Plant Circular RNA Database

Detail information of Zm00001d005638_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d005638_circ_g.1
					
						ID in PlantcircBase
						zma_circ_007315
					
						Alias
						zma_circ_0000850
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 181608876-181610521  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d005638						
					
						Parent gene annotation
						
							Retinol dehydrogenase 13
							
						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
						Zm00001d005638_T006:2
Zm00001d005638_T011:2
Zm00001d005638_T009:2
Zm00001d005638_T014:2
Zm00001d005638_T012:2
Zm00001d005638_T002:2
Zm00001d005638_T001:2
Zm00001d005638_T016:2
Zm00001d005638_T004:2
Zm00001d005638_T007:2

General Information
CircRNA Name	Zm00001d005638_circ_g.1
ID in PlantcircBase	zma_circ_007315
Alias	zma_circ_0000850
Organism	Zea mays
Position	chr2: 181608876-181610521 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d005638
Parent gene annotation	Retinol dehydrogenase 13
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	Zm00001d005638_T006:2 Zm00001d005638_T011:2 Zm00001d005638_T009:2 Zm00001d005638_T014:2 Zm00001d005638_T012:2 Zm00001d005638_T002:2 Zm00001d005638_T001:2 Zm00001d005638_T016:2 Zm00001d005638_T004:2 Zm00001d005638_T007:2

			
						 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  
						
							TCCGCCATGCCTCATACTCTTGAGGATCAGAGAAATCTGATGCCTTGAATTGCTGCAAGAATTC
CAAGGGCAACACCATAGATTCTGCACGCCTGCCAAGctcttgcttcaaattccggtcaacccat
ccctttagtctgtctactctttcttttatccacactttcaccagattagcaattgcattttcag
cttcatat

									
								

					

						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
						
							CTCTTGCTTCAAATTCCGGTCAACCCATCCCTTTAGTCTGTCTACTCTTTCTTTTATCCACACT
TTCACCAGATTAGCAATTGCATTTTCAGCTTCATATGGCGGCATCTCTCTGATTAGTGACTTGC
CTCCATCATCACTATCCACAGAATCTTCTACAGCTATATTAACAAGGTCCTTCTCTAATTTGTC
TGCTGATTTAAGTACTTCAACTGTATCAGGGGTCAGCTCTGTAAGCCCAGCTACAAACTGCTTC
AGCTCATTTCCATAACAAGAATGAAGGGTTGCAACAGCAACACCAGAAGCAAGAGGATGCCATG
TCTTCAGTATTGGACTGTACAATTTTTTCTCCTTCGTAGCTAGGTCACTAATGTCCTTCGCAAG
GATAGAAAGAACTGGAGTAGGGTTTCTTGATGATCGTTTTGAATCTGCTTCTTCCATTCTCTAC
ACAGGTCGAAGTAACATCAATAACAGAAGAGCTTGTGCACAATACCAAAATATCAATTTTATGA
AACCTAGCATCTCAATCCATGCATAAAAGAGAACAGCTAAGTACAAATATAAGTTGAGATCATG
GAAAATGATTTTCTACAGTTTCTAGGTTAAAACTTTCTAGTCATTCCTTTACCAAACATGGCAT
GGGTTGTGAGCAATAAATTGATGTGGCAAAACAAAAACAACAAATGCACATGGGTATTTTGACT
TTTGAGGTACAGAAACAACATTATTCATATATGTTAAACCAAAGATTGAGGATGATATTTACGA
CTAACAAGACTTACTTGAGCAAAAGCTGTCCGTAGTGAAGACCTTATGTATGTCTCTACCCTGC
TTCGAGCTACATCAGTCTCTTCTTTTCTTCTACGGCGGTATTCATGGGATATATCTTCAACAAG
AACCCTTGCAGCTGACACTCCAATGGAGACAATGCCTTGCATAGACTCAATATTACTTGTATTG
AAGGTTTCATGATATGCCAGAAGTCTTTTCTCTGTCCAGCCCATTATTGAGCTTAATGTTGAGC
TCAATACTTTACAGTAATTTGGATCTTTTGTGGTTTTCGCATCCTTAGCCACTTCAGCTAACTG
GTTCTCTGCTGCAGAAAGTAGCTCGATATCTACTTGACCAGACATAACAAAATGGTTGAACAAT
GCCCAAGTAAAGCAAAGATTGTGGAGCAACTCATTAATTCCAAGAATAACCCAGGTTTTCTTCA
AGAGCTCCATCACCTCATCGATCTCATCAACCACAGTGCCCTCATCATTATCAAAGCAAGCTTC
TACCAACGTTTGGTACAGATGGAGATTCAATGGGAAGCCATCTGCCCAGTGGCATCCATCAGAA
GTACCATCATGAGATCTTCCAGCAAGGGACATGACACAAGTACGTAGACCCTGCATTGACTCAG
AGTTTTTCCCAGTTTCAAGTGGCCTATCATATGCACCCCGTATAATTTGCCGCAACCGTTGCAC
AGAACTGTCTGATTTGTTCAATGGAACGAGTGGATGAACAAGTAGACCAGCCTCAAGAAGCTTC
AGATTCCTACTCCGCCATGCCTCATACTCTTGAGGATCAGAGAAATCTGATGCCTTGAATTGCT
GCAAGAATTCCAAGGGCAACACCATAGATTCTGCACGCCTGCCAAG
						
