTGTTCCT
CGGTTCTTAAAAACTTGAGGATACACAAAAGGATCTCGGTTTTGCTTTATGCTCATAAGTGAAG
GCCTTGAAATTCCAATATCTACAAATGCTCCTCCCATATGAGGAACGAGCTTTGTTACTACACC
TAGATAAATACTATCACACTGTACATTGTTCTTGATGGGTTCCAGCAAGAGTTCAACTAGTTTT
CCATCTTCTAATACTGCAATTCTCTGCATAGTGCAGACAGAGGAATTCATAAGTATAACTCTTG
ATGACGGTTCACCACCAGTCGGTTTACTCTCATCCAAAGGCGTTAAAGGTTTTTCTATTTTCCT
TAATTTTCTGATAATGTCCCTTGCTTCTACTTTTCCATCAGCAAGAACTATAGTTTCATTTAGT
TCCAATATAGATTGAAATAACCATGGCTCTTCAACAGGCTGATACTGTTCATGCATGTTTTTAC
TAACTCCACTCAAAGTGTGCTTATAATTTACAAGCTTCTTTTGCCCTTTCTTATCTTTGACTTT
TGCAACTGGTTTCTTTGCAGACACAATTGATTCAAGAATCCATGGCTCCTCTACGACTTGAGGC
CTTCCATATTGGCTTATATAACTGGCATTTGGTATTTCAGTTACACAGTTGTGCATGATGGTAG
ATTGATTATCCGACAACAGTTTTGCATGTAATGGTGTGCCATTCCCAAGCTTCAATATAATATG
ATCACCTACAGATAAGCCTTGATTCCGTGTATCCCTGACAGAGTGATCTTTCACAATGTTCTGG
TTATTTCCACCATCAAAAAGTTCACCTTCAAGAGAATCAGCTTCCATCAGCCATGATCCCCATG
TAGGAGTAGGAAGACCTGGTAGACTGGTTTTCATCCATAGGTCTTTCACAATAATAACCTGCTT
TTTCTGGCCATCTGAAGGTATTGATAAGGAGTATACTGGACCTGGCCTCCATATAATATCAGAA
GAGGAACTCATTTCTTCTCGAACAAAATAACTATATTTGAAATGCACTCCATATGGTACCTTTA
TTTCAGCTGTCCATATATTATTGCTTTCAACAGAAGGAGCCAACTGAACAGCCATGTTGGATTC
CCAACAGCCCAGGGTAAGCGGGTCTCCTGTTATGAATATTAAGCACCCATCTTGTAAATCTGCT
TTCAGGTTCCATAATATTGTACAGAATCCTTTACAGGTTATGGCTGAATCAT
						
					

						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.						
					

			
		

