Plant Circular RNA Database

Detail information of Zm00001d040191_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d040191_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007541
					
						Alias
						zma_circ_0001435
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 31623124-31625516  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d040191						
					
						Parent gene annotation
						
							zinc ion binding
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d040191_circ_g.1 						
					
						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
						Zm00001d040191_T001:5
Zm00001d040191_T005:6
Zm00001d040191_T006:5
Zm00001d040191_T004:5
Zm00001d040191_T008:3
Zm00001d040191_T003:5
Zm00001d040191_T007:5
Zm00001d040191_T002:5

General Information
CircRNA Name	Zm00001d040191_circ_g.2
ID in PlantcircBase	zma_circ_007541
Alias	zma_circ_0001435
Organism	Zea mays
Position	chr3: 31623124-31625516 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d040191
Parent gene annotation	zinc ion binding
Parent gene strand	-
Alternative splicing	Zm00001d040191_circ_g.1
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	Zm00001d040191_T001:5 Zm00001d040191_T005:6 Zm00001d040191_T006:5 Zm00001d040191_T004:5 Zm00001d040191_T008:3 Zm00001d040191_T003:5 Zm00001d040191_T007:5 Zm00001d040191_T002:5

			
						 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  
						
							CCAGTGTTGCTCTTATCAGATTTCACAGGGCATACACCACCACCAGTGGTGGCTCCCGCGAAAG
GGCAGATCGAGCTCATGATTATTCACTCGTCCTTCCctgggaagccacagcagagtgttctttt
actgcatttctgcgaacatccaatgaacgggcataatagtttcttgcagattggaggtcgccat
catagtag

									
								

					

						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: 962
Transcript exons: 31623124-31623270,31623347-31623434,31624551-31624696,31
624850-31625078,31625165-31625516
CTGGGAAGCCACAGCAGAGTGTTCTTTTACTGCATTTCTGCGAACATCCAATGAACGGGCATAA
TAGTTTCTTGCAGATTGGAGGTCGCCATCATAGTAGCGAAGGTCACCGATTTTATTTAGTGAAA
CAGAGAGAGTATGAACCAGCTCAAGATCTTTTGCAGGGGGCTTTGAGAGGAACTCAGCACTTTC
TTCATAGTAGGTGATTGCTGCAGGAACATCTCCCAAGGTCCGACAGCAGTCCCCAAGCATTCCT
AACACAGCTCCAAGCTGTGAACATAGGTCTAAGTTATCTTCTGAAGATTTTAACTCCTCCCTGA
TGTCGTCTGCACACATAGTGAGCCTTGACTTTGCACTTTCAATGTTTCGGGCACGAAAAGCCCT
CATAGCTTGCTGCACCAGAAAAGCCCCTCTCTCCATGGAAACATCCTCATATATGACTTTGTTC
TTGCCATCTGCTGCTTCCACATCCCCTGCAGCATGTGATCGCTTGATTCTGGCATGACCATCAA
TGAAGCGGTCAACAAGAGCTTGAAGTTCCGCATCAGGCTCAATACCCTCTATATCAGCACCACA
TAGTGGGCAGTCTTTAAAGCGTGATATACATGCCTTGCAAAATTTATGGGCACACGGCTTGCAT
TTGCTACTTTCATGGAGTAGTGCCTGGCAGACAATGCAGCTAAGCGGACCCAGCTTGAAAGTGT
TGGAGTCATAGCCGAATGGGCATTTTGCTGGTACGACACGAGGATCGGTGCCCTTTTCTTCACC
ATGATCACCACTTTCCTTGAGCTTGCTACCATGATCCTTGCCAGTGACAGGGCATACACCACTG
ATGCTCTTGTCAGATTTTGCAGGGCACACCCCAGTGTTGCTCTTATCAGATTTCACAGGGCATA
CACCACCACCAGTGGTGGCTCCCGCGAAAGGGCAGATCGAGCTCATGATTATTCACTCGTCCTT
CC
						
					

						Genomic sequence
						
							CTGGGAAGCCACAGCAGAGTGTTCTTTTACTGCATTTCTGCGAACATCCAATGAACGGGCATAA
TAGTTTCTTGCAGATTGGAGGTCGCCATCATAGTAGCGAAGGTCACCGATTTTATTTAGTGAAA
CAGAGAGAGTATGAACCAGCTGCAGATAAGTGTAAAAGATAAATCAGCATGTGAAATTTCAATG
TTATTACAGTTACACTAAAATTGAATAGAACCTCAAGATCTTTTGCAGGGGGCTTTGAGAGGAA
CTCAGCACTTTCTTCATAGTAGGTGATTGCTGCAGGAACATCTCCCAAGGTCCGACTGAAAACA
CAATACAATGAAAAGGATGCAGTGTGGAATGAGTTCCATGATTAAATGATCAATAAAATGAGCA
AAATTGTGTCGATCAATACCAAATGAATCGCAAACAGGCCGGAAGACCAAGACAATTATATGAA
AAGTGACGCATGGTATTATAAGTGTGACAGGAGTGAAGATTCACTGATGATAAGTAGAAAAATG
AAGTCACCACAGATTCAGAGACATCACAGATCCTATGCTTGTCGAATACAAGGTGGCTAGATAT
CCCAATCCAGATCGTGTTAACTTGCAATTAGCTTAATGCATGAGGCACGAATCCGTAATTAAGA
TGATGCTTGGCACAGGCCACAGAGTTTTTTCCATTTGGCGAAATACCATCCAAACAAGTTGCAA
GCAGCTGAAGACTGGCATAATTATCAGGCTAGAACCCTACTAAAAGTTCCTAGCTGCATTAGCC
AGTCCACAGTCTAGACAAAAACATTGGCTCATACATGTCAAGTCGTTTAAAAGTAGGCAGCAAA
TTTGGAAAAGATTTCAGGTAGTTAAAAACTAAGAATGTTCAGATACACAACATGAACAAAATTT
GCACTTTGAAAGAGCACAGCTATGCAGGAAGCTAGCTCAATATACAGTTAAAATATCAATGTAA
CATCTGCAGAATTCATTTTATTTGCTCCCTTAGACCATAATGCACACTTTTGGCGTCCAGACTA
ACACACTCCTATATACAGAGGGGGTAGCAAAAGAAACATATGTGGTAGAAATATCTTTGTGTGT
TAAATCAACAGCACATATCTTTTGTTTTTCTAATCCTGGTATGACTCATCATTAGGGGGTGCAA
ATGGTACGGATGTTTTCTGGCCATATCCAAGCTCGAATTCGTTTAGAGTTAAAAATCCATCCGT
ATCTGAGTCGGATAAACTATATCCAAAACCGTATCCGCATCCGAATACTGAAATCATATCCATA
TTCTAATCCAAGAAACAATATAGCTATCCATGTTCATATCCGTAGGTATCCAACCATTTGCACC
CTAGTAATCATAGTATTTTCTTAGTTTGCTGATGAAGTGAATAAAAACATTTGAGGGAAATAGT
TAAGAGCCAACAGACATACCAGCAGTCCCCAAGCATTCCTAACACAGCTCCAAGCTGTGAACAT
AGGTCTAAGTTATCTTCTGAAGATTTTAACTCCTCCCTGATGTCGTCTGCACACATAGTGAGCC
TTGACTTTGCACTTTCAATGTTTCGGGCACGAAAAGCCTAGAGCCAAACAGTTAAGGCCTTGTT
GTAAGTTGTAACACCAATATTGTAAATAAATCCATGAATAATAGACAATGATTAGTTATTAAAA
TTTATCAGGTTCAAGAATCTATTTCAACATAAGAGGCTAAAGCAGTTAACTTAATTACTGACCC
TCATAGCTTGCTGCACCAGAAAAGCCCCTCTCTCCATGGAAACATCCTCATATATGACTTTGTT
CTTGCCATCTGCTGCTTCCACATCCCCTGCAGCATGTGATCGCTTGATTCTGGCATGACCATCA
ATGAAGCGGTCAACAAGAGCTTGAAGTTCCGCATCAGGCTCAATACCCTCTATATCAGCACCAC
ATAGTGGGCAGTCTTTAAAGCGTGATATACATGCCCTGCCAAGGAAATCCAGTAAGAACCTATT
GAAGCAACGAATGAAACACAAAATGCAATTGAGCTGGATGTGAGGCACGAAACACACTTGCAAA
ATTTATGGGCACACGGCTTGCATTTGCTACTTTCATGGAGTAGTGCCTGGCAGACAATGCAGCT
AAGCGGACCCAGCTTGAAAGTGTTGGAGTCATAGCCGAATGGGCATTTTGCTGGTACGACACGA
GGATCGGTGCCCTTTTCTTCACCATGATCACCACTTTCCTTGAGCTTGCTACCATGATCCTTGC
CAGTGACAGGGCATACACCACTGATGCTCTTGTCAGATTTTGCAGGGCACACCCCAGTGTTGCT
CTTATCAGATTTCACAGGGCATACACCACCACCAGTGGTGGCTCCCGCGAAAGGGCAGATCGAG
CTCATGATTATTCACTCGTCCTTCC
						
					

			
		

Sequences
Splice junction sequence	CCAGTGTTGCTCTTATCAGATTTCACAGGGCATACACCACCACCAGTGGTGGCTCCCGCGAAAG GGCAGATCGAGCTCATGATTATTCACTCGTCCTTCCctgggaagccacagcagagtgttctttt actgcatttctgcgaacatccaatgaacgggcataatagtttcttgcagattggaggtcgccat catagtag
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: 962 Transcript exons: 31623124-31623270,31623347-31623434,31624551-31624696,31 624850-31625078,31625165-31625516 CTGGGAAGCCACAGCAGAGTGTTCTTTTACTGCATTTCTGCGAACATCCAATGAACGGGCATAA TAGTTTCTTGCAGATTGGAGGTCGCCATCATAGTAGCGAAGGTCACCGATTTTATTTAGTGAAA CAGAGAGAGTATGAACCAGCTCAAGATCTTTTGCAGGGGGCTTTGAGAGGAACTCAGCACTTTC TTCATAGTAGGTGATTGCTGCAGGAACATCTCCCAAGGTCCGACAGCAGTCCCCAAGCATTCCT AACACAGCTCCAAGCTGTGAACATAGGTCTAAGTTATCTTCTGAAGATTTTAACTCCTCCCTGA TGTCGTCTGCACACATAGTGAGCCTTGACTTTGCACTTTCAATGTTTCGGGCACGAAAAGCCCT CATAGCTTGCTGCACCAGAAAAGCCCCTCTCTCCATGGAAACATCCTCATATATGACTTTGTTC TTGCCATCTGCTGCTTCCACATCCCCTGCAGCATGTGATCGCTTGATTCTGGCATGACCATCAA TGAAGCGGTCAACAAGAGCTTGAAGTTCCGCATCAGGCTCAATACCCTCTATATCAGCACCACA TAGTGGGCAGTCTTTAAAGCGTGATATACATGCCTTGCAAAATTTATGGGCACACGGCTTGCAT TTGCTACTTTCATGGAGTAGTGCCTGGCAGACAATGCAGCTAAGCGGACCCAGCTTGAAAGTGT TGGAGTCATAGCCGAATGGGCATTTTGCTGGTACGACACGAGGATCGGTGCCCTTTTCTTCACC ATGATCACCACTTTCCTTGAGCTTGCTACCATGATCCTTGCCAGTGACAGGGCATACACCACTG ATGCTCTTGTCAGATTTTGCAGGGCACACCCCAGTGTTGCTCTTATCAGATTTCACAGGGCATA CACCACCACCAGTGGTGGCTCCCGCGAAAGGGCAGATCGAGCTCATGATTATTCACTCGTCCTT CC
Genomic sequence	CTGGGAAGCCACAGCAGAGTGTTCTTTTACTGCATTTCTGCGAACATCCAATGAACGGGCATAA TAGTTTCTTGCAGATTGGAGGTCGCCATCATAGTAGCGAAGGTCACCGATTTTATTTAGTGAAA CAGAGAGAGTATGAACCAGCTGCAGATAAGTGTAAAAGATAAATCAGCATGTGAAATTTCAATG TTATTACAGTTACACTAAAATTGAATAGAACCTCAAGATCTTTTGCAGGGGGCTTTGAGAGGAA CTCAGCACTTTCTTCATAGTAGGTGATTGCTGCAGGAACATCTCCCAAGGTCCGACTGAAAACA CAATACAATGAAAAGGATGCAGTGTGGAATGAGTTCCATGATTAAATGATCAATAAAATGAGCA AAATTGTGTCGATCAATACCAAATGAATCGCAAACAGGCCGGAAGACCAAGACAATTATATGAA AAGTGACGCATGGTATTATAAGTGTGACAGGAGTGAAGATTCACTGATGATAAGTAGAAAAATG AAGTCACCACAGATTCAGAGACATCACAGATCCTATGCTTGTCGAATACAAGGTGGCTAGATAT CCCAATCCAGATCGTGTTAACTTGCAATTAGCTTAATGCATGAGGCACGAATCCGTAATTAAGA TGATGCTTGGCACAGGCCACAGAGTTTTTTCCATTTGGCGAAATACCATCCAAACAAGTTGCAA GCAGCTGAAGACTGGCATAATTATCAGGCTAGAACCCTACTAAAAGTTCCTAGCTGCATTAGCC AGTCCACAGTCTAGACAAAAACATTGGCTCATACATGTCAAGTCGTTTAAAAGTAGGCAGCAAA TTTGGAAAAGATTTCAGGTAGTTAAAAACTAAGAATGTTCAGATACACAACATGAACAAAATTT GCACTTTGAAAGAGCACAGCTATGCAGGAAGCTAGCTCAATATACAGTTAAAATATCAATGTAA CATCTGCAGAATTCATTTTATTTGCTCCCTTAGACCATAATGCACACTTTTGGCGTCCAGACTA ACACACTCCTATATACAGAGGGGGTAGCAAAAGAAACATATGTGGTAGAAATATCTTTGTGTGT TAAATCAACAGCACATATCTTTTGTTTTTCTAATCCTGGTATGACTCATCATTAGGGGGTGCAA ATGGTACGGATGTTTTCTGGCCATATCCAAGCTCGAATTCGTTTAGAGTTAAAAATCCATCCGT ATCTGAGTCGGATAAACTATATCCAAAACCGTATCCGCATCCGAATACTGAAATCATATCCATA TTCTAATCCAAGAAACAATATAGCTATCCATGTTCATATCCGTAGGTATCCAACCATTTGCACC CTAGTAATCATAGTATTTTCTTAGTTTGCTGATGAAGTGAATAAAAACATTTGAGGGAAATAGT TAAGAGCCAACAGACATACCAGCAGTCCCCAAGCATTCCTAACACAGCTCCAAGCTGTGAACAT AGGTCTAAGTTATCTTCTGAAGATTTTAACTCCTCCCTGATGTCGTCTGCACACATAGTGAGCC TTGACTTTGCACTTTCAATGTTTCGGGCACGAAAAGCCTAGAGCCAAACAGTTAAGGCCTTGTT GTAAGTTGTAACACCAATATTGTAAATAAATCCATGAATAATAGACAATGATTAGTTATTAAAA TTTATCAGGTTCAAGAATCTATTTCAACATAAGAGGCTAAAGCAGTTAACTTAATTACTGACCC TCATAGCTTGCTGCACCAGAAAAGCCCCTCTCTCCATGGAAACATCCTCATATATGACTTTGTT CTTGCCATCTGCTGCTTCCACATCCCCTGCAGCATGTGATCGCTTGATTCTGGCATGACCATCA ATGAAGCGGTCAACAAGAGCTTGAAGTTCCGCATCAGGCTCAATACCCTCTATATCAGCACCAC ATAGTGGGCAGTCTTTAAAGCGTGATATACATGCCCTGCCAAGGAAATCCAGTAAGAACCTATT GAAGCAACGAATGAAACACAAAATGCAATTGAGCTGGATGTGAGGCACGAAACACACTTGCAAA ATTTATGGGCACACGGCTTGCATTTGCTACTTTCATGGAGTAGTGCCTGGCAGACAATGCAGCT AAGCGGACCCAGCTTGAAAGTGTTGGAGTCATAGCCGAATGGGCATTTTGCTGGTACGACACGA GGATCGGTGCCCTTTTCTTCACCATGATCACCACTTTCCTTGAGCTTGCTACCATGATCCTTGC CAGTGACAGGGCATACACCACTGATGCTCTTGTCAGATTTTGCAGGGCACACCCCAGTGTTGCT CTTATCAGATTTCACAGGGCATACACCACCACCAGTGGTGGCTCCCGCGAAAGGGCAGATCGAG CTCATGATTATTCACTCGTCCTTCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.096660985

Conservation Information
Conserved circRNAs	NA
PMCS	0.096660985

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							31625324-31623184(+)
31625388-31623402(+)
31625498-31625501(-)
						
						Potential amino acid sequence
						
							MITTFLELATMILASDRAYTTDALVRFCRAHPSVALIRFHRAYTTTSGGSRERADRAHDYSLVL
PWEATAECSFTAFLRTSNERA*(+)
MLLSDFAGHTPVLLLSDFTGHTPPPVVAPAKGQIELMIIHSSFPGKPQQSVLLLHFCEHPMNGH
NSFLQIGGRHHSSEGHRFYLVKQREYEPAQDLLQGALRGTQHFLHSR*(+)
MSSICPFAGATTGGGVCPVKSDKSNTGVCPAKSDKSISGVCPVTGKDHGSKLKESGDHGEEKGT
DPRVVPAKCPFGYDSNTFKLGPLSCIVCQALLHESSKCKPCAHKFCKACISRFKDCPLCGADIE
GIEPDAELQALVDRFIDGHARIKRSHAAGDVEAADGKNKVIYEDVSMERGAFLVQQAMRVIFNY
LKSFPNLLPTFKRLDIRTLGDVPAAITYYEESAEFLSKPPAKDLELVHTLSVSLNKIGDLRYYD
GDLQSARNYYARSLDVRRNAVKEHSAVASQGRTSE*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	31625324-31623184(+) 31625388-31623402(+) 31625498-31625501(-)
Potential amino acid sequence	MITTFLELATMILASDRAYTTDALVRFCRAHPSVALIRFHRAYTTTSGGSRERADRAHDYSLVL PWEATAECSFTAFLRTSNERA(+) MLLSDFAGHTPVLLLSDFTGHTPPPVVAPAKGQIELMIIHSSFPGKPQQSVLLLHFCEHPMNGH NSFLQIGGRHHSSEGHRFYLVKQREYEPAQDLLQGALRGTQHFLHSR(+) MSSICPFAGATTGGGVCPVKSDKSNTGVCPAKSDKSISGVCPVTGKDHGSKLKESGDHGEEKGT DPRVVPAKCPFGYDSNTFKLGPLSCIVCQALLHESSKCKPCAHKFCKACISRFKDCPLCGADIE GIEPDAELQALVDRFIDGHARIKRSHAAGDVEAADGKNKVIYEDVSMERGAFLVQQAMRVIFNY LKSFPNLLPTFKRLDIRTLGDVPAAITYYEESAEFLSKPPAKDLELVHTLSVSLNKIGDLRYYD GDLQSARNYYARSLDVRRNAVKEHSAVASQGRTSE*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d040191_circ_g.2

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