RetrogeneDB - Retrocopy retro_eeur

						
>retro_eeur_320
ATGTCTTCCAGTAGTGACCAAGTTGTTATCACAATGCCACAAAGCAACGGCCTCCCCACGGTGACTCTCAACAACCTTAA

TACTTTTACTAAGGGGTCTATGCTAAGTTTTCATAACATATGCTACAGGGTGAAAGTGAAGTGCGGCTCTCTCCTTGATG

GAAGCACATGGGAGAAAGAAATACTCAAGAATGTCAATGGGATCATGGGACCTGGCCTCAATGCCATTCTGGGACCCACA

GGTGGAGGCAAATCTTCCTTGTTGGATGTTCTAGCTGCAAGGAAAGATCCACAGGGATTATCTGGGGATGTTTTGATAAA

TGGAAAACCTCGCCCTGCCAATTTCAAATGCATTTCCGGTTATGTGGTACAGGATGACGTGGTGATGGGAACGCTGACCG

TGAGAGAAAACCTACAGTTCTCAGCAGCGCTGCGGCTCCCTGAGACCATGACCATGGGCGAAAAAAATCAAAGGGTCTGC

CAGATCCTTCAAGAGTTGGGTCTGGATAACGTGGCAGATTCCAAAGTTGGGACTCAGTTTACCCGTGGTGTGTCTGGAGG

AGAGAGAAAAAGGACTAGCATTGGGATGGAGCTTATTACTGACCCATCCATCTTGTTCCTTGATGAGCCCACCACTGGCT

TAGATTCAAGCACAGCAAATGCTGTCCTTTTGCTCCTGAAGAGGATGTCGAAGCAAGGGAGGACCATCATCTTCTCTATC

CATCAGCCTCGCTATTCCATCTTCCGGCTGTTTGATAGCCTCACCTTATTGGCCTCTGGAAGACTGGTGTTCCATGGGCC

GGCTCAGGAGGCCTTGGGGTACTTTGAATCTGCTGGTTACCAGTGTGAGGCCTATAATAACCCTGCAGACTTCTTCCTGG

ACGTCATCAATGGAGACTCCTCTGCTGTGATATTAAACAGAGACAATGAAAGTGATGAAACCAGGGGCATCATGGAGCCC

ACCCAAATAGAGACTCTATGCATAGAAAAATTAGCTGAGTTGTATGTCAACTCCACCTTTTTCAGAGAGACGAACATTGT

ATTAAGTCATCTCTCAGTCGTCCTAAGACAGAAAGAGCCCCACTTTCTGAAGAGGATCACCTATGCCACCTCCTTCTGTC

ACCAACTTAAG

ORF - retro_eeur_320 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	74.41 %
Parental protein coverage:	57.71 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalMSCRTEQVFITMSERNVNGLPGATRNNLKTCSEGSVLSFHNICYRVKVKSGFLFCGKTVEKEILSGINGI
		MS....QV.ITM...N..GLP..T.NNL.T...GS.LSFHNICYRVKVK.G.L..G.T.EKEIL...NGI
RetrocopyMSSSSDQVVITMPQSN--GLPTVTLNNLNTFTKGSMLSFHNICYRVKVKCGSLLDGSTWEKEILKNVNGI
ParentalMRPGLNAILGPTGGGKSSLLDILAARKDPRGLSGDVLINGGPRPANFKCISGYVVQDDVVMGTLTVRENL
		M.PGLNAILGPTGGGKSSLLD.LAARKDP.GLSGDVLING.PRPANFKCISGYVVQDDVVMGTLTVRENL
RetrocopyMGPGLNAILGPTGGGKSSLLDVLAARKDPQGLSGDVLINGKPRPANFKCISGYVVQDDVVMGTLTVRENL
ParentalQFSAALRLPTMMDSREKNERIDKIIKELGLDKVADSKVGTQFIRGVSGGERKRTSIGMELITDPSILFLD
		QFSAALRLP..M...EKN.R...I..ELGLD.VADSKVGTQF.RGVSGGERKRTSIGMELITDPSILFLD
RetrocopyQFSAALRLPETMTMGEKNQRVCQILQELGLDNVADSKVGTQFTRGVSGGERKRTSIGMELITDPSILFLD
ParentalEPTTGLDSSTASAVLLLLKRMSRQGRTIIFSIHQPRYSIFKLFDSLTLLASGRLMFHGPAQEALGYFETA
		EPTTGLDSSTA.AVLLLLKRMS.QGRTIIFSIHQPRYSIF.LFDSLTLLASGRL.FHGPAQEALGYFE.A
RetrocopyEPTTGLDSSTANAVLLLLKRMSKQGRTIIFSIHQPRYSIFRLFDSLTLLASGRLVFHGPAQEALGYFESA
ParentalGYHCEAYNNPADFFLDVINGDSTAVALNQEEEADAAKDLAEAPKRDTSVVKRLAEFYISSSFFRDSQAEL
		GY.CEAYNNPADFFLDVINGDS.AV.LN...E.D......E.....T.....LAE.Y..S.FFR.....L
RetrocopyGYQCEAYNNPADFFLDVINGDSSAVILNRDNESDETRGIMEPTQIETLCIEKLAELYVNSTFFRETNIVL
ParentalDQLLEVPQKKNTAF-NEVTYATSFFHQLR
		..L..V...K...F....TYATSF.HQL.
RetrocopySHLSVVLRQKEPHFLKRITYATSFCHQLK

