Plant Circular RNA Database

Detail information of Zm00001d027392_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d027392_circ_g.3
					
						ID in PlantcircBase
						zma_circ_006356
					
						Alias
						Zm01circ00009, zma_circ_0000020, ZmciR74
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 4245157-4246335  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d027392						
					
						Parent gene annotation
						
							Callose synthase 9
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d027392_circ_g.4 Zm00001d027392_circ_g.5 Zm00001d027392_circ_g.6 Zm00001d027392_circ_g.7 Zm00001d027392_circ_g.8 Zm00001d027392_circ_g.9 Zm00001d027392_circ_g.10 						
					
						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  
						
							GT-AG							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
						Zm00001d027392_T056:6
Zm00001d027392_T012:6
Zm00001d027392_T055:6
Zm00001d027392_T016:6
Zm00001d027392_T042:6
Zm00001d027392_T059:6
Zm00001d027392_T051:6
Zm00001d027392_T007:6
Zm00001d027392_T049:6
Zm00001d027392_T065:6
Zm00001d027392_T002:6
Zm00001d027392_T027:5
Zm00001d027392_T023:6
Zm00001d027392_T062:6
Zm00001d027392_T029:6
Zm00001d027392_T033:6
Zm00001d027392_T064:6
Zm00001d027392_T054:6
Zm00001d027392_T025:6
Zm00001d027392_T038:6
Zm00001d027392_T046:6
Zm00001d027392_T041:6
Zm00001d027392_T011:4
Zm00001d027392_T030:6
Zm00001d027392_T045:6
Zm00001d027392_T036:6
Zm00001d027392_T006:6
Zm00001d027392_T004:6
Zm00001d027392_T034:6
Zm00001d027392_T052:6
Zm00001d027392_T019:6
Zm00001d027392_T060:6
Zm00001d027392_T050:6
Zm00001d027392_T020:6
Zm00001d027392_T015:6
Zm00001d027392_T003:6

General Information
CircRNA Name	Zm00001d027392_circ_g.3
ID in PlantcircBase	zma_circ_006356
Alias	Zm01circ00009, zma_circ_0000020, ZmciR74
Organism	Zea mays
Position	chr1: 4245157-4246335 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d027392
Parent gene annotation	Callose synthase 9
Parent gene strand	+
Alternative splicing	Zm00001d027392_circ_g.4 Zm00001d027392_circ_g.5 Zm00001d027392_circ_g.6 Zm00001d027392_circ_g.7 Zm00001d027392_circ_g.8 Zm00001d027392_circ_g.9 Zm00001d027392_circ_g.10
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	GT-AG 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	Zm00001d027392_T056:6 Zm00001d027392_T012:6 Zm00001d027392_T055:6 Zm00001d027392_T016:6 Zm00001d027392_T042:6 Zm00001d027392_T059:6 Zm00001d027392_T051:6 Zm00001d027392_T007:6 Zm00001d027392_T049:6 Zm00001d027392_T065:6 Zm00001d027392_T002:6 Zm00001d027392_T027:5 Zm00001d027392_T023:6 Zm00001d027392_T062:6 Zm00001d027392_T029:6 Zm00001d027392_T033:6 Zm00001d027392_T064:6 Zm00001d027392_T054:6 Zm00001d027392_T025:6 Zm00001d027392_T038:6 Zm00001d027392_T046:6 Zm00001d027392_T041:6 Zm00001d027392_T011:4 Zm00001d027392_T030:6 Zm00001d027392_T045:6 Zm00001d027392_T036:6 Zm00001d027392_T006:6 Zm00001d027392_T004:6 Zm00001d027392_T034:6 Zm00001d027392_T052:6 Zm00001d027392_T019:6 Zm00001d027392_T060:6 Zm00001d027392_T050:6 Zm00001d027392_T020:6 Zm00001d027392_T015:6 Zm00001d027392_T003:6

			
						 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  
						
							TTCGTTTATGCAGATTTACCTTTTGGACATTCATGTATTCTACACTGTATTGTCTGCTATTTAT
GGATTTCTCCTTGGTGCACGTGATCGCCTGGGAGAGcaagacacttcaagatggcacagagtca
gcaacattcaagatatatgtttttgtaatcagtgcatatgtgggcattaagataattttcagcc
tacttatg

									
								

					

						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: 511
Transcript exons: 4245157-4245334,4245430-4245482,4245565-4245625,4245702-
4245783,4245975-4246024,4246249-4246335
CAAGACACTTCAAGATGGCACAGAGTCAGCAACATTCAAGATATATGTTTTTGTAATCAGTGCA
TATGTGGGCATTAAGATAATTTTCAGCCTACTTATGAGTGTCCCTTGTTGCCATGGTTTGGCTG
AGGCTTGCTATCGCTGGTCTGCTGTACGCCTTGTTAAGTGGATGCATCAGGAGAATAATTATGT
TGGAAGAGGCATGCATGAGAGTCCCCTTGACTATATCAAATACGCCACTTTCTGGATTGCAATT
CTTGGTGCAAAATTTTCATTCACCTATTTTCTTCAGATAAAACCTCTTGTAGAACCAACAAGAA
CTATAATCAATTTCACTGGCCTGCAGTATGCTTGGCATGATTTTTTCTCGAAGAATAATCATAA
TGCTCTTACAATCCTTTCTTTATGGGCTCCAGTGCTGTCAATTTACCTTTTGGACATTCATGTA
TTCTACACTGTATTGTCTGCTATTTATGGATTTCTCCTTGGTGCACGTGATCGCCTGGGAGAG
						
					

						Genomic sequence
						
							CAAGACACTTCAAGATGGCACAGAGTCAGCAACATTCAAGATATATGTTTTTGTAATCAGTGCA
TATGTGGGCATTAAGATAATTTTCAGCCTACTTATGAGTGTCCCTTGTTGCCATGGTTTGGCTG
AGGCTTGCTATCGCTGGTCTGCTGTACGCCTTGTTAAGTGGATGCATCAGGTTTTGTCCTTTAG
CAGATTCTGACTTCTTATCTTATCATTTGAAATCTTTGTATGCGATGTCTTCTGCTAATAATAT
CTGTCATTTATTTGAAGGAGAATAATTATGTTGGAAGAGGCATGCATGAGAGTCCCCTTGACTA
TATCAAGTAACTGGAACTTCGAATCATAATTCTGTCTTCCATCTCACAAATTGGAAGTTCGTAA
TTATTTACTATATTTTCTGTGCAGATACGCCACTTTCTGGATTGCAATTCTTGGTGCAAAATTT
TCATTCACCTATTTTCTTCAGGAAAGCTTAGTTTTTCATTGTCAGCCATTCATAGTTATTGACC
TCTGGACCCTAAAACATGGCTTTTATTTTGCAGATAAAACCTCTTGTAGAACCAACAAGAACTA
TAATCAATTTCACTGGCCTGCAGTATGCTTGGCATGATTTTTTCTCGAAGAGTATGAATACATT
ACTTTTTTCCACAAATGTCACCATTATATTTTTTACTTGTCCACACCCTGTGATTCTATAAATT
TTCATTATTGTGTATTTGGAAATTGTTCCTTTCAGAACTTTGAGAAGTGTCTATCTGTTTCCAA
ATATTTATGATTAAATGTGTGTAACCGAGTCGTTCTTACAATGTTTGCAGATAATCATAATGCT
CTTACAATCCTTTCTTTATGGGCTCCAGTGCTGTCAGTAAGTAACCTTTGGTTGCTTCTAGTTC
TAGCTCTCTTGACTCCTTTATGTGTCAGAATCACAGGCACAATATGCAAACAACTATGACTGTT
GCAAAAAATAATATTAGATAATCTAGATGAAAATGTCCTAAGCTCATAATAAAGTAATGAGTCA
ATTTCTGTCTAGTTTCTCTTGACCACATTTGAAAATTATATTCTTGGATTAAGCATTCGTTTAT
GCAGATTTACCTTTTGGACATTCATGTATTCTACACTGTATTGTCTGCTATTTATGGATTTCTC
CTTGGTGCACGTGATCGCCTGGGAGAG
						
					

			
		

