Plant Circular RNA Database

Detail information of Zm00001d053316_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d053316_circ_g.2
					
						ID in PlantcircBase
						zma_circ_008272
					
						Alias
						Zm04circ00104, zma_circ_0001621, GRMZM2G147026_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 225861976-225864447  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d053316						
					
						Parent gene annotation
						
							Casein kinase I isoform delta-like; Putative casein kinase famil
y protein  
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d053316_circ_g.1 						
					
						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
						Zm00001d053316_T009:8
Zm00001d053316_T016:5
Zm00001d053316_T003:8
Zm00001d053316_T013:8
Zm00001d053316_T012:8
Zm00001d053316_T011:8
Zm00001d053316_T004:8
Zm00001d053316_T008:8
Zm00001d053316_T015:8
Zm00001d053316_T007:5
Zm00001d053316_T017:8
Zm00001d053316_T006:7
Zm00001d053316_T014:8
Zm00001d053316_T005:8
Zm00001d053316_T001:8
Zm00001d053316_T002:8
Zm00001d053316_T010:8

General Information
CircRNA Name	Zm00001d053316_circ_g.2
ID in PlantcircBase	zma_circ_008272
Alias	Zm04circ00104, zma_circ_0001621, GRMZM2G147026_C1
Organism	Zea mays
Position	chr4: 225861976-225864447 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d053316
Parent gene annotation	Casein kinase I isoform delta-like; Putative casein kinase famil y protein
Parent gene strand	-
Alternative splicing	Zm00001d053316_circ_g.1
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	Zm00001d053316_T009:8 Zm00001d053316_T016:5 Zm00001d053316_T003:8 Zm00001d053316_T013:8 Zm00001d053316_T012:8 Zm00001d053316_T011:8 Zm00001d053316_T004:8 Zm00001d053316_T008:8 Zm00001d053316_T015:8 Zm00001d053316_T007:5 Zm00001d053316_T017:8 Zm00001d053316_T006:7 Zm00001d053316_T014:8 Zm00001d053316_T005:8 Zm00001d053316_T001:8 Zm00001d053316_T002:8 Zm00001d053316_T010:8

			
						 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  
						
							AGCAATGGGTTTTAAAATCATTAGCTCACCTATAAGGTATATGGCGGTTGGTGGCTGAATCACG
ATATCTCTTTGCAAGCCCGAAGTCAATTACATAAACcaatctctcaggatgcagattattggaa
cggctgtttaattgcattctgattgccgggcgttgttctgcttcaagcagacctgaagcattaa
ttgggcgt

									
								

					

						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: 657
Transcript exons: 225861976-225862085,225862310-225862364,225862536-225862
618,225862711-225862837,225862927-225863011,225863947-22
5864010,225864188-225864249,225864377-225864447
CAATCTCTCAGGATGCAGATTATTGGAACGGCTGTTTAATTGCATTCTGATTGCCGGGCGTTGT
TCTGCTTCAAGCAGACCTGAAGCATTAATTGGGCGTGCAACACCAACTTGGTGCTTGTCCACGT
TTGTTGCAACTGGACGGCTGCTTACGCCTGCATCATGAGAGCATCCTTGCTGAACCTTAGCCTT
CTGGGATTGCTTACACTTCAACAAAGTCCAGTCATACACATAATCAAATTGATAGCCTTCGCGC
TCAAACAATTCTCGAAAGACATGCCTCAAGAAACTATAATCGGGACGCTGATCAAATGTCAGAG
AATGGCAGTAGTGGAAATAGGAAGCAAATTCCACAGGATGGGATTTACATAGAGCCTCAATAGG
AGTCGAAAGCTTCTTCTCACTTATTTTGTCATACTTCTGTTTCTTTGTGGCTGCTTTCAAGCCC
TGCCAAGGAAGACTTCCCCTAAGGAAATACAGAAGAACGTATCCGATCGATTCCAAATCATCTC
TGCGGCTTTGCTCAATCCCAAGATGAGTATTACGGCTAGCATAGCGAGCTGTGCCAGTCAAGTT
TTTATTTTCTCTATAAGGTATATGGCGGTTGGTGGCTGAATCACGATATCTCTTTGCAAGCCCG
AAGTCAATTACATAAAC
						
