RetrogeneDB - Retrocopy retro_eeur

						
>retro_eeur_363
AAGGTACCCAAAACCCCCGGGTACAGTTCACAAGGTACAGACAATTAGAGTGATTCACACGACCCTGTGACAGAGTGATG

ATGGTGGCTTCAGTGAAGAGTGGGAAGCCCAGAGGGATAGCCACCTGGGGCCTCAGCGTTCCACCTTGGAGTCACAAGCT

GCTGTCCAGGAACTTTCCAGCAGCATCCTTGCCAATAAGGACCAGAGGAAAGGGAAGTAAAACCTGGATTAGGATATTTC

ATTTTCTACAGTGTTCTGGTTGGTAAAGCTTCTGCAATGGCCAGTGGTGACTGGAACACAACCATTGCCTGTTTTGTAGC

CATATTAATTGGTTTGTGCCTTACATTATCACTCCTCACCACTTTCAAGAAAGCATAGCCGGCTCTTCCAATCCCTATCG

CCTTTGGGCTTAATTTCTACTTTGCCACAGATTATCTTGTACAGCCCTTTATGGACCTATTAGAATTCCATCAATAT

ORF - retro_eeur_363 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	82.1 %
Parental protein coverage:	51.47 %
Number of stop codons detected:	2
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalKASKTPRYSSQGTDN--DSRDPVTE-SDDGGFSEEWEAQRDSRLGPQRSTSESRAAVQELSSSILASED-
		K..KTP.YSSQGTDN..DS.DPVTE..D.G.FSEEWEAQRDS.LGPQRST.ES.AAVQELSSSILA..D.
RetrocopyKVPKTPGYSSQGTDN*SDSHDPVTE>DDGG-FSEEWEAQRDSHLGPQRSTLESQAAVQELSSSILANKD<
ParentalPEERGVKLGLGDFIFYSVLVGKASAMASGDWNTTIACFVAILIGLCLTLLLLAIFKKALPALPISITFGL
		PEER.VK.GLG.FIFYSVLVGKASAMASGDWNTTIACFVAILIGLCLTL.LL..FKKA.PALPI.I.FGL
RetrocopyPEEREVKPGLGYFIFYSVLVGKASAMASGDWNTTIACFVAILIGLCLTLSLLTTFKKA*PALPIPIAFGL
ParentalIFYFATDYLVQPFMDQLAFHQF
		.FYFATDYLVQPFMD.L.FHQ.
RetrocopyNFYFATDYLVQPFMDLLEFHQY

							

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

						

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0 .00 RPM	20 .30 RPM
SRP017611_kidney	0 .00 RPM	46 .51 RPM
SRP017611_liver	0 .16 RPM	20 .58 RPM

ChIP-Seq - click to see more details

Erinaceus europaeus was not studied using ChIP-Seq data.

EST - click to see more details

Erinaceus europaeus was not studied using EST data.

TSS - click to see more details

Erinaceus europaeus was not studied using FANTOM5 data.

Lab - click to see more details

retro_eeur_363 was not experimentally validated.

Retrocopy orthology:

Erinaceus europaeus 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
Erinaceus europaeus	ENSEEUG00000007027	1 retrocopy	retro_eeur_363 ,

	RetrogeneDB ID:	retro_eeur_363
Retrocopy location	Organism:	*Hedgehog (Erinaceus europaeus)*
	Coordinates:	scaffold_269964:4563..5040(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	PSEN1
	Ensembl ID:	ENSEEUG00000007027
	Aliases:	None
	Description:	presenilin 1 [Source:HGNC Symbol;Acc:9508]

Parental	KASKTPRYSSQGTDN--DSRDPVTE-SDDGGFSEEWEAQRDSRLGPQRSTSESRAAVQELSSSILASED-
	K..KTP.YSSQGTDN..DS.DPVTE..D.G.FSEEWEAQRDS.LGPQRST.ES.AAVQELSSSILA..D.
Retrocopy	KVPKTPGYSSQGTDN*SDSHDPVTE>DDGG-FSEEWEAQRDSHLGPQRSTLESQAAVQELSSSILANKD<

Parental	PEERGVKLGLGDFIFYSVLVGKASAMASGDWNTTIACFVAILIGLCLTLLLLAIFKKALPALPISITFGL
	PEER.VK.GLG.FIFYSVLVGKASAMASGDWNTTIACFVAILIGLCLTL.LL..FKKA.PALPI.I.FGL
Retrocopy	PEEREVKPGLGYFIFYSVLVGKASAMASGDWNTTIACFVAILIGLCLTLSLLTTFKKA*PALPIPIAFGL

Parental	IFYFATDYLVQPFMDQLAFHQF
	.FYFATDYLVQPFMD.L.FHQ.
Retrocopy	NFYFATDYLVQPFMDLLEFHQY

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

RetrogeneDB ID:

retro_eeur_363