					

			
		

Sequences
Splice junction sequence	TCCGCCATGCCTCATACTCTTGAGGATCAGAGAAATCTGATGCCTTGAATTGCTGCAAGAATTC CAAGGGCAACACCATAGATTCTGCACGCCTGCCAAGctcttgcttcaaattccggtcaacccat ccctttagtctgtctactctttcttttatccacactttcaccagattagcaattgcattttcag cttcatat
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	CTCTTGCTTCAAATTCCGGTCAACCCATCCCTTTAGTCTGTCTACTCTTTCTTTTATCCACACT TTCACCAGATTAGCAATTGCATTTTCAGCTTCATATGGCGGCATCTCTCTGATTAGTGACTTGC CTCCATCATCACTATCCACAGAATCTTCTACAGCTATATTAACAAGGTCCTTCTCTAATTTGTC TGCTGATTTAAGTACTTCAACTGTATCAGGGGTCAGCTCTGTAAGCCCAGCTACAAACTGCTTC AGCTCATTTCCATAACAAGAATGAAGGGTTGCAACAGCAACACCAGAAGCAAGAGGATGCCATG TCTTCAGTATTGGACTGTACAATTTTTTCTCCTTCGTAGCTAGGTCACTAATGTCCTTCGCAAG GATAGAAAGAACTGGAGTAGGGTTTCTTGATGATCGTTTTGAATCTGCTTCTTCCATTCTCTAC ACAGGTCGAAGTAACATCAATAACAGAAGAGCTTGTGCACAATACCAAAATATCAATTTTATGA AACCTAGCATCTCAATCCATGCATAAAAGAGAACAGCTAAGTACAAATATAAGTTGAGATCATG GAAAATGATTTTCTACAGTTTCTAGGTTAAAACTTTCTAGTCATTCCTTTACCAAACATGGCAT GGGTTGTGAGCAATAAATTGATGTGGCAAAACAAAAACAACAAATGCACATGGGTATTTTGACT TTTGAGGTACAGAAACAACATTATTCATATATGTTAAACCAAAGATTGAGGATGATATTTACGA CTAACAAGACTTACTTGAGCAAAAGCTGTCCGTAGTGAAGACCTTATGTATGTCTCTACCCTGC TTCGAGCTACATCAGTCTCTTCTTTTCTTCTACGGCGGTATTCATGGGATATATCTTCAACAAG AACCCTTGCAGCTGACACTCCAATGGAGACAATGCCTTGCATAGACTCAATATTACTTGTATTG AAGGTTTCATGATATGCCAGAAGTCTTTTCTCTGTCCAGCCCATTATTGAGCTTAATGTTGAGC TCAATACTTTACAGTAATTTGGATCTTTTGTGGTTTTCGCATCCTTAGCCACTTCAGCTAACTG GTTCTCTGCTGCAGAAAGTAGCTCGATATCTACTTGACCAGACATAACAAAATGGTTGAACAAT GCCCAAGTAAAGCAAAGATTGTGGAGCAACTCATTAATTCCAAGAATAACCCAGGTTTTCTTCA AGAGCTCCATCACCTCATCGATCTCATCAACCACAGTGCCCTCATCATTATCAAAGCAAGCTTC TACCAACGTTTGGTACAGATGGAGATTCAATGGGAAGCCATCTGCCCAGTGGCATCCATCAGAA GTACCATCATGAGATCTTCCAGCAAGGGACATGACACAAGTACGTAGACCCTGCATTGACTCAG AGTTTTTCCCAGTTTCAAGTGGCCTATCATATGCACCCCGTATAATTTGCCGCAACCGTTGCAC AGAACTGTCTGATTTGTTCAATGGAACGAGTGGATGAACAAGTAGACCAGCCTCAAGAAGCTTC AGATTCCTACTCCGCCATGCCTCATACTCTTGAGGATCAGAGAAATCTGATGCCTTGAATTGCT GCAAGAATTCCAAGGGCAACACCATAGATTCTGCACGCCTGCCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.2217621

