RetrogeneDB - Retrocopy retro_eeur

						
>retro_eeur_390
ATGTCACTGTACGAAGACCTGGGCGTGGAGAGGAGTGACTCCAAGATGGAAGGCTGGTCCAGGAACTTCATGCTGTTGCA

GTCTCAGCTGCAGGTAAAGAAGGCGGCTCTCATGCAGGCCAAGAGCCAGAAGACCAAGCAAAGCACCGTCCTGGCGCCAG

TGATCGACCTGAAGCGCGGTGGCTCCTCGGACAAACGGCAGATCGTGGACACGTGGCCGCACGTGGCCGCCGGCCTCAAG

GACCCTGTCCCCAGTGGATGTTCTGCGGGAGGAATGCTGATTCCCTTGGCCGACGAATATGACCCCATGTCCCCTAACGA

CTACGAGAAGGTAGTGAAGCGCCAGAGAGAGAAGCGACAGAGGCAGCGAGAGCTGGTAAGACTGAAAGAAAAAGGAGAGA

CAGCGAAGAGGCGGAAGGATAGATGCGAAGCCGGTGCCGGGTATTCCAGGCGGCCAGATCTAGATTCTGATGAGGATGAA

GATTATGAACGAGAAAGGCGCGAAAAAAGAAAGGGCGGAGTTGCCATCGCACCCCCCACTTCTCTTGTAACAAAGGGCCC

GGCGTTGCCCCCAGATTTTCCTTACGAGGAGGATTCCCGGCCTCGCTCACCGTCTCCCAAAGCTACTACTCCTCCCCCCA

TGTACGAGGATCAAGACAGACCCCGCTCCCCGGCTGGGCCCGGCAGCTCCTTCCTTGCCAGCATGGGTGGCACGGTGGCG

CATAAAATCATGCAGAAGTACGGCTTCCGGGAAGGCCAGGGGCTGGGGAAGCACGAGCAGGGGCTGAGCGTGGCCTTGTC

GGTGGAGAAGACCAGCAAGTGTGGGGGCAAGATCGTAGTGGGCGAAGTC

ORF - retro_eeur_390 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	78.52 %
Parental protein coverage:	83.18 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalMFMNHNLGVETSE--MEGWS----LLQAQLQVKNMTLKQIKSQRTKQSTVLAPVIDLKRGGGSADERQIV
		M.....LGVE.S...MEGWS....LLQ.QLQVK...L.Q.KSQ.TKQSTVLAPVIDLKRGG.S.D.RQIV
RetrocopyMSLYEDLGVERSDSKMEGWSRNFMLLQSQLQVKKAALMQAKSQKTKQSTVLAPVIDLKRGG-SSDKRQIV
ParentalDTPPHVAAGLKDPVPSGFSAGEVLIPLADEYDPMFPNDYEKVVKRQREERQRQRELERQKEIEEREKRRK
		DT.PHVAAGLKDPVPSG.SAG..LIPLADEYDPM.PNDYEKVVKRQRE.RQRQREL.R.KE..E..KRRK
RetrocopyDTWPHVAAGLKDPVPSGCSAGGMLIPLADEYDPMSPNDYEKVVKRQREKRQRQRELVRLKEKGETAKRRK
ParentalDRHEA-SGFSRRPDPDSDEDEDYERERRKRSMGGAAIAPPTSLVEKDKELPRDFPYEEDSRPRSQSSKAA
		DR.EA..G.SRRPD.DSDEDEDYERERR....GG.AIAPPTSLV.K...LP.DFPYEEDSRPRS.S.KA.
RetrocopyDRCEAGAGYSRRPDLDSDEDEDYERERREKRKGGVAIAPPTSLVTKGPALPPDFPYEEDSRPRSPSPKAT
ParentalIPPPVYEDQDRPRSPPGPGNSFLANMGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSVEKTSKRGGKII
		.PPP.YEDQDRPRSP.GPG.SFLA.MGGTVAHKIMQKYGFREGQGLGKHEQGLS.ALSVEKTSK.GGKI.
RetrocopyTPPPMYEDQDRPRSPAGPGSSFLASMGGTVAHKIMQKYGFREGQGLGKHEQGLSVALSVEKTSKCGGKIV
ParentalVGEV
		VGEV
RetrocopyVGEV