Sequences
Splice junction sequence	AGCGGGTCTCCTGTTATGAATATTAAGCACCCATCTTGTAAATCTGCTTTCAGGTTCCATAATA TTGTACAGAATCCTTTACAGGTTATGGCTGAATCATccaaaatcggcttcgcaggcatggaaat ggactaagtgttggacctttcgtacccaatccttctttgacaacttgaaccattacttttgtgc ccttgcga
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: 1652 Transcript exons: 204969766-204970922,204971030-204971339,204975888-204976 072 CCAAAATCGGCTTCGCAGGCATGGAAATGGACTAAGTGTTGGACCTTTCGTACCCAATCCTTCT TTGACAACTTGAACCATTACTTTTGTGCCCTTGCGAACTTGAGACCATCTGCTTCCATTTGTGT CATCATTAGATTCTCTTAAAGCATGCTGAATTGAAGATAAAGTCTTGAGATCATTGGAAATTTC TGATTGATATCCTTGCAGTATGCCCTCACTATATTCATCTTCCATGTGGTCATTTTCTTCATCT TTGTCTACGTCATAAACAGAAATGCTGTCAACTTCATCATCATCGACATTGTTATCTGTAACAT TCTCAACTGGAAATGATGAACCATCATGAGCTTCTTCATCTGCAAATTCGTCGTCACTCATATC ATCATCGTTTTCATAAGCTGGAAGGTTCTCTTCATTACAATAATCACCAACATGATCTGTTCCT CGGTTCTTAAAAACTTGAGGATACACAAAAGGATCTCGGTTTTGCTTTATGCTCATAAGTGAAG GCCTTGAAATTCCAATATCTACAAATGCTCCTCCCATATGAGGAACGAGCTTTGTTACTACACC TAGATAAATACTATCACACTGTACATTGTTCTTGATGGGTTCCAGCAAGAGTTCAACTAGTTTT CCATCTTCTAATACTGCAATTCTCTGCATAGTGCAGACAGAGGAATTCATAAGTATAACTCTTG ATGACGGTTCACCACCAGTCGGTTTACTCTCATCCAAAGGCGTTAAAGGTTTTTCTATTTTCCT TAATTTTCTGATAATGTCCCTTGCTTCTACTTTTCCATCAGCAAGAACTATAGTTTCATTTAGT TCCAATATAGATTGAAATAACCATGGCTCTTCAACAGGCTGATACTGTTCATGCATGTTTTTAC TAACTCCACTCAAAGTGTGCTTATAATTTACAAGCTTCTTTTGCCCTTTCTTATCTTTGACTTT TGCAACTGGTTTCTTTGCAGACACAATTGATTCAAGAATCCATGGCTCCTCTACGACTTGAGGC CTTCCATATTGGCTTATATAACTGGCATTTGGTATTTCAGTTACACAGTTGTGCATGATGGTAG ATTGATTATCCGACAACAGTTTTGCATGTAATGGTGTGCCATTCCCAAGCTTCAATATAATATG ATCACCTACAGATAAGCCTTGATTCCGTGTATCCCTGACAGAGTGATCTTTCACAATGTTCTGG TTATTTCCACCATCAAAAAGTTCACCTTCAAGAGAATCAGCTTCCATCAGCCATGATCCCCATG TAGGAGTAGGAAGACCTGGTAGACTGGTTTTCATCCATAGGTCTTTCACAATAATAACCTGCTT TTTCTGGCCATCTGAAGGTATTGATAAGGAGTATACTGGACCTGGCCTCCATATAATATCAGAA GAGGAACTCATTTCTTCTCGAACAAAATAACTATATTTGAAATGCACTCCATATGGTACCTTTA TTTCAGCTGTCCATATATTATTGCTTTCAACAGAAGGAGCCAACTGAACAGCCATGTTGGATTC CCAACAGCCCAGGGTAAGCGGGTCTCCTGTTATGAATATTAAGCACCCATCTTGTAAATCTGCT TTCAGGTTCCATAATATTGTACAGAATCCTTTACAGGTTATGGCTGAATCAT
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.069994569

Conservation Information
Conserved circRNAs	NA
PMCS	0.069994569

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							204975947-204969797(+)
204969789-204976060(-)
204975949-204976060(-)
						