Sequences
Splice junction sequence	TTCGTTTATGCAGATTTACCTTTTGGACATTCATGTATTCTACACTGTATTGTCTGCTATTTAT GGATTTCTCCTTGGTGCACGTGATCGCCTGGGAGAGcaagacacttcaagatggcacagagtca gcaacattcaagatatatgtttttgtaatcagtgcatatgtgggcattaagataattttcagcc tacttatg
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: 511 Transcript exons: 4245157-4245334,4245430-4245482,4245565-4245625,4245702- 4245783,4245975-4246024,4246249-4246335 CAAGACACTTCAAGATGGCACAGAGTCAGCAACATTCAAGATATATGTTTTTGTAATCAGTGCA TATGTGGGCATTAAGATAATTTTCAGCCTACTTATGAGTGTCCCTTGTTGCCATGGTTTGGCTG AGGCTTGCTATCGCTGGTCTGCTGTACGCCTTGTTAAGTGGATGCATCAGGAGAATAATTATGT TGGAAGAGGCATGCATGAGAGTCCCCTTGACTATATCAAATACGCCACTTTCTGGATTGCAATT CTTGGTGCAAAATTTTCATTCACCTATTTTCTTCAGATAAAACCTCTTGTAGAACCAACAAGAA CTATAATCAATTTCACTGGCCTGCAGTATGCTTGGCATGATTTTTTCTCGAAGAATAATCATAA TGCTCTTACAATCCTTTCTTTATGGGCTCCAGTGCTGTCAATTTACCTTTTGGACATTCATGTA TTCTACACTGTATTGTCTGCTATTTATGGATTTCTCCTTGGTGCACGTGATCGCCTGGGAGAG
Genomic sequence	CAAGACACTTCAAGATGGCACAGAGTCAGCAACATTCAAGATATATGTTTTTGTAATCAGTGCA TATGTGGGCATTAAGATAATTTTCAGCCTACTTATGAGTGTCCCTTGTTGCCATGGTTTGGCTG AGGCTTGCTATCGCTGGTCTGCTGTACGCCTTGTTAAGTGGATGCATCAGGTTTTGTCCTTTAG CAGATTCTGACTTCTTATCTTATCATTTGAAATCTTTGTATGCGATGTCTTCTGCTAATAATAT CTGTCATTTATTTGAAGGAGAATAATTATGTTGGAAGAGGCATGCATGAGAGTCCCCTTGACTA TATCAAGTAACTGGAACTTCGAATCATAATTCTGTCTTCCATCTCACAAATTGGAAGTTCGTAA TTATTTACTATATTTTCTGTGCAGATACGCCACTTTCTGGATTGCAATTCTTGGTGCAAAATTT TCATTCACCTATTTTCTTCAGGAAAGCTTAGTTTTTCATTGTCAGCCATTCATAGTTATTGACC TCTGGACCCTAAAACATGGCTTTTATTTTGCAGATAAAACCTCTTGTAGAACCAACAAGAACTA TAATCAATTTCACTGGCCTGCAGTATGCTTGGCATGATTTTTTCTCGAAGAGTATGAATACATT ACTTTTTTCCACAAATGTCACCATTATATTTTTTACTTGTCCACACCCTGTGATTCTATAAATT TTCATTATTGTGTATTTGGAAATTGTTCCTTTCAGAACTTTGAGAAGTGTCTATCTGTTTCCAA ATATTTATGATTAAATGTGTGTAACCGAGTCGTTCTTACAATGTTTGCAGATAATCATAATGCT CTTACAATCCTTTCTTTATGGGCTCCAGTGCTGTCAGTAAGTAACCTTTGGTTGCTTCTAGTTC TAGCTCTCTTGACTCCTTTATGTGTCAGAATCACAGGCACAATATGCAAACAACTATGACTGTT GCAAAAAATAATATTAGATAATCTAGATGAAAATGTCCTAAGCTCATAATAAAGTAATGAGTCA ATTTCTGTCTAGTTTCTCTTGACCACATTTGAAAATTATATTCTTGGATTAAGCATTCGTTTAT GCAGATTTACCTTTTGGACATTCATGTATTCTACACTGTATTGTCTGCTATTTATGGATTTCTC CTTGGTGCACGTGATCGCCTGGGAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.163156618

Conservation Information
Conserved circRNAs	NA
PMCS	0.163156618

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4245255-4245231(+)
4245758-4245231(+)
4245193-4246298(-)
						
						Potential amino acid sequence
						
							MSVPCCHGLAEACYRWSAVRLVKWMHQENNYVGRGMHESPLDYIKYATFWIAILGAKFSFTYFL
QIKPLVEPTRTIINFTGLQYAWHDFFSKNNHNALTILSLWAPVLSIYLLDIHVFYTVLSAIYGF
LLGARDRLGEQDTSRWHRVSNIQDICFCNQCICGH*(+)
MLGMIFSRRIIIMLLQSFLYGLQCCQFTFWTFMYSTLYCLLFMDFSLVHVIAWESKTLQDGTES
ATFKIYVFVISAYVGIKIIFSLLMSVPCCHGLAEACYRWSAVRLVKWMHQENNYVGRGMHESPL
DYIKYATFWIAILGAKFSFTYFLQIKPLVEPTRTIINFTGLQYAWHDFFSKNNHNALTILSLWA
PVLSIYLLDIHVFYTVLSAIYGFLLGARDRLGEQDTSRWHRVSNIQDICFCNQCICGH*(+)
MLLTLCHLEVSCSPRRSRAPRRNP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	4245255-4245231(+) 4245758-4245231(+) 4245193-4246298(-)
Potential amino acid sequence	MSVPCCHGLAEACYRWSAVRLVKWMHQENNYVGRGMHESPLDYIKYATFWIAILGAKFSFTYFL QIKPLVEPTRTIINFTGLQYAWHDFFSKNNHNALTILSLWAPVLSIYLLDIHVFYTVLSAIYGF LLGARDRLGEQDTSRWHRVSNIQDICFCNQCICGH(+) MLGMIFSRRIIIMLLQSFLYGLQCCQFTFWTFMYSTLYCLLFMDFSLVHVIAWESKTLQDGTES ATFKIYVFVISAYVGIKIIFSLLMSVPCCHGLAEACYRWSAVRLVKWMHQENNYVGRGMHESPL DYIKYATFWIAILGAKFSFTYFLQIKPLVEPTRTIINFTGLQYAWHDFFSKNNHNALTILSLWA PVLSIYLLDIHVFYTVLSAIYGFLLGARDRLGEQDTSRWHRVSNIQDICFCNQCICGH(+) MLLTLCHLEVSCSPRRSRAPRRNP*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d027392_circ_g.3

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