Plant Circular RNA Database

Detail information of Gh_D04G0310_circ_g.1

			
						 General Information
					
						CircRNA Name
						Gh_D04G0310_circ_g.1
					
						ID in PlantcircBase
						ghi_circ_002128
					
						Alias
						D04:4702511|4703638
					
						Organism
						
							Gossypium hirsutum						
					
						Position
						
							chrD04: 4702511-4703638  JBrowse»						
					
						Reference genome
						
							v1.1						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Gh_D04G0310						
					
						Parent gene annotation
						
							SIMILAR TO: AT2G30800, helicase in vascular tissue and tapetum
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						4
					
						Tissues
						ovule
					
						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
						Gh_D04G0310:1

General Information
CircRNA Name	Gh_D04G0310_circ_g.1
ID in PlantcircBase	ghi_circ_002128
Alias	D04:4702511\|4703638
Organism	Gossypium hirsutum
Position	chrD04: 4702511-4703638 JBrowse»
Reference genome	v1.1
Type	e-circRNA
Identification method	CIRI
Parent gene	Gh_D04G0310
Parent gene annotation	SIMILAR TO: AT2G30800, helicase in vascular tissue and tapetum
Parent gene strand	-
Alternative splicing	NA
Support reads	4
Tissues	ovule
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	Gh_D04G0310:1

			
						 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  
						
							GAAGGACTCTAAGTGCATTATGTACAGTTTCAGAAACAGGAGGGTCCAATGTCTTTCGCAAGAA
ATCCTCTACTTTGCAAGCTGGGTCAAGCAATTTCACcttgaacaagattgctgccaataatcgt
tctctcaagcagtaaatttgagcaacatcaagggctgttgatctgaatgatagccagcgatcaa
caaccacc

						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
						
							CTTGAACAAGATTGCTGCCAATAATCGTTCTCTCAAGCAGTAAATTTGAGCAACATCAAGGGCT
GTTGATCTGAATGATAGCCAGCGATCAACAACCACCATAACAGAATTATCGGGAGAGGACATGA
CCTTATCTTCTTTTCCACCTGACTTACTAACAGCCAACTTTTCATCTCCATCAGTGTTGCATGC
ATCACCATCACCATCATCACTTCCATCATCATCATCACCATCACCATCAGCCCCATCATCATCT
TCATCTTCATCATAAACAATGCCTTTTATAGGAGCCACTGCAATCTCTGTTGCAAGAAATAACA
ATGGAAATGGCCCAACAACAGTACAGTTCCTTATGAACATACCCCCATCCCCACGTGTTATTTC
ATCATACATAATCAAGGGGCAATCTTCGGGTTTCTTGGGTACTAACTTTGAATTAACAGAGCGA
GTGTGTAACCGAACTTTACTGCCATTGGCAGCCTCTATAATTAATCGTTTACCCTGTTTTACAG
GGAGTATCCTCCCCACCATTGGATACAAACCAGCCACAAGGACTGCATGGAGTATTCCAGGGTG
ATTTGCATTTAGACTACAACTTGAGACATCATCTGGAATAAACCCATGCCGTATTAGTTCACCC
TGGAGCTGCTTACGCATGCCAAACAGCAAGTTCATGGTGCTTGATGAGACAAAGTATTGTGAAC
AAAAACGTCGCTCTAGACCCTTTCTTTTAGCATTCTTCCAGCACTCAAACGCAGCTATGAGTGC
CAGCTGATCACTTTGCCCACCATACAGAGACGCAAGCTCATGCCTGGCAGCGGCAGCCTTCTGC
TTTTCATTTGGTCGCATGGGAAGGACAAATGGATCCTTGAAGTCTGATGCACATGCTAGTGTCA
ATGCCGGATCAAGGCAATTCATCAATATGGCAAAGAAAAGCATCCTGCATGTCAATGGATGAAC
AGGAAGATAACCAAGCTTCTCTCCAAGTTCTGTCAGTTCCTCATCTTGCGTGAAAGCCCCAATA
TCTTGAAGGACTCTAAGTGCATTATGTACAGTTTCAGAAACAGGAGGGTCCAATGTCTTTCGCA
AGAAATCCTCTACTTTGCAAGCTGGGTCAAGCAATTTCAC