Conservation Information
Conserved circRNAs	NA
PMCS	0.2217621

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							181610502-181608878(-)
						
					

						Potential amino acid sequence
						
							MVLPLEFLQQFKASDFSDPQEYEAWRSRNLKLLEAGLLVHPLVPLNKSDSSVQRLRQIIRGAYD
RPLETGKNSESMQGLRTCVMSLAGRSHDGTSDGCHWADGFPLNLHLYQTLVEACFDNDEGTVVD
EIDEVMELLKKTWVILGINELLHNLCFTWALFNHFVMSGQVDIELLSAAENQLAEVAKDAKTTK
DPNYCKVLSSTLSSIMGWTEKRLLAYHETFNTSNIESMQGIVSIGVSAARVLVEDISHEYRRRR
KEETDVARSRVETYIRSSLRTAFAQRMEEADSKRSSRNPTPVLSILAKDISDLATKEKKLYSPI
LKTWHPLASGVAVATLHSCYGNELKQFVAGLTELTPDTVEVLKSADKLEKDLVNIAVEDSVDSD
DGGKSLIREMPPYEAENAIANLVKVWIKERVDRLKGWVDRNLKQELGRRAESMVLPLEFLQQFK
ASDFSDPQEYEAWRSRNLKLLEAGLLVHPLVPLNKSDSSVQRLRQIIRGAYDRPLETGKNSESM
QGLRTCVMSLAGRSHDGTSDGCHWADGFPLNLHLYQTLVEACFDNDEGTVVDEIDEVMELLKKT
WVILGINELLHNLCFTWALFNHFVMSGQVDIELLSAAENQLAEVAKDAKTTKDPNYCKVLSSTL
SSIMGWTEKRLLAYHETFNTSNIESMQGIVSIGVSAARVLVEDISHEYRRRRKEETDVARSRVE
TYIRSSLRTAFAQRMEEADSKRSSRNPTPVLSILAKDISDLATKEKKLYSPILKTWHPLASGVA
VATLHSCYGNELKQFVAGLTELTPDTVEVLKSADKLEKDLVNIAVEDSVDSDDGGKSLIREMPP
YEAENAIANLVKVWIKERVDRLKGWVDRNLKQELGRRAESMVLPLEFLQQFKASDFSDPQEYEA
WRSRNLKLLEAGLLVHPLVPLNKSDSSVQRLRQIIRGAYDRPLETGKNSESMQGLRTCVMSLAG
RSHDGTSDGCHWADGFPLNLHLYQTLVEACFDNDEGTVVDEIDEVMELLKKTWVILGINELLHN
LCFTWALFNHFVMSGQVDIELLSAAENQLAEVAKDAKTTKDPNYCKVLSSTLSSIMGWTEKRLL
AYHETFNTSNIESMQGIVSIGVSAARVLVEDISHEYRRRRKEETDVARSRVETYIRSSLRTAFA
QRMEEADSKRSSRNPTPVLSILAKDISDLATKEKKLYSPILKTWHPLASGVAVATLHSCYGNEL
KQFVAGLTELTPDTVEVLKSADKLEKDLVNIAVEDSVDSDDGGKSLIREMPPYEAENAIANLVK
VWIKERVDRLKGWVDRNLKQELGRRAESMVLPLEFLQQFKASDFSDPQEYEAWRSRNLKLLEAG
LLVHPLVPLNKSDSSVQRLRQIIRGAYDRPLETGKNSESMQGLRTCVMSLAGRSHDGTSDGCHW
ADGFPLNLHLYQTLVEACFDNDEGTVVDEIDEVMELLKKTWVILGINELLHNLCFTWALFNHFV
MSGQVDIELLSAAENQLAEVAKDAKTTKDPNYCKVLSSTLSSIMGWTEKRLLAYHETFNTSNIE
SMQGIVSIGVSAARVLVEDISHEYRRRRKEETDVARSRVETYIRSSLRTAFAQRMEEADSKRSS
RNPTPVLSILAKDISDLATKEKKLYSPILKTWHPLASGVAVATLHSCYGNELKQFVAGLTELTP
DTVEVLKSADKLEKDLVNIAVEDSVDSDDGGKSLIREMPPYEAENAIANLVKVWIKERVDRLKG
