RetrogeneDB - Retrocopy retro_eeur

						
>retro_eeur_403
TCCCGCGATGGCACCGTGGCTCTCTGCGGGTGGATCCCGACATGTTCAATGGCAGCATTGCCTGGCACAGTGATGCGGGG

CTCCCGGTGTATGCCCACATCCGGCCCAGGGACATGGAGGCCATCCCCAGGTCTAACACCAACCCCGGTAACCGCAAGGT

GAGGGCTCTGGCCTTCAGCAACCAGAATCAGGAGCTGGGAGCCTTATCGCTGGATGGTTTCTTCCACTTGTGGAAAGTCC

AGAACAACTTGACCAGGCAGCTGTCCTTCAGGCTGCCCTACTGCCGAGAGAATGTGTGCCTGACCTACTGCCATGAGCCA

GCCTTGTTCGCAGTGGGCTCCCAGTCCCACATCTCCTTCCTGGATCTGCGCCAGGGTCAGCAAAATATCTGGCCTCTGTG

CTCCAGAGAGGGAGGCACAGGCGTGCGCTCACTGAGCTTCTACCATCATATCCTCACTGTGGGCACAGGCCATGGGAGCC

TACTTTTCTATGACATCCGTGCCCAGAAGTTCCTGGAAGAGAGTGCCAACAGAAGCTCCTTACCTGAACCCAGGAGAAAG

CTCAAGCTCACCTGCGGCAGAGGCTGGCTTAACCATGATGATATGTGGGTGAACTACTTCGGTGGTGTCGCAGAGTTCCC

CAATGCGCTCTATACCCACTGCTACAACTGGCCTGAGATGAAGCTTTTTGTGGCAGGGGGGCCTCTCCCTTCAGGCCTCC

ATGGGCACTATGCAGGCCTCTGGAGC

ORF - retro_eeur_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	61.26 %
Parental protein coverage:	55.63 %
Number of stop codons detected:	0
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalSRDGSMGLW-EVTDDVLTKSDAMHNVSRVPVYAHITHKALKDIPKENTNPDNCKVRALAFNNKNKELGAV
		SRDG...L...V..D....S.A.H.....PVYAHI.......IP..NTNP.N.KVRALAF.N.N.ELGA.
RetrocopySRDGTVALC<RVDPDMFNGSIAWHSDAGLPVYAHIRPRDMEAIPRSNTNPGNRKVRALAFSNQNQELGAL
ParentalSLDGYFHLWKAENTLTKLLSTKLPYCRENVCLAYGSEWSVYAVGSQAHVSFLDPRQPSYNVKSVCSREQG
		SLDG.FHLWK..N.LT..LS..LPYCRENVCL.Y..E....AVGSQ.H.SFLD.RQ...N....CSRE.G
RetrocopySLDGFFHLWKVQNNLTRQLSFRLPYCRENVCLTYCHEPALFAVGSQSHISFLDLRQGQQNIWPLCSREGG
ParentalSGIRSVSFYEHIITVGTGQGSLLFYDIRAQRFLEERLSAYCGSKPRLAGENLKLTTGKGWLNHDETWRNY
		.G.RS.SFY.HI.TVGTG.GSLLFYDIRAQ.FLEE.........PR.....LKLT.G.GWLNHD..W.NY
RetrocopyTGVRSLSFYHHILTVGTGHGSLLFYDIRAQKFLEESANRSSLPEPR---RKLKLTCGRGWLNHDDMWVNY
ParentalFSDIDFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYAGLWS
		F.....FPNA.YTHCY.....KLFVAGGPLPSGLHG.YAGLWS
RetrocopyFGGVAEFPNALYTHCYNWPEMKLFVAGGPLPSGLHGHYAGLWS

							