					

						Genomic sequence
						
							CAATCTCTCAGGATGCAGATTATTGGAACGGCTGTTTAATTGCATTCTGATTGCCGGGCGTTGT
TCTGCTTCAAGCAGACCTGAAGCATTAATTGGGCGTGCAACACCAACTGAAAAAGGTTGTTATA
AACATGCCACTGTGAATTGACATCCTATAGAAGTTACAACTAAAGAAGTACATTTTTTGACAAA
AAAAAAACTAACACCACAAAGAAGCATTATGCACGAAAACTTGAAATCCAGAAAGCAAAATGCA
CTGTACAAATAGAGAAAAATGACTACAAACAGCACTAGTTTTATACTACATCACCTAGTTTTAT
ACTACATAGACTACCTTGGTGCTTGTCCACGTTTGTTGCAACTGGACGGCTGCTTACGCCTGCA
TCATGCTGCCACGGCGGGAGAACAATCAGCAAAACCGCTAAAACAATTGGGGAAGATACACTCG
TTTATTTGTTGCATCAAATCCATATTAGAAAGTATCACTTTCTGGAAACCTCCAACATATTTAA
AATGAAATACTGAGGGAAGTTATAACTCCAAAAACAAGCAGTACTTACAGAGCATCCTTGCTGA
ACCTTAGCCTTCTGGGATTGCTTACACTTCAACAAAGTCCAGTCATACACATAATCAAATTGAT
AGCCTAGAGAAGATCAAATAATAAACAAGTTATCAAGCTTTTCATAATTAATAAGATATGATGG
GAGATTGCACACCAGAATTCCAAATGTTTACCTTCGCGCTCAAACAATTCTCGAAAGACATGCC
TCAAGAAACTATAATCGGGACGCTGATCAAATGTCAGAGAATGGCAGTAGTGGAAATAGGAAGC
AAATTCCACAGGATGGGATTTACATAGAGCCTATAATGACAAAAGTCATGAGTACTCTTCCTGT
CAACGATATCAAAGGAGTTAACATTCGTAAATGCAAAGCAAGTTACTCAAACAACCTCAATAGG
AGTCGAAAGCTTCTTCTCACTTATTTTGTCATACTTCTGTTTCTTTGTGGCTGCTTTCAAGCCC
TGCCAAGGAAGACTGGACAGAACAGATAGTTAGTTAGTTACACTTACACCAAGTCCATAAAATG
TTTCATACACAACAAATTACGATCAAAATGTTTCATACACAAGAAATCACAATCAAAGATAGCT
GGCATATTGAGTTATTGACCACTGGTTTTCAGGACAGATTTGAGAAAAATGTACTAGTTGTTTT
GCTTCAGGCATAACCACATAATATATTGGGGGAAAGTGTTTTTGCCCTGTCCAAAATTTCAATT
GTGATTTACTGAGCCATTTGCCATTTGCATGTCCATTATTTGGACGGAGATTAAACGATCTAAA
AAATAAAACACATAAAACCAGATGCAAAATGACCGAATTGCCCTTATCCAAGCTATCCAACCAG
GCCCATCCCAACCGTCTCGATAGCCCAAACTTAGGGAAGACGGCGCACGGGTGCAGACACGAGC
AGCACACAGGCAGGACCCGCGTGGGTCGGTCATTGCCAGTGCGGCGTGTAGGCACTAGCCAGTA
CTCTTATCTGTTTCGTTTCGCACAGGGCAGCCTCGGCGAGCTGATTTCATTTCGCTTTTGTGTG
AGTGTCTTCTAATCTGTTTCGGCAACGTTTTTTCCTGTCTGTGCCCAGACCTGTGTGCTCAAGG
TGAATATTCACTGTGATGGCTGCACAAAGAAGGTGAAGAAGGTCCTTCACAAGATTGATGATAA
GTTGCGGGAGCAAGAAAGATCTTTTTTAAAATGCAAATTGCTTGCTTTTTTCCATTCTTGTGTG
TGCGTCTTACTGCTACTGTGATGCCGCCAGGGTGAGAGGGTCTATTCAGTTCGGTTCAGCTGTG
CTATTTTGTTTTTCTCTGTAACATGGTTTTCATTAATGACTGCTACACATGCAGCATTATTCTA
GGACAATGGTGAAAGAAATAAACTATCGAGATCTTTAGCACAAAATAATACCTTCCCCTAAGGA
AATACAGAAGAACGTATCCGATCGATTCCAAATCATCTCTGCGGCTTTGCTCTGGCAACAAAAC
TTAGTGATAGTGAACCAAAGGAAAAATAAATGGCTATAATTTTGTCCGATAATCTATAGAACCA
GTGCTATTTTAGTGTTATAATAATATACATGTGCACAATACAAGCATTCAAAGTAATGACACAA
GAGATAAATGCAAAATAGAACGGCCATATTACTCACCAATCCCAAGATGAGTATTACGGCTAGC
ATAGCGAGCTGTGCCAGTCAAGTTTTTATTTTCTCTGTAAAAACAATTATGTTAACTGGTCAAA
AAAATAAACAGGTATTACCACAATTGCAAAAATAAGAATAAAATGAAACAAAAACTGATAGTTC
CGGAAGCAATGGGTTTTAAAATCATTAGCTCACCTATAAGGTATATGGCGGTTGGTGGCTGAAT
CACGATATCTCTTTGCAAGCCCGAAGTCAATTACATAAAC
						