WVDRNLKQE(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	181610502-181608878(-)
Potential amino acid sequence	MVLPLEFLQQFKASDFSDPQEYEAWRSRNLKLLEAGLLVHPLVPLNKSDSSVQRLRQIIRGAYD RPLETGKNSESMQGLRTCVMSLAGRSHDGTSDGCHWADGFPLNLHLYQTLVEACFDNDEGTVVD EIDEVMELLKKTWVILGINELLHNLCFTWALFNHFVMSGQVDIELLSAAENQLAEVAKDAKTTK DPNYCKVLSSTLSSIMGWTEKRLLAYHETFNTSNIESMQGIVSIGVSAARVLVEDISHEYRRRR KEETDVARSRVETYIRSSLRTAFAQRMEEADSKRSSRNPTPVLSILAKDISDLATKEKKLYSPI LKTWHPLASGVAVATLHSCYGNELKQFVAGLTELTPDTVEVLKSADKLEKDLVNIAVEDSVDSD DGGKSLIREMPPYEAENAIANLVKVWIKERVDRLKGWVDRNLKQELGRRAESMVLPLEFLQQFK ASDFSDPQEYEAWRSRNLKLLEAGLLVHPLVPLNKSDSSVQRLRQIIRGAYDRPLETGKNSESM QGLRTCVMSLAGRSHDGTSDGCHWADGFPLNLHLYQTLVEACFDNDEGTVVDEIDEVMELLKKT WVILGINELLHNLCFTWALFNHFVMSGQVDIELLSAAENQLAEVAKDAKTTKDPNYCKVLSSTL SSIMGWTEKRLLAYHETFNTSNIESMQGIVSIGVSAARVLVEDISHEYRRRRKEETDVARSRVE TYIRSSLRTAFAQRMEEADSKRSSRNPTPVLSILAKDISDLATKEKKLYSPILKTWHPLASGVA VATLHSCYGNELKQFVAGLTELTPDTVEVLKSADKLEKDLVNIAVEDSVDSDDGGKSLIREMPP YEAENAIANLVKVWIKERVDRLKGWVDRNLKQELGRRAESMVLPLEFLQQFKASDFSDPQEYEA WRSRNLKLLEAGLLVHPLVPLNKSDSSVQRLRQIIRGAYDRPLETGKNSESMQGLRTCVMSLAG RSHDGTSDGCHWADGFPLNLHLYQTLVEACFDNDEGTVVDEIDEVMELLKKTWVILGINELLHN LCFTWALFNHFVMSGQVDIELLSAAENQLAEVAKDAKTTKDPNYCKVLSSTLSSIMGWTEKRLL AYHETFNTSNIESMQGIVSIGVSAARVLVEDISHEYRRRRKEETDVARSRVETYIRSSLRTAFA QRMEEADSKRSSRNPTPVLSILAKDISDLATKEKKLYSPILKTWHPLASGVAVATLHSCYGNEL KQFVAGLTELTPDTVEVLKSADKLEKDLVNIAVEDSVDSDDGGKSLIREMPPYEAENAIANLVK VWIKERVDRLKGWVDRNLKQELGRRAESMVLPLEFLQQFKASDFSDPQEYEAWRSRNLKLLEAG LLVHPLVPLNKSDSSVQRLRQIIRGAYDRPLETGKNSESMQGLRTCVMSLAGRSHDGTSDGCHW ADGFPLNLHLYQTLVEACFDNDEGTVVDEIDEVMELLKKTWVILGINELLHNLCFTWALFNHFV MSGQVDIELLSAAENQLAEVAKDAKTTKDPNYCKVLSSTLSSIMGWTEKRLLAYHETFNTSNIE SMQGIVSIGVSAARVLVEDISHEYRRRRKEETDVARSRVETYIRSSLRTAFAQRMEEADSKRSS RNPTPVLSILAKDISDLATKEKKLYSPILKTWHPLASGVAVATLHSCYGNELKQFVAGLTELTP DTVEVLKSADKLEKDLVNIAVEDSVDSDDGGKSLIREMPPYEAENAIANLVKVWIKERVDRLKG WVDRNLKQE(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d005638_circ_g.1

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