						Potential amino acid sequence
						
							MLDSQQPRVSGSPVMNIKHPSCKSAFRFHNIVQNPLQVMAESSKIGFAGMEMD*(+)
MPAKPILDDSAITCKGFCTILWNLKADLQDGCLIFITGDPLTLGCWESNMAVQLAPSVESNNIW
TAEIKVPYGVHFKYSYFVREEMSSSSDIIWRPGPVYSLSIPSDGQKKQVIIVKDLWMKTSLPGL
PTPTWGSWLMEADSLEGELFDGGNNQNIVKDHSVRDTRNQGLSVGDHIILKLGNGTPLHAKLLS
DNQSTIMHNCVTEIPNASYISQYGRPQVVEEPWILESIVSAKKPVAKVKDKKGQKKLVNYKHTL
SGVSKNMHEQYQPVEEPWLFQSILELNETIVLADGKVEARDIIRKLRKIEKPLTPLDESKPTGG
EPSSRVILMNSSVCTMQRIAVLEDGKLVELLLEPIKNNVQCDSIYLGVVTKLVPHMGGAFVDIG
ISRPSLMSIKQNRDPFVYPQVFKNRGTDHVGDYCNEENLPAYENDDDMSDDEFADEEAHDGSSF
PVENVTDNNVDDDEVDSISVYDVDKDEENDHMEDEYSEGILQGYQSEISNDLKTLSSIQHALRE
SNDDTNGSRWSQVRKGTKVMVQVVKEGLGTKGPTLSPFPCLRSRFWMIQP*(-)
MAVQLAPSVESNNIWTAEIKVPYGVHFKYSYFVREEMSSSSDIIWRPGPVYSLSIPSDGQKKQV
IIVKDLWMKTSLPGLPTPTWGSWLMEADSLEGELFDGGNNQNIVKDHSVRDTRNQGLSVGDHII
LKLGNGTPLHAKLLSDNQSTIMHNCVTEIPNASYISQYGRPQVVEEPWILESIVSAKKPVAKVK
DKKGQKKLVNYKHTLSGVSKNMHEQYQPVEEPWLFQSILELNETIVLADGKVEARDIIRKLRKI
EKPLTPLDESKPTGGEPSSRVILMNSSVCTMQRIAVLEDGKLVELLLEPIKNNVQCDSIYLGVV
TKLVPHMGGAFVDIGISRPSLMSIKQNRDPFVYPQVFKNRGTDHVGDYCNEENLPAYENDDDMS
DDEFADEEAHDGSSFPVENVTDNNVDDDEVDSISVYDVDKDEENDHMEDEYSEGILQGYQSEIS
NDLKTLSSIQHALRESNDDTNGSRWSQVRKGTKVMVQVVKEGLGTKGPTLSPFPCLRSRFWMIQ
P*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	204975947-204969797(+) 204969789-204976060(-) 204975949-204976060(-)
Potential amino acid sequence	MLDSQQPRVSGSPVMNIKHPSCKSAFRFHNIVQNPLQVMAESSKIGFAGMEMD(+) MPAKPILDDSAITCKGFCTILWNLKADLQDGCLIFITGDPLTLGCWESNMAVQLAPSVESNNIW TAEIKVPYGVHFKYSYFVREEMSSSSDIIWRPGPVYSLSIPSDGQKKQVIIVKDLWMKTSLPGL PTPTWGSWLMEADSLEGELFDGGNNQNIVKDHSVRDTRNQGLSVGDHIILKLGNGTPLHAKLLS DNQSTIMHNCVTEIPNASYISQYGRPQVVEEPWILESIVSAKKPVAKVKDKKGQKKLVNYKHTL SGVSKNMHEQYQPVEEPWLFQSILELNETIVLADGKVEARDIIRKLRKIEKPLTPLDESKPTGG EPSSRVILMNSSVCTMQRIAVLEDGKLVELLLEPIKNNVQCDSIYLGVVTKLVPHMGGAFVDIG ISRPSLMSIKQNRDPFVYPQVFKNRGTDHVGDYCNEENLPAYENDDDMSDDEFADEEAHDGSSF PVENVTDNNVDDDEVDSISVYDVDKDEENDHMEDEYSEGILQGYQSEISNDLKTLSSIQHALRE SNDDTNGSRWSQVRKGTKVMVQVVKEGLGTKGPTLSPFPCLRSRFWMIQP(-) MAVQLAPSVESNNIWTAEIKVPYGVHFKYSYFVREEMSSSSDIIWRPGPVYSLSIPSDGQKKQV IIVKDLWMKTSLPGLPTPTWGSWLMEADSLEGELFDGGNNQNIVKDHSVRDTRNQGLSVGDHII LKLGNGTPLHAKLLSDNQSTIMHNCVTEIPNASYISQYGRPQVVEEPWILESIVSAKKPVAKVK DKKGQKKLVNYKHTLSGVSKNMHEQYQPVEEPWLFQSILELNETIVLADGKVEARDIIRKLRKI EKPLTPLDESKPTGGEPSSRVILMNSSVCTMQRIAVLEDGKLVELLLEPIKNNVQCDSIYLGVV TKLVPHMGGAFVDIGISRPSLMSIKQNRDPFVYPQVFKNRGTDHVGDYCNEENLPAYENDDDMS DDEFADEEAHDGSSFPVENVTDNNVDDDEVDSISVYDVDKDEENDHMEDEYSEGILQGYQSEIS NDLKTLSSIQHALRESNDDTNGSRWSQVRKGTKVMVQVVKEGLGTKGPTLSPFPCLRSRFWMIQ P*(-)
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 Zm00001d031873_circ_g.4

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