					

			
		

Sequences
Splice junction sequence	AGCAATGGGTTTTAAAATCATTAGCTCACCTATAAGGTATATGGCGGTTGGTGGCTGAATCACG ATATCTCTTTGCAAGCCCGAAGTCAATTACATAAACcaatctctcaggatgcagattattggaa cggctgtttaattgcattctgattgccgggcgttgttctgcttcaagcagacctgaagcattaa ttgggcgt
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: 657 Transcript exons: 225861976-225862085,225862310-225862364,225862536-225862 618,225862711-225862837,225862927-225863011,225863947-22 5864010,225864188-225864249,225864377-225864447 CAATCTCTCAGGATGCAGATTATTGGAACGGCTGTTTAATTGCATTCTGATTGCCGGGCGTTGT TCTGCTTCAAGCAGACCTGAAGCATTAATTGGGCGTGCAACACCAACTTGGTGCTTGTCCACGT TTGTTGCAACTGGACGGCTGCTTACGCCTGCATCATGAGAGCATCCTTGCTGAACCTTAGCCTT CTGGGATTGCTTACACTTCAACAAAGTCCAGTCATACACATAATCAAATTGATAGCCTTCGCGC TCAAACAATTCTCGAAAGACATGCCTCAAGAAACTATAATCGGGACGCTGATCAAATGTCAGAG AATGGCAGTAGTGGAAATAGGAAGCAAATTCCACAGGATGGGATTTACATAGAGCCTCAATAGG AGTCGAAAGCTTCTTCTCACTTATTTTGTCATACTTCTGTTTCTTTGTGGCTGCTTTCAAGCCC TGCCAAGGAAGACTTCCCCTAAGGAAATACAGAAGAACGTATCCGATCGATTCCAAATCATCTC TGCGGCTTTGCTCAATCCCAAGATGAGTATTACGGCTAGCATAGCGAGCTGTGCCAGTCAAGTT TTTATTTTCTCTATAAGGTATATGGCGGTTGGTGGCTGAATCACGATATCTCTTTGCAAGCCCG AAGTCAATTACATAAAC
Genomic sequence	CAATCTCTCAGGATGCAGATTATTGGAACGGCTGTTTAATTGCATTCTGATTGCCGGGCGTTGT TCTGCTTCAAGCAGACCTGAAGCATTAATTGGGCGTGCAACACCAACTGAAAAAGGTTGTTATA AACATGCCACTGTGAATTGACATCCTATAGAAGTTACAACTAAAGAAGTACATTTTTTGACAAA AAAAAAACTAACACCACAAAGAAGCATTATGCACGAAAACTTGAAATCCAGAAAGCAAAATGCA CTGTACAAATAGAGAAAAATGACTACAAACAGCACTAGTTTTATACTACATCACCTAGTTTTAT ACTACATAGACTACCTTGGTGCTTGTCCACGTTTGTTGCAACTGGACGGCTGCTTACGCCTGCA TCATGCTGCCACGGCGGGAGAACAATCAGCAAAACCGCTAAAACAATTGGGGAAGATACACTCG TTTATTTGTTGCATCAAATCCATATTAGAAAGTATCACTTTCTGGAAACCTCCAACATATTTAA AATGAAATACTGAGGGAAGTTATAACTCCAAAAACAAGCAGTACTTACAGAGCATCCTTGCTGA ACCTTAGCCTTCTGGGATTGCTTACACTTCAACAAAGTCCAGTCATACACATAATCAAATTGAT AGCCTAGAGAAGATCAAATAATAAACAAGTTATCAAGCTTTTCATAATTAATAAGATATGATGG