RetrogeneDB - Retrocopy retro_ocun

						
>retro_ocun_413
CAAAACCGCAAATTCCACTGTGAAATTCAGGACTTGATGGTCCAGGGTGGAAGCTTCACCAGGGGAGAGAGCACAGGAGG

AAAGAGAATCTATGGGGATGCTTCCCCGACCAGAATTTCAAGTTGACATACTACTGACCCGGCTGGGGGAGGAGCATGCC

CAGTGCAGACAGACAGTGATGGCTCCTGGTTCTTTATCACCACAACGAGAAGCCCTGGAAGGATGGCAAACACGCATTGT

TTGGCAAAGTTCTAGAGGGCATGGAGGTGGTGTGGAAGGTAGAGAGCACGAGGACAGACTGGGGACAAACCCCTGAAAAA

ORF - retro_ocun_413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	60.91 %
Parental protein coverage:	57.38 %
Number of stop codons detected:	1
Number of frameshifts detected	3

Retrocopy - Parental Gene Alignment:

									ParentalKNSKFHRVIKDFMIQGGDFTRGDGTGGKSIYGER-FPDENFKLKHYGPGWV-SMANAG-DTNGSQFFITT
		.N.KFH..I.D.M.QGG.FTRG..TGGK.IYG...FPD.NFKL..Y.PGW..SM..A..D..GS.FFITT
RetrocopyQNRKFHCEIQDLMVQGGSFTRGESTGGKRIYGDA<FPDQNFKLTYY*PGWGRSMPSAD>DSDGSWFFITT
ParentalVKTA-WLDGKHVVFG-VLEGMEVVRKVESTKTDSRDKPLK
		.....W.DGKH..FG.VLEGMEVV.KVEST.TD....P.K
RetrocopyTRSP<WKDGKHALFGKVLEGMEVVWKVESTRTDWGQTPEK

							

							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	91 .39 RPM
SRP017611_kidney	0 .00 RPM	177 .07 RPM
SRP017611_liver	0 .00 RPM	111 .37 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_413 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_413 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ocun_413 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017053	1 retrocopy	retro_cfam_1999,
Equus caballus	ENSECAG00000017164	1 retrocopy	retro_ecab_617,
Echinops telfairi	ENSETEG00000012671	1 retrocopy	retro_etel_1493,
Loxodonta africana	ENSLAFG00000018698	1 retrocopy	retro_lafr_521,
Oryctolagus cuniculus	ENSOCUG00000007046	2 retrocopies	retro_ocun_1493, retro_ocun_1759,
Oryctolagus cuniculus	ENSOCUG00000007696	2 retrocopies	retro_ocun_661, retro_ocun_892,
Oryctolagus cuniculus	ENSOCUG00000011453	1 retrocopy	retro_ocun_1195,
Oryctolagus cuniculus	ENSOCUG00000012012	1 retrocopy	retro_ocun_413 ,

	RetrogeneDB ID:	retro_ocun_413
Retrocopy location	Organism:	*Rabbit (Oryctolagus cuniculus)*
	Coordinates:	1:177120190..177120510(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	PPIB
	Ensembl ID:	ENSOCUG00000012012
	Aliases:	None
	Description:	peptidylprolyl isomerase B (cyclophilin B) [Source:HGNC Symbol;Acc:9255]

Parental	KNSKFHRVIKDFMIQGGDFTRGDGTGGKSIYGER-FPDENFKLKHYGPGWV-SMANAG-DTNGSQFFITT
	.N.KFH..I.D.M.QGG.FTRG..TGGK.IYG...FPD.NFKL..Y.PGW..SM..A..D..GS.FFITT
Retrocopy	QNRKFHCEIQDLMVQGGSFTRGESTGGKRIