Plant Circular RNA Database

Detail information of Zm00001d004667_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d004667_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007260
					
						Alias
						Zm02circ00077, GRMZM2G075680_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 128171252-128173456  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d004667						
					
						Parent gene annotation
						
							Protein transport protein Sec24-like CEF
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d004667_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d004667_T009:7
Zm00001d004667_T044:7
Zm00001d004667_T011:7
Zm00001d004667_T042:7
Zm00001d004667_T007:7
Zm00001d004667_T040:7
Zm00001d004667_T034:7
Zm00001d004667_T018:7
Zm00001d004667_T038:7
Zm00001d004667_T003:7
Zm00001d004667_T046:7
Zm00001d004667_T023:7
Zm00001d004667_T037:7
Zm00001d004667_T043:7
Zm00001d004667_T030:7
Zm00001d004667_T001:7
Zm00001d004667_T026:7
Zm00001d004667_T036:7
Zm00001d004667_T014:7
Zm00001d004667_T005:7
Zm00001d004667_T006:7
Zm00001d004667_T008:7
Zm00001d004667_T029:7
Zm00001d004667_T045:7
Zm00001d004667_T022:7
Zm00001d004667_T004:7
Zm00001d004667_T024:7
Zm00001d004667_T002:7
Zm00001d004667_T021:7

General Information
CircRNA Name	Zm00001d004667_circ_g.3
ID in PlantcircBase	zma_circ_007260
Alias	Zm02circ00077, GRMZM2G075680_C1
Organism	Zea mays
Position	chr2: 128171252-128173456 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d004667
Parent gene annotation	Protein transport protein Sec24-like CEF
Parent gene strand	-
Alternative splicing	Zm00001d004667_circ_g.2
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d004667_T009:7 Zm00001d004667_T044:7 Zm00001d004667_T011:7 Zm00001d004667_T042:7 Zm00001d004667_T007:7 Zm00001d004667_T040:7 Zm00001d004667_T034:7 Zm00001d004667_T018:7 Zm00001d004667_T038:7 Zm00001d004667_T003:7 Zm00001d004667_T046:7 Zm00001d004667_T023:7 Zm00001d004667_T037:7 Zm00001d004667_T043:7 Zm00001d004667_T030:7 Zm00001d004667_T001:7 Zm00001d004667_T026:7 Zm00001d004667_T036:7 Zm00001d004667_T014:7 Zm00001d004667_T005:7 Zm00001d004667_T006:7 Zm00001d004667_T008:7 Zm00001d004667_T029:7 Zm00001d004667_T045:7 Zm00001d004667_T022:7 Zm00001d004667_T004:7 Zm00001d004667_T024:7 Zm00001d004667_T002:7 Zm00001d004667_T021:7

			
						 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  
						
							AGACTCAAGTGTGCAATACCTGCTGCTGAGCACGTTTAAGACTGTAGAAGTGAATAGCAGAATC
AAATGTTGCAATTCCAACCATTGTCCGAGGACCTTCccggccacctgtagtttgaggcacaacg
gatatagaagcaatatcaacataggattgtgtggtgaggaatacatccacacagacctgaaaga
ggggagaa

									
								

					

						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: 540
Transcript exons: 128171252-128171335,128171426-128171497,128171656-128171
732,128172311-128172365,128172528-128172620,128172728-12
8172805,128173376-128173456
CCGGCCACCTGTAGTTTGAGGCACAACGGATATAGAAGCAATATCAACATAGGATTGTGTGGTG
AGGAATACATCCACACAGACCTGATACTCAGCAAATTCTAGTGCCATTGTCTTGAGGGTGTTGT
CAACAGGCTGCAAAAGTTTATGGGCTTCCTTGTCACCAGTTGTAATGTTTGCTCTACCTTCAGC
TTCCCTAGCTGATAAAGAACCAATCCCAAGTGATGGCAGCACTGATTGGAAAACCAGAAGTTTT
CCGCCGGTAGATTTCATCGCCAGGAAGCCAGCCTTCATAGCTGCTCCAAAAGCAGAATCAGCAA
CCCTATTATTCTCAAACATGCTTGGGATACTTTCTAGCAACTGCTCCAGATTGTCCCGGCACTC
AGAAACTGGGAGAATAAGATCAGTCTGAAGAGGTGTATATACATCTTGAACATCAGGAACGATG
AGCATCAAAGGCTGCTGCTGAGCACGTTTAAGACTGTAGAAGTGAATAGCAGAATCAAATGTTG
CAATTCCAACCATTGTCCGAGGACCTTC
						
