RetrogeneDB - Retrocopy retro_rnor

						
>retro_rnor_976
ATGAGCAGGGAAGAGGAGAACCCGGCCAGCAAGACCACACCTGTGCAGGATATGCAGAGCAAGGGGCTCTAGATGTCTCT

GCACCATCAATTTGTGGTGGACAGCAAAGACAAGGGACCCGAAGTCATCCTTATCTGGGACTCCTTGGTTCAGCTAATTC

ACCAGTGTGAGATCTCGTGGGAGCTCTTCTCACCTCTGCATGCACTTAACTTTGGCACTGGTGGTGACAGCACATAGCAT

GCACTCTGGGAGCTTGAAAATGGGGAGCTGCAACACATCCAGCCCAAGATTGTGGTGGTCTTGGTGGGCACCAATAACCA

CAGCCACACAGCAGAAGAAGTGAAGGGTGGCATCAAAGCCATGGTA

ORF - retro_rnor_976 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	77.87 %
Parental protein coverage:	52.59 %
Number of stop codons detected:	2
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalMSGEGENPASKPTPVQDVQGDGRWMSLHHRFVADSKDKEPEVVFIGDSLVQLMHQCEIWRELFSPLHALN
		MS.E.ENPASK.TPVQD.Q..G..MSLHH.FV.DSKDK.PEV..I.DSLVQL.HQCEI..ELFSPLHALN
RetrocopyMSREEENPASKTTPVQDMQSKGL*MSLHHQFVVDSKDKGPEVILIWDSLVQLIHQCEISWELFSPLHALN
ParentalFGIGGDSTQHVLWRLENGELEHIRPKIVVVWVGTNNHSHTAEQVTGGIKAIV
		FG.GGDST.H.LW.LENGEL.HI.PKIVVV.VGTNNHSHTAE.V.GGIKA.V
RetrocopyFGTGGDST*HALWELENGELQHIQPKIVVVLVGTNNHSHTAEEVKGGIKAMV

							

							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	3 .81 RPM
SRP017611_kidney	0 .00 RPM	3 .70 RPM
SRP017611_liver	0 .00 RPM	0 .47 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_976 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_976 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_976 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019787	1 retrocopy	retro_btau_547,
Canis familiaris	ENSCAFG00000004847	1 retrocopy	retro_cfam_610,
Dasypus novemcinctus	ENSDNOG00000002870	1 retrocopy	retro_dnov_1276,
Macaca mulatta	ENSMMUG00000012172	1 retrocopy	retro_mmul_18,
Mustela putorius furo	ENSMPUG00000007574	1 retrocopy	retro_mputfur_351,
Rattus norvegicus	ENSRNOG00000018032	1 retrocopy	retro_rnor_2585,
Rattus norvegicus	ENSRNOG00000020481	1 retrocopy	retro_rnor_976 ,

	RetrogeneDB ID:	retro_rnor_976
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	13:90814457..90814823(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Pafah1b3
	Ensembl ID:	ENSRNOG00000020481
	Aliases:	None
	Description:	Platelet-activating factor acetylhydrolase IB subunit gamma [Source:UniProtKB/Swiss-Prot;Acc:O35263]

Parental	MSGEGENPASKPTPVQDVQGDGRWMSLHHRFVADSKDKEPEVVFIGDSLVQLMHQCEIWRELFSPLHALN
	MS.E.ENPASK.TPVQD.Q..G..MSLHH.FV.DSKDK.PEV..I.DSLVQL.HQCEI..ELFSPLHALN
Retrocopy	MSREEENPASKTTPVQDMQSKGL*MSLHHQFVVDSKDKGPEVILIWDSLVQLIHQCEISWELFSPLHALN

Parental	FGIGGDSTQHVLWRLENGELEHIRPKIVVVWVGTNNHSHTAEQVTGGIKAIV
	FG.GGDST.H.LW.LENGEL.HI.PKIVVV.VGTNNHSHTAE.V.GGIKA.V
Retrocopy	FGTGGDST*HALWELENGELQHIQPKIVVVLVGTNNHSHTAEEVKGGIKAMV

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

RetrogeneDB ID:

retro_rnor_976