Sequences
Splice junction sequence	GAAGGACTCTAAGTGCATTATGTACAGTTTCAGAAACAGGAGGGTCCAATGTCTTTCGCAAGAA ATCCTCTACTTTGCAAGCTGGGTCAAGCAATTTCACcttgaacaagattgctgccaataatcgt tctctcaagcagtaaatttgagcaacatcaagggctgttgatctgaatgatagccagcgatcaa caaccacc
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	CTTGAACAAGATTGCTGCCAATAATCGTTCTCTCAAGCAGTAAATTTGAGCAACATCAAGGGCT GTTGATCTGAATGATAGCCAGCGATCAACAACCACCATAACAGAATTATCGGGAGAGGACATGA CCTTATCTTCTTTTCCACCTGACTTACTAACAGCCAACTTTTCATCTCCATCAGTGTTGCATGC ATCACCATCACCATCATCACTTCCATCATCATCATCACCATCACCATCAGCCCCATCATCATCT TCATCTTCATCATAAACAATGCCTTTTATAGGAGCCACTGCAATCTCTGTTGCAAGAAATAACA ATGGAAATGGCCCAACAACAGTACAGTTCCTTATGAACATACCCCCATCCCCACGTGTTATTTC ATCATACATAATCAAGGGGCAATCTTCGGGTTTCTTGGGTACTAACTTTGAATTAACAGAGCGA GTGTGTAACCGAACTTTACTGCCATTGGCAGCCTCTATAATTAATCGTTTACCCTGTTTTACAG GGAGTATCCTCCCCACCATTGGATACAAACCAGCCACAAGGACTGCATGGAGTATTCCAGGGTG ATTTGCATTTAGACTACAACTTGAGACATCATCTGGAATAAACCCATGCCGTATTAGTTCACCC TGGAGCTGCTTACGCATGCCAAACAGCAAGTTCATGGTGCTTGATGAGACAAAGTATTGTGAAC AAAAACGTCGCTCTAGACCCTTTCTTTTAGCATTCTTCCAGCACTCAAACGCAGCTATGAGTGC CAGCTGATCACTTTGCCCACCATACAGAGACGCAAGCTCATGCCTGGCAGCGGCAGCCTTCTGC TTTTCATTTGGTCGCATGGGAAGGACAAATGGATCCTTGAAGTCTGATGCACATGCTAGTGTCA ATGCCGGATCAAGGCAATTCATCAATATGGCAAAGAAAAGCATCCTGCATGTCAATGGATGAAC AGGAAGATAACCAAGCTTCTCTCCAAGTTCTGTCAGTTCCTCATCTTGCGTGAAAGCCCCAATA TCTTGAAGGACTCTAAGTGCATTATGTACAGTTTCAGAAACAGGAGGGTCCAATGTCTTTCGCA AGAAATCCTCTACTTTGCAAGCTGGGTCAAGCAATTTCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							gra_circ_001303* 						
					
						PMCS

Conservation Information
Conserved circRNAs	gra_circ_001303*
PMCS

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							4703451-4702513(-)
4703466-4702531(+)
						
					