					

						Genomic sequence
						
							CCGGCCACCTGTAGTTTGAGGCACAACGGATATAGAAGCAATATCAACATAGGATTGTGTGGTG
AGGAATACATCCACACAGACCTGAAAGAGGGGAGAAAATAAAACATCATATAACAGCAACATGG
CAACTCTTAACCCAGAAAAACAACTCAAATGATGAACATAGCATGCCTGATACTCAGCAAATTC
TAGTGCCATTGTCTTGAGGGTGTTGTCAACAGGCTGCAAAAGTTTATGGGCTTCCTATGAATCA
CACAAGGTTATTAGTATTTTAACTGGGTATTCTTGATAAAAGGAACATGAGCTCCTGATGAAAC
AAATATATGGAGTTAGATCGTATTTACAATGTGCCATTGTTAGTAAGACAAAATAAGTATATGC
AAGTATGCAACAATGCATACCTTGTCACCAGTTGTAATGTTTGCTCTACCTTCAGCTTCCCTAG
CTGATAAAGAACCAATCCCAAGTGATGGCAGCACTGCCAAGTGCCAACAGTGCACATTGCCACA
TTATTAACACAAGAGCATCGAAATTTAAGACTTAAAAAAAAATCTCACAGAAATATGTACGGCA
AATTAGCAGCAATTGAAACAAATCCTTTATTAAGATAAAAAACAAACATGAGTCCACTTGCCAG
ACTTAGAGCTAGTTTGGGAACACCAATTTATCAAGAGATTTCTATTTTCCCATGGGAAAATGAA
CTAATTTCCCTTGGGAAAATGAAAATCCCTTGGAAAATTGGGGTTCCCAAACTAGCCCTTAAAG
TAAAACTGTCAAATATCTTACGAAGACCAACTATAAATTTATGTGGCAGGTGTATAGCGCTAGG
TCATTTGATATAGCACTGCCGTTCCAATCTGGTACCAATAACAGGCAAAACTTCCTGAAGTAGA
ATGCAAATATACTCACTACGAAGACCAAACTAACAAATTGAAAATATAGCTCTCCAAATAAGCC
AGCATGCATTAGGAAAAAAAGCGCCCAAGTAAACTAAGAAACCACTTAACAGAGTCAGCATAAA
TATGCATCTTATCTCTGATAAGTTAACAAGCATACCTGATTGGAAAACCAGAAGTTTTCCGCCG
GTAGATTTCATCGCCAGGAAGCCAGCCTACAGAACAAAACAATAAGCACAAAGTTATCCGATCA
ACAATGAGAATGGAACTCTGGAAAGGGAATACTGAATAAAAAATGATGAATTTGATCTGTAGCC
CATCCAGACCTAACACCAAAAGAAAATAGAACCAGCACCCATAAAACATAGACCAAGTACCTTC
ATAGCTGCTCCAAAAGCAGAATCAGCAACCCTATTATTCTCAAACATGCTTGGGATACTTTCTA
GCAACTGCTCCAGATTGTCCCGGCACTAAAAACATGAAGTAAACATAAGAATAATTCAAAAAAT
AATTTCTCTCAAATCTTGAAGATGACATGAAATAAAAGTTAATGTCAAATTTCAGTTTAAATAC
AAACCTCAGAAACTGGGAGAATAAGATCAGTCTGAAGAGGTGTATATACATCTTGAACATCAGG
AACGATGAGCATCAAAGGCTGCAAGGGAAAAAGGTTGCATAGACAATTCATATCTCTCTAAAAT
GAGATTCATTAAGAAACAAACTGTAGAGAGAGAGAGAGATGGAATAGAAGACAAGAAAATTTTA
TATGTTATTTCCGCATACATAAATAATTTATTATAGTCTCAACCAATAAAAAATCCATATGACT
CTATTCTAAACTTAACTATGTCTAACCAGAGAAACAGAGTTGCTGACAAATTCAGAAGTTTCAC
TCCGACGAGCAAAAAGGAAAACTGAGACAAACTACCATTCCCACTGTAAATTTCAAAATACCCA
TAGTGATATGTCAGAAAGAAAAGGTCAGGATGCAGTTATTGTGCTCTGCTGCACTCCGCAGCAG
AATCTCCTTGTTAGGGAATAACTTCCCAATGACAATTGATCTTGTGAATCCAAAAAGTATGGTT
CTACAGGAAAAGCTACACAACACAAAACCAAATTGGTAACACTAAGTCATGCTGAGGCCAAGTT
TACAGAGAGGCAAAGTTACAATACAACATTTGGTGTGCCTTCAAATCACTGCTGACAAGACTCA
AGTGTGCAATACCTGCTGCTGAGCACGTTTAAGACTGTAGAAGTGAATAGCAGAATCAAATGTT
GCAATTCCAACCATTGTCCGAGGACCTTC
						
					

			
		

Sequences
Splice junction sequence	AGACTCAAGTGTGCAATACCTGCTGCTGAGCACGTTTAAGACTGTAGAAGTGAATAGCAGAATC AAATGTTGCAATTCCAACCATTGTCCGAGGACCTTCccggccacctgtagtttgaggcacaacg gatatagaagcaatatcaacataggattgtgtggtgaggaatacatccacacagacctgaaaga ggggagaa
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: 540 Transcript exons: 128171252-128171335,128171426-128171497,128171656-128171 732,128172311-128172365,128172528-128172620,128172728-12 8172805,128173376-128173456 CCGGCCACCTGTAGTTTGAGGCACAACGGATATAGAAGCAATATCAACATAGGATTGTGTGGTG AGGAATACATCCACACAGACCTGATACTCAGCAAATTCTAGTGCCATTGTCTTGAGGGTGTTGT CAACAGGCTGCAAAAGTTTATGGGCTTCCTTGTCACCAGTTGTAATGTTTGCTCTACCTTCAGC TTCCCTAGCTGATAAAGAACCAATCCCAAGTGATGGCAGCACTGATTGGAAAACCAGAAGTTTT CCGCCGGTAGATTTCATCGCCAGGAAGCCAGCCTTCATAGCTGCTCCAAAAGCAGAATCAGCAA CCCTATTATTCTCAAACATGCTTGGGATACTTTCTAGCAACTGCTCCAGATTGTCCCGGCACTC AGAAACTGGGAGAATAAGATCAGTCTGAAGAGGTGTATATACATCTTGAACATCAGGAACGATG AGCATCAAAGGCTGCTGCTGAGCACGTTTAAGACTGTAGAAGTGAATAGCAGAATCAAATGTTG CAATTCCAACCATTGTCCGAGGACCTTC
Genomic sequence	CCGGCCACCTGTAGTTTGAGGCACAACGGATATAGAAGCAATATCAACATAGGATTGTGTGGTG AGGAATACATCCACACAGACCTGAAAGAGGGGAGAAAATAAAACATCATATAACAGCAACATGG CAACTCTTAACCCAGAAAAACAACTCAAATGATGAACATAGCATGCCTGATACTCAGCAAATTC TAGTGCCATTGTCTTGAGGGTGTTGTCAACAGGCTGCAAAAGTTTATGGGCTTCCTATGAATCA CACAAGGTTATTAGTATTTTAACTGGGTATTCTTGATAAAAGGAACATGAGCTCCTGATGAAAC AAATATATGGAGTTAGATCGTATTTACAATGTGCCATTGTTAGTAAGACAAAATAAGTATATGC AAGTATGCAACAATGCATACCTTGTCACCAGTTGTAATGTTTGCTCTACCTTCAGCTTCCCTAG CTGATAAAGAACCAATCCCAAGTGATGGCAGCACTGCCAAGTGCCAACAGTGCACATTGCCACA TTATTAACACAAGAGCATCGAAATTTAAGACTTAAAAAAAAATCTCACAGAAATATGTACGGCA AATTAGCAGCAATTGAAACAAATCCTTTATTAAGATAAAAAACAAACATGAGTCCACTTGCCAG