GAGATTGCACACCAGAATTCCAAATGTTTACCTTCGCGCTCAAACAATTCTCGAAAGACATGCC TCAAGAAACTATAATCGGGACGCTGATCAAATGTCAGAGAATGGCAGTAGTGGAAATAGGAAGC AAATTCCACAGGATGGGATTTACATAGAGCCTATAATGACAAAAGTCATGAGTACTCTTCCTGT CAACGATATCAAAGGAGTTAACATTCGTAAATGCAAAGCAAGTTACTCAAACAACCTCAATAGG AGTCGAAAGCTTCTTCTCACTTATTTTGTCATACTTCTGTTTCTTTGTGGCTGCTTTCAAGCCC TGCCAAGGAAGACTGGACAGAACAGATAGTTAGTTAGTTACACTTACACCAAGTCCATAAAATG TTTCATACACAACAAATTACGATCAAAATGTTTCATACACAAGAAATCACAATCAAAGATAGCT GGCATATTGAGTTATTGACCACTGGTTTTCAGGACAGATTTGAGAAAAATGTACTAGTTGTTTT GCTTCAGGCATAACCACATAATATATTGGGGGAAAGTGTTTTTGCCCTGTCCAAAATTTCAATT GTGATTTACTGAGCCATTTGCCATTTGCATGTCCATTATTTGGACGGAGATTAAACGATCTAAA AAATAAAACACATAAAACCAGATGCAAAATGACCGAATTGCCCTTATCCAAGCTATCCAACCAG GCCCATCCCAACCGTCTCGATAGCCCAAACTTAGGGAAGACGGCGCACGGGTGCAGACACGAGC AGCACACAGGCAGGACCCGCGTGGGTCGGTCATTGCCAGTGCGGCGTGTAGGCACTAGCCAGTA CTCTTATCTGTTTCGTTTCGCACAGGGCAGCCTCGGCGAGCTGATTTCATTTCGCTTTTGTGTG AGTGTCTTCTAATCTGTTTCGGCAACGTTTTTTCCTGTCTGTGCCCAGACCTGTGTGCTCAAGG TGAATATTCACTGTGATGGCTGCACAAAGAAGGTGAAGAAGGTCCTTCACAAGATTGATGATAA GTTGCGGGAGCAAGAAAGATCTTTTTTAAAATGCAAATTGCTTGCTTTTTTCCATTCTTGTGTG TGCGTCTTACTGCTACTGTGATGCCGCCAGGGTGAGAGGGTCTATTCAGTTCGGTTCAGCTGTG CTATTTTGTTTTTCTCTGTAACATGGTTTTCATTAATGACTGCTACACATGCAGCATTATTCTA GGACAATGGTGAAAGAAATAAACTATCGAGATCTTTAGCACAAAATAATACCTTCCCCTAAGGA AATACAGAAGAACGTATCCGATCGATTCCAAATCATCTCTGCGGCTTTGCTCTGGCAACAAAAC TTAGTGATAGTGAACCAAAGGAAAAATAAATGGCTATAATTTTGTCCGATAATCTATAGAACCA GTGCTATTTTAGTGTTATAATAATATACATGTGCACAATACAAGCATTCAAAGTAATGACACAA GAGATAAATGCAAAATAGAACGGCCATATTACTCACCAATCCCAAGATGAGTATTACGGCTAGC ATAGCGAGCTGTGCCAGTCAAGTTTTTATTTTCTCTGTAAAAACAATTATGTTAACTGGTCAAA AAAATAAACAGGTATTACCACAATTGCAAAAATAAGAATAAAATGAAACAAAAACTGATAGTTC CGGAAGCAATGGGTTTTAAAATCATTAGCTCACCTATAAGGTATATGGCGGTTGGTGGCTGAAT CACGATATCTCTTTGCAAGCCCGAAGTCAATTACATAAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.104868254