						Potential amino acid sequence
						
							MLFFAILMNCLDPALTLACASDFKDPFVLPMRPNEKQKAAAARHELASLYGGQSDQLALIAAFE
CWKNAKRKGLERRFCSQYFVSSSTMNLLFGMRKQLQGELIRHGFIPDDVSSCSLNANHPGILHA
VLVAGLYPMVGRILPVKQGKRLIIEAANGSKVRLHTRSVNSKLVPKKPEDCPLIMYDEITRGDG
GMFIRNCTVVGPFPLLFLATEIAVAPIKGIVYDEDEDDDGADGDGDDDDGSDDGDGDACNTDGD
EKLAVSKSGGKEDKVMSSPDNSVMVVVDRWLSFRSTALDVAQIYCLRERLLAAILFKVKLLDPA
CKVEDFLRKTLDPPVSETVHNALRVLQDIGAFTQDEELTELGEKLGYLPVHPLTCRMLFFAILM
NCLDPALTLACASDFKDPFVLPMRPNEKQKAAAARHELASLYGGQSDQLALIAAFECWKNAKRK
GLERRFCSQYFVSSSTMNLLFGMRKQLQGELIRHGFIPDDVSSCSLNANHPGILHAVLVAGLYP
MVGRILPVKQGKRLIIEAANGSKVRLHTRSVNSKLVPKKPEDCPLIMYDEITRGDGGMFIRNCT
VVGPFPLLFLATEIAVAPIKGIVYDEDEDDDGADGDGDDDDGSDDGDGDACNTDGDEKLAVSKS
GGKEDKVMSSPDNSVMVVVDRWLSFRSTALDVAQIYCLRERLLAAILFKVKLLDPACKVEDFLR
KTLDPPVSETVHNALRVLQDIGAFTQDEELTELGEKLGYLPVHPLTCRMLFFAILMNCLDPALT
LACASDFKDPFVLPMRPNEKQKAAAARHELASLYGGQSDQLALIAAFECWKNAKRKGLERRFCS
QYFVSSSTMNLLFGMRKQLQGELIRHGFIPDDVSSCSLNANHPGILHAVLVAGLYPMVGRILPV
KQGKRLIIEAANGSKVRLHTRSVNSKLVPKKPEDCPLIMYDEITRGDGGMFIRNCTVVGPFPLL
FLATEIAVAPIKGIVYDEDEDDDGADGDGDDDDGSDDGDGDACNTDGDEKLAVSKSGGKEDKVM
SSPDNSVMVVVDRWLSFRSTALDVAQIYCLRERLLAAILFKVKLLDPACKVEDFLRKTLDPPVS
ETVHNALRVLQDIGAFTQDEELTELGEKLGYLPVHPLTCRMLFFAILMNCLDPALTLACASDFK
DPFVLPMRPNEKQKAAAARHELASLYGGQSDQLALIAAFECWKNAKRKGLERRFCSQYFVSSST
MNLLFGMRKQLQGELIRHGFIPDDVSSCSLNANHPGILHAVLVAGLYPMVGRILPVKQGKRLII
EAANGSKVRLHTRSVNSKLVPKKPEDCPLIMYDEITRGDGGMFIRNCTVVGPFPLLFLATEIAV
APIKGIVYDEDEDDDGADGDGDDDDGSDDGDGDACNTDGDEKLAVSKSGGKEDKVMSSPDNSVM
VVVDRWLSFRSTALDVAQIYCLRERLLAAILFK(-)
MNRKITKLLSKFCQFLILRESPNILKDSKCIMYSFRNRRVQCLSQEILYFASWVKQFHLEQDCC
Q*(+)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	4703451-4702513(-) 4703466-4702531(+)
Potential amino acid sequence	MLFFAILMNCLDPALTLACASDFKDPFVLPMRPNEKQKAAAARHELASLYGGQSDQLALIAAFE CWKNAKRKGLERRFCSQYFVSSSTMNLLFGMRKQLQGELIRHGFIPDDVSSCSLNANHPGILHA VLVAGLYPMVGRILPVKQGKRLIIEAANGSKVRLHTRSVNSKLVPKKPEDCPLIMYDEITRGDG GMFIRNCTVVGPFPLLFLATEIAVAPIKGIVYDEDEDDDGADGDGDDDDGSDDGDGDACNTDGD EKLAVSKSGGKEDKVMSSPDNSVMVVVDRWLSFRSTALDVAQIYCLRERLLAAILFKVKLLDPA CKVEDFLRKTLDPPVSETVHNALRVLQDIGAFTQDEELTELGEKLGYLPVHPLTCRMLFFAILM NCLDPALTLACASDFKDPFVLPMRPNEKQKAAAARHELASLYGGQSDQLALIAAFECWKNAKRK GLERRFCSQYFVSSSTMNLLFGMRKQLQGELIRHGFIPDDVSSCSLNANHPGILHAVLVAGLYP MVGRILPVKQGKRLIIEAANGSKVRLHTRSVNSKLVPKKPEDCPLIMYDEITRGDGGMFIRNCT VVGPFPLLFLATEIAVAPIKGIVYDEDEDDDGADGDGDDDDGSDDGDGDACNTDGDEKLAVSKS GGKEDKVMSSPDNSVMVVVDRWLSFRSTALDVAQIYCLRERLLAAILFKVKLLDPACKVEDFLR KTLDPPVSETVHNALRVLQDIGAFTQDEELTELGEKLGYLPVHPLTCRMLFFAILMNCLDPALT LACASDFKDPFVLPMRPNEKQKAAAARHELASLYGGQSDQLALIAAFECWKNAKRKGLERRFCS QYFVSSSTMNLLFGMRKQLQGELIRHGFIPDDVSSCSLNANHPGILHAVLVAGLYPMVGRILPV KQGKRLIIEAANGSKVRLHTRSVNSKLVPKKPEDCPLIMYDEITRGDGGMFIRNCTVVGPFPLL FLATEIAVAPIKGIVYDEDEDDDGADGDGDDDDGSDDGDGDACNTDGDEKLAVSKSGGKEDKVM SSPDNSVMVVVDRWLSFRSTALDVAQIYCLRERLLAAILFKVKLLDPACKVEDFLRKTLDPPVS ETVHNALRVLQDIGAFTQDEELTELGEKLGYLPVHPLTCRMLFFAILMNCLDPALTLACASDFK DPFVLPMRPNEKQKAAAARHELASLYGGQSDQLALIAAFECWKNAKRKGLERRFCSQYFVSSST MNLLFGMRKQLQGELIRHGFIPDDVSSCSLNANHPGILHAVLVAGLYPMVGRILPVKQGKRLII EAANGSKVRLHTRSVNSKLVPKKPEDCPLIMYDEITRGDGGMFIRNCTVVGPFPLLFLATEIAV APIKGIVYDEDEDDDGADGDGDDDDGSDDGDGDACNTDGDEKLAVSKSGGKEDKVMSSPDNSVM VVVDRWLSFRSTALDVAQIYCLRERLLAAILFK(-) MNRKITKLLSKFCQFLILRESPNILKDSKCIMYSFRNRRVQCLSQEILYFASWVKQFHLEQDCC Q*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017b

circRNA

Detail information of Gh_D04G0310_circ_g.1

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