ACTTAGAGCTAGTTTGGGAACACCAATTTATCAAGAGATTTCTATTTTCCCATGGGAAAATGAA CTAATTTCCCTTGGGAAAATGAAAATCCCTTGGAAAATTGGGGTTCCCAAACTAGCCCTTAAAG TAAAACTGTCAAATATCTTACGAAGACCAACTATAAATTTATGTGGCAGGTGTATAGCGCTAGG TCATTTGATATAGCACTGCCGTTCCAATCTGGTACCAATAACAGGCAAAACTTCCTGAAGTAGA ATGCAAATATACTCACTACGAAGACCAAACTAACAAATTGAAAATATAGCTCTCCAAATAAGCC AGCATGCATTAGGAAAAAAAGCGCCCAAGTAAACTAAGAAACCACTTAACAGAGTCAGCATAAA TATGCATCTTATCTCTGATAAGTTAACAAGCATACCTGATTGGAAAACCAGAAGTTTTCCGCCG GTAGATTTCATCGCCAGGAAGCCAGCCTACAGAACAAAACAATAAGCACAAAGTTATCCGATCA ACAATGAGAATGGAACTCTGGAAAGGGAATACTGAATAAAAAATGATGAATTTGATCTGTAGCC CATCCAGACCTAACACCAAAAGAAAATAGAACCAGCACCCATAAAACATAGACCAAGTACCTTC ATAGCTGCTCCAAAAGCAGAATCAGCAACCCTATTATTCTCAAACATGCTTGGGATACTTTCTA GCAACTGCTCCAGATTGTCCCGGCACTAAAAACATGAAGTAAACATAAGAATAATTCAAAAAAT AATTTCTCTCAAATCTTGAAGATGACATGAAATAAAAGTTAATGTCAAATTTCAGTTTAAATAC AAACCTCAGAAACTGGGAGAATAAGATCAGTCTGAAGAGGTGTATATACATCTTGAACATCAGG AACGATGAGCATCAAAGGCTGCAAGGGAAAAAGGTTGCATAGACAATTCATATCTCTCTAAAAT GAGATTCATTAAGAAACAAACTGTAGAGAGAGAGAGAGATGGAATAGAAGACAAGAAAATTTTA TATGTTATTTCCGCATACATAAATAATTTATTATAGTCTCAACCAATAAAAAATCCATATGACT CTATTCTAAACTTAACTATGTCTAACCAGAGAAACAGAGTTGCTGACAAATTCAGAAGTTTCAC TCCGACGAGCAAAAAGGAAAACTGAGACAAACTACCATTCCCACTGTAAATTTCAAAATACCCA TAGTGATATGTCAGAAAGAAAAGGTCAGGATGCAGTTATTGTGCTCTGCTGCACTCCGCAGCAG AATCTCCTTGTTAGGGAATAACTTCCCAATGACAATTGATCTTGTGAATCCAAAAAGTATGGTT CTACAGGAAAAGCTACACAACACAAAACCAAATTGGTAACACTAAGTCATGCTGAGGCCAAGTT TACAGAGAGGCAAAGTTACAATACAACATTTGGTGTGCCTTCAAATCACTGCTGACAAGACTCA AGTGTGCAATACCTGCTGCTGAGCACGTTTAAGACTGTAGAAGTGAATAGCAGAATCAAATGTT GCAATTCCAACCATTGTCCGAGGACCTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.060008689