							

							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	18 .21 RPM
SRP017611_kidney	0 .00 RPM	9 .75 RPM
SRP017611_liver	0 .00 RPM	109 .01 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_320 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000011333	1 retrocopy	retro_eeur_320 ,
Tupaia belangeri	ENSTBEG00000004706	1 retrocopy	retro_tbel_3110,
Tursiops truncatus	ENSTTRG00000015227	1 retrocopy	retro_ttru_313,

	RetrogeneDB ID:	retro_eeur_320
Retrocopy location	Organism:	*Hedgehog (Erinaceus europaeus)*
	Coordinates:	scaffold_252947:3334..4465(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	ABCG2
	Ensembl ID:	ENSEEUG00000011333
	Aliases:	None
	Description:	ATP-binding cassette, sub-family G (WHITE), member 2 [Source:HGNC Symbol;Acc:74]

Parental	MSCRTEQVFITMSERNVNGLPGATRNNLKTCSEGSVLSFHNICYRVKVKSGFLFCGKTVEKEILSGINGI
	MS....QV.ITM...N..GLP..T.NNL.T...GS.LSFHNICYRVKVK.G.L..G.T.EKEIL...NGI
Retrocopy	MSSSSDQVVITMPQSN--GLPTVTLNNLNTFTKGSMLSFHNICYRVKVKCGSLLDGSTWEKEILKNVNGI

Parental	MRPGLNAILGPTGGGKSSLLDILAARKDPRGLSGDVLINGGPRPANFKCISGYVVQDDVVMGTLTVRENL
	M.PGLNAILGPTGGGKSSLLD.LAARKDP.GLSGDVLING.PRPANFKCISGYVVQDDVVMGTLTVRENL
Retrocopy	MGPGLNAILGPTGGGKSSLLDVLAARKDPQGLSGDVLINGKPRPANFKCISGYVVQDDVVMGTLTVRENL

Parental	QFSAALRLPTMMDSREKNERIDKIIKELGLDKVADSKVGTQFIRGVSGGERKRTSIGMELITDPSILFLD
	QFSAALRLP..M...EKN.R...I..ELGLD.VADSKVGTQF.RGVSGGERKRTSIGMELITDPSILFLD
Retrocopy	QFSAALRLPETMTMGEKNQRVCQILQELGLDNVADSKVGTQFTRGVSGGERKRTSIGMELITDPSILFLD

Parental	EPTTGLDSSTASAVLLLLKRMSRQGRTIIFSIHQPRYSIFKLFDSLTLLASGRLMFHGPAQEALGYFETA
	EPTTGLDSSTA.AVLLLLKRMS.QGRTIIFSIHQPRYSIF.LFDSLTLLASGRL.FHGPAQEALGYFE.A
Retrocopy	EPTTGLDSSTANAVLLLLKRMSKQGRTIIFSIHQPRYSIFRLFDSLTLLASGRLVFHGPAQEALGYFESA

Parental	GYHCEAYNNPADFFLDVINGDSTAVALNQEEEADAAKDLAEAPKRDTSVVKRLAEFYISSSFFRDSQAEL
	GY.CEAYNNPADFFLDVINGDS.AV.LN...E.D......E.....T.....LAE.Y..S.FFR.....L
Retrocopy	GYQCEAYNNPADFFLDVINGDSSAVILNRDNESDETRGIMEPTQIETLCIEKLAELYVNSTFFRETNIVL

Parental	DQLLEVPQKKNTAF-NEVTYATSFFHQLR
	..L..V...K...F....TYATSF.HQL.
Retrocopy	SHLSVVLRQKEPHFLKRITYATSFCHQLK

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

RetrogeneDB ID:

retro_eeur_320