							

							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	7 .90 RPM
SRP017611_kidney	0 .19 RPM	8 .25 RPM
SRP017611_liver	0 .00 RPM	5 .79 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_390 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 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021951	2 retrocopies	retro_btau_1057, retro_btau_530,
Canis familiaris	ENSCAFG00000005206	1 retrocopy	retro_cfam_844,
Callithrix jacchus	ENSCJAG00000020573	1 retrocopy	retro_cjac_432,
Equus caballus	ENSECAG00000008939	1 retrocopy	retro_ecab_547,
Erinaceus europaeus	ENSEEUG00000013077	1 retrocopy	retro_eeur_390 ,
Homo sapiens	ENSG00000134453	1 retrocopy	retro_hsap_1551,
Macropus eugenii	ENSMEUG00000011347	1 retrocopy	retro_meug_438,
Macaca mulatta	ENSMMUG00000015152	2 retrocopies	retro_mmul_1209, retro_mmul_771,
Mus musculus	ENSMUSG00000037197	1 retrocopy	retro_mmus_2855,
Otolemur garnettii	ENSOGAG00000015687	1 retrocopy	retro_ogar_1119,
Pongo abelii	ENSPPYG00000002067	1 retrocopy	retro_pabe_1284,
Pan troglodytes	ENSPTRG00000002265	1 retrocopy	retro_ptro_1044,
Ictidomys tridecemlineatus	ENSSTOG00000013591	1 retrocopy	retro_itri_1376,
Tursiops truncatus	ENSTTRG00000001344	1 retrocopy	retro_ttru_1758,

	RetrogeneDB ID:	retro_eeur_390
Retrocopy location	Organism:	*Hedgehog (Erinaceus europaeus)*
	Coordinates:	scaffold_281589:8550..9399(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	RBM17
	Ensembl ID:	ENSEEUG00000013077
	Aliases:	None
	Description:	RNA binding motif protein 17 [Source:HGNC Symbol;Acc:16944]

Parental	MFMNHNLGVETSE--MEGWS----LLQAQLQVKNMTLKQIKSQRTKQSTVLAPVIDLKRGGGSADERQIV
	M.....LGVE.S...MEGWS....LLQ.QLQVK...L.Q.KSQ.TKQSTVLAPVIDLKRGG.S.D.RQIV
Retrocopy	MSLYEDLGVERSDSKMEGWSRNFMLLQSQLQVKKAALMQAKSQKTKQSTVLAPVIDLKRGG-SSDKRQIV

Parental	DTPPHVAAGLKDPVPSGFSAGEVLIPLADEYDPMFPNDYEKVVKRQREERQRQRELERQKEIEEREKRRK
	DT.PHVAAGLKDPVPSG.SAG..LIPLADEYDPM.PNDYEKVVKRQRE.RQRQREL.R.KE..E..KRRK
Retrocopy	DTWPHVAAGLKDPVPSGCSAGGMLIPLADEYDPMSPNDYEKVVKRQREKRQRQRELVRLKEKGETAKRRK

Parental	DRHEA-SGFSRRPDPDSDEDEDYERERRKRSMGGAAIAPPTSLVEKDKELPRDFPYEEDSRPRSQSSKAA
	DR.EA..G.SRRPD.DSDEDEDYERERR....GG.AIAPPTSLV.K...LP.DFPYEEDSRPRS.S.KA.
Retrocopy	DRCEAGAGYSRRPDLDSDEDEDYERERREKRKGGVAIAPPTSLVTKGPALPPDFPYEEDSRPRSPSPKAT

Parental	IPPPVYEDQDRPRSPPGPGNSFLANMGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSVEKTSKRGGKII
	.PPP.YEDQDRPRSP.GPG.SFLA.MGGTVAHKIMQKYGFREGQGLGKHEQGLS.ALSVEKTSK.GGKI.
Retrocopy	TPPPMYEDQDRPRSPAGPGSSFLASMGGTVAHKIMQKYGFREGQGLGKHEQGLSVALSVEKTSKCGGKIV

Parental	VGEV
	VGEV
Retrocopy	VGEV

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

RetrogeneDB ID:

retro_eeur_390