Conservation Information
Conserved circRNAs	NA
PMCS	0.060008689

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							128173443-128171254(-)
128171327-128172801(-)
						
						Potential amino acid sequence
						
							MVGIATFDSAIHFYSLKRAQQQPLMLIVPDVQDVYTPLQTDLILPVSECRDNLEQLLESIPSMF
ENNRVADSAFGAAMKAGFLAMKSTGGKLLVFQSVLPSLGIGSLSAREAEGRANITTGDKEAHKL
LQPVDNTLKTMALEFAEYQVCVDVFLTTQSYVDIASISVVPQTTGGREGPRTMVGIATFDSAIH
FYSLKRAQQQPLMLIVPDVQDVYTPLQTDLILPVSECRDNLEQLLESIPSMFENNRVADSAFGA
AMKAGFLAMKSTGGKLLVFQSVLPSLGIGSLSAREAEGRANITTGDKEAHKLLQPVDNTLKTMA
LEFAEYQVCVDVFLTTQSYVDIASISVVPQTTGGREGPRTMVGIATFDSAIHFYSLKRAQQQPL
MLIVPDVQDVYTPLQTDLILPVSECRDNLEQLLESIPSMFENNRVADSAFGAAMKAGFLAMKST
GGKLLVFQSVLPSLGIGSLSAREAEGRANITTGDKEAHKLLQPVDNTLKTMALEFAEYQVCVDV
FLTTQSYVDIASISVVPQTTGGREGPRTMVGIATFDSAIHFYSLKRAQQQPLMLIVPDVQDVYT
PLQTDLILPVSECRDNLEQLLESIPSMFENNRVADSAFGAAMKAGFLAMKSTGGKLLVFQSVLP
SLGIGSLSAREAEGRANITTGDKEAHKLLQPVDNTLKTMALEFAEYQVCVDVFLTTQSYVDIAS
ISVVPQTTGGR(-)
MYSSPHNPMLILLLYPLCLKLQVAGKVLGQWLELQHLILLFTSTVLNVLSSSL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	128173443-128171254(-) 128171327-128172801(-)
Potential amino acid sequence	MVGIATFDSAIHFYSLKRAQQQPLMLIVPDVQDVYTPLQTDLILPVSECRDNLEQLLESIPSMF ENNRVADSAFGAAMKAGFLAMKSTGGKLLVFQSVLPSLGIGSLSAREAEGRANITTGDKEAHKL LQPVDNTLKTMALEFAEYQVCVDVFLTTQSYVDIASISVVPQTTGGREGPRTMVGIATFDSAIH FYSLKRAQQQPLMLIVPDVQDVYTPLQTDLILPVSECRDNLEQLLESIPSMFENNRVADSAFGA AMKAGFLAMKSTGGKLLVFQSVLPSLGIGSLSAREAEGRANITTGDKEAHKLLQPVDNTLKTMA LEFAEYQVCVDVFLTTQSYVDIASISVVPQTTGGREGPRTMVGIATFDSAIHFYSLKRAQQQPL MLIVPDVQDVYTPLQTDLILPVSECRDNLEQLLESIPSMFENNRVADSAFGAAMKAGFLAMKST GGKLLVFQSVLPSLGIGSLSAREAEGRANITTGDKEAHKLLQPVDNTLKTMALEFAEYQVCVDV FLTTQSYVDIASISVVPQTTGGREGPRTMVGIATFDSAIHFYSLKRAQQQPLMLIVPDVQDVYT PLQTDLILPVSECRDNLEQLLESIPSMFENNRVADSAFGAAMKAGFLAMKSTGGKLLVFQSVLP SLGIGSLSAREAEGRANITTGDKEAHKLLQPVDNTLKTMALEFAEYQVCVDVFLTTQSYVDIAS ISVVPQTTGGR(-) MYSSPHNPMLILLLYPLCLKLQVAGKVLGQWLELQHLILLFTSTVLNVLSSSL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Zm00001d004667_circ_g.3

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