							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	1 .61 RPM	16 .92 RPM
SRP017611_kidney	0 .00 RPM	23 .63 RPM
SRP017611_liver	0 .00 RPM	13 .34 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_403 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000309	1 retrocopy	retro_amel_73,
Bos taurus	ENSBTAG00000021573	3 retrocopies	retro_btau_1794, retro_btau_1795, retro_btau_1796,
Equus caballus	ENSECAG00000023064	2 retrocopies	retro_ecab_1128, retro_ecab_1129,
Erinaceus europaeus	ENSEEUG00000013279	1 retrocopy	retro_eeur_403 ,
Microcebus murinus	ENSMICG00000005881	1 retrocopy	retro_mmur_14,
Macaca mulatta	ENSMMUG00000017458	1 retrocopy	retro_mmul_202,
Nomascus leucogenys	ENSNLEG00000004996	1 retrocopy	retro_nleu_6,
Otolemur garnettii	ENSOGAG00000015799	1 retrocopy	retro_ogar_237,
Ochotona princeps	ENSOPRG00000001281	2 retrocopies	retro_opri_1178, retro_opri_470,
Pongo abelii	ENSPPYG00000019127	1 retrocopy	retro_pabe_64,
Pteropus vampyrus	ENSPVAG00000008654	1 retrocopy	retro_pvam_16,
Sus scrofa	ENSSSCG00000010986	1 retrocopy	retro_sscr_17,
Ictidomys tridecemlineatus	ENSSTOG00000006904	1 retrocopy	retro_itri_168,
Tarsius syrichta	ENSTSYG00000014394	1 retrocopy	retro_tsyr_1965,
Tursiops truncatus	ENSTTRG00000010591	1 retrocopy	retro_ttru_8,

	RetrogeneDB ID:	retro_eeur_403
Retrocopy location	Organism:	*Hedgehog (Erinaceus europaeus)*
	Coordinates:	scaffold_285983:55..801(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSEEUG00000006361
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	DCAF12
	Ensembl ID:	ENSEEUG00000013279
	Aliases:	None
	Description:	DDB1 and CUL4 associated factor 12 [Source:HGNC Symbol;Acc:19911]

Parental	SRDGSMGLW-EVTDDVLTKSDAMHNVSRVPVYAHITHKALKDIPKENTNPDNCKVRALAFNNKNKELGAV
	SRDG...L...V..D....S.A.H.....PVYAHI.......IP..NTNP.N.KVRALAF.N.N.ELGA.
Retrocopy	SRDGTVALC<RVDPDMFNGSIAWHSDAGLPVYAHIRPRDMEAIPRSNTNPGNRKVRALAFSNQNQELGAL

Parental	SLDGYFHLWKAENTLTKLLSTKLPYCRENVCLAYGSEWSVYAVGSQAHVSFLDPRQPSYNVKSVCSREQG
	SLDG.FHLWK..N.LT..LS..LPYCRENVCL.Y..E....AVGSQ.H.SFLD.RQ...N....CSRE.G
Retrocopy	SLDGFFHLWKVQNNLTRQLSFRLPYCRENVCLTYCHEPALFAVGSQSHISFLDLRQGQQNIWPLCSREGG

Parental	SGIRSVSFYEHIITVGTGQGSLLFYDIRAQRFLEERLSAYCGSKPRLAGENLKLTTGKGWLNHDETWRNY
	.G.RS.SFY.HI.TVGTG.GSLLFYDIRAQ.FLEE.........PR.....LKLT.G.GWLNHD..W.NY
Retrocopy	TGVRSLSFYHHILTVGTGHGSLLFYDIRAQKFLEESANRSSLPEPR---RKLKLTCGRGWLNHDDMWVNY

Parental	FSDIDFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYAGLWS
	F.....FPNA.YTHCY.....KLFVAGGPLPSGLHG.YAGLWS
Retrocopy	FGGVAEFPNALYTHCYNWPEMKLFVAGGPLPSGLHGHYAGLWS

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

RetrogeneDB ID:

retro_eeur_403