RetrogeneDB - Retrocopy retro_brap

	RetrogeneDB ID:	retro_brap_44
Retrocopy location	Organism:	*Chinese cabbage (Brassica rapa)*
	Coordinates:	A04:10380159..10380387(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	None
	Ensembl ID:	Bra030324
	Aliases:	None
	Description:	None

Retrocopy-Parental alignment summary:

						
>retro_brap_44
GGTAGAGGAGCTTATGGCGGAGGTGGAGGAGTGGATAACGTAAGTGGAACTTGTGGATGTGGATATGAAAGTTATGGTGG

TCAAAGATGTGGTTAGCCGTCATGGAAGCGGTGGTGGCAAAGGCAGCGAAGGGAGAAGAACCAGAGGTGGAGATAGATCT

ACACTTATACTCCTCGGTGGCGGTAGAGAAAGTGGCGGTGGAGAAGCTTATGGCGGAGTGGAGTTTAT

ORF - retro_brap_44 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	52.44 %
Parental protein coverage:	64.96 %
Number of stop codons detected:	0
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalGVGSYGGGEGGRAGRGA-VDVDQKL---EEVVSSHGAGGGSYCGSAYVGRNQRR-ERSTIIPSSGGRGSG
		G.G.YGGG.G.....G..VDVD.K......VVS.HG.GG....G....GR..R...RST.I...GGR.SG
RetrocopyGRGAYGGGGGVDNVSGT>VDVDMKVMVVKDVVSRHGSGG----GKGSEGRRTRGGDRSTLILLGGGRESG
ParentalGGEAYGG-GGVY
		GGEAYGG..GVY
RetrocopyGGEAYGG<SGVY

							

							Legend:
							
								*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide

						

RNA-Seq - click to see more details

Brassica rapa was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Brassica rapa was not studied using ChIP-Seq data.

EST - click to see more details

Brassica rapa was not studied using EST data.

TSS - click to see more details

Brassica rapa was not studied using FANTOM5 data.

Lab - click to see more details

retro_brap_44 was not experimentally validated.

Retrocopy orthology:

Brassica rapa does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra030324	1 retrocopy	retro_brap_44 ,

Parental	GVGSYGGGEGGRAGRGA-VDVDQKL---EEVVSSHGAGGGSYCGSAYVGRNQRR-ERSTIIPSSGGRGSG
	G.G.YGGG.G.....G..VDVD.K......VVS.HG.GG....G....GR..R...RST.I...GGR.SG
Retrocopy	GRGAYGGGGGVDNVSGT>VDVDMKVMVVKDVVSRHGSGG----GKGSEGRRTRGGDRSTLILLGGGRESG

Parental	GGEAYGG-GGVY
	GGEAYGG..GVY
Retrocopy	GGEAYGG<SGVY

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_brap_44