RetrogeneDB - Retrocopy retro_rnor

	RetrogeneDB ID:	retro_rnor_552
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	1:273367834..273368039(+)
	Located in intron of:	ENSRNOG00000026048
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Lyrm7
	Ensembl ID:	ENSRNOG00000045961
	Aliases:	None
	Description:	LYR motif-containing protein 7 [Source:UniProtKB/Swiss-Prot;Acc:B4F7A1]

Retrocopy-Parental alignment summary:

                        
>retro_rnor_552
AATGATAAGACAACATTAGAAGCAGCTAGAGTTAAGGTAGTTGAAGAATTTAAAAATCATTAAAGTGAGACTTCACCAGA

GAACAGAGAAGAGCTGATGAAGATAAGCTCCGGTGTTAAACTGTTCCTCAGACATCTGTTAAACAAGTGTTCACACTGAC

CACCATGCACTGACGCATCTCTCCAGGAAAGAGCTTCATCCAGAG

ORF - retro_rnor_552 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	57.75 %
Parental protein coverage:	66.35 %
Number of stop codons detected:	1
Number of frameshifts detected:	2

Retrocopy - Parental Gene Alignment:

                                ParentalNDKRALEAARVKINEEFKKHKNETSPEKIKEMLKIGSDVELLLR-TSVIQ-GIHTDHDTLQLVPRKDLLT
NDK..LEAARVK..EEFK.H..ETSPE...E..KI.S.V.L.LR.TSV.Q...HTDH..L....RK.L..
RetrocopyNDKTTLEAARVKVVEEFKNH*SETSPENREELMKISSGVKLFLR<TSVKQ<SVHTDHHALTHLSRKELHP
ParentalE
E
RetrocopyE

                            

                            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	12 .94 RPM
SRP017611_kidney	0 .00 RPM	16 .19 RPM
SRP017611_liver	0 .07 RPM	3 .97 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_552 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_552 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_552 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017776	1 retrocopy	retro_amel_1472,
Canis familiaris	ENSCAFG00000000736	1 retrocopy	retro_cfam_1279,
Choloepus hoffmanni	ENSCHOG00000006766	6 retrocopies	retro_chof_1440, retro_chof_2015, retro_chof_2366, retro_chof_2681, retro_chof_488, retro_chof_688,
Echinops telfairi	ENSETEG00000010130	1 retrocopy	retro_etel_1126,
Oryctolagus cuniculus	ENSOCUG00000000166	1 retrocopy	retro_ocun_1740,
Ochotona princeps	ENSOPRG00000015568	4 retrocopies	retro_opri_1182, retro_opri_212, retro_opri_361, retro_opri_611,
Rattus norvegicus	ENSRNOG00000045961	1 retrocopy	retro_rnor_552 ,

Parental	NDKRALEAARVKINEEFKKHKNETSPEKIKEMLKIGSDVELLLR-TSVIQ-GIHTDHDTLQLVPRKDLLT
	NDK..LEAARVK..EEFK.H..ETSPE...E..KI.S.V.L.LR.TSV.Q...HTDH..L....RK.L..
Retrocopy	NDKTTLEAARVKVVEEFKNH*SETSPENREELMKISSGVKLFLR<TSVKQ<SVHTDHHALTHLSRKELHP

Parental	E
	E
Retrocopy	E

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

RetrogeneDB ID:

retro_rnor_552