Conservation Information
Conserved circRNAs	NA
PMCS	0.104868254

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							225862022-225861978(-)
						
						Potential amino acid sequence
						
							MQLNSRSNNLHPERLVYVIDFGLAKRYRDSATNRHIPYRENKNLTGTARYASRNTHLGIEQSRR
DDLESIGYVLLYFLRGSLPWQGLKAATKKQKYDKISEKKLSTPIEALCKSHPVEFASYFHYCHS
LTFDQRPDYSFLRHVFRELFEREGYQFDYVYDWTLLKCKQSQKAKVQQGCSHDAGVSSRPVATN
VDKHQVGVARPINASGLLEAEQRPAIRMQLNSRSNNLHPERLVYVIDFGLAKRYRDSATNRHIP
YRENKNLTGTARYASRNTHLGIEQSRRDDLESIGYVLLYFLRGSLPWQGLKAATKKQKYDKISE
KKLSTPIEALCKSHPVEFASYFHYCHSLTFDQRPDYSFLRHVFRELFEREGYQFDYVYDWTLLK
CKQSQKAKVQQGCSHDAGVSSRPVATNVDKHQVGVARPINASGLLEAEQRPAIRMQLNSRSNNL
HPERLVYVIDFGLAKRYRDSATNRHIPYRENKNLTGTARYASRNTHLGIEQSRRDDLESIGYVL
LYFLRGSLPWQGLKAATKKQKYDKISEKKLSTPIEALCKSHPVEFASYFHYCHSLTFDQRPDYS
FLRHVFRELFEREGYQFDYVYDWTLLKCKQSQKAKVQQGCSHDAGVSSRPVATNVDKHQVGVAR
PINASGLLEAEQRPAIRMQLNSRSNNLHPERL(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	225862022-225861978(-)
Potential amino acid sequence	MQLNSRSNNLHPERLVYVIDFGLAKRYRDSATNRHIPYRENKNLTGTARYASRNTHLGIEQSRR DDLESIGYVLLYFLRGSLPWQGLKAATKKQKYDKISEKKLSTPIEALCKSHPVEFASYFHYCHS LTFDQRPDYSFLRHVFRELFEREGYQFDYVYDWTLLKCKQSQKAKVQQGCSHDAGVSSRPVATN VDKHQVGVARPINASGLLEAEQRPAIRMQLNSRSNNLHPERLVYVIDFGLAKRYRDSATNRHIP YRENKNLTGTARYASRNTHLGIEQSRRDDLESIGYVLLYFLRGSLPWQGLKAATKKQKYDKISE KKLSTPIEALCKSHPVEFASYFHYCHSLTFDQRPDYSFLRHVFRELFEREGYQFDYVYDWTLLK CKQSQKAKVQQGCSHDAGVSSRPVATNVDKHQVGVARPINASGLLEAEQRPAIRMQLNSRSNNL HPERLVYVIDFGLAKRYRDSATNRHIPYRENKNLTGTARYASRNTHLGIEQSRRDDLESIGYVL LYFLRGSLPWQGLKAATKKQKYDKISEKKLSTPIEALCKSHPVEFASYFHYCHSLTFDQRPDYS FLRHVFRELFEREGYQFDYVYDWTLLKCKQSQKAKVQQGCSHDAGVSSRPVATNVDKHQVGVAR PINASGLLEAEQRPAIRMQLNSRSNNLHPERL(-)
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 Zm00001d053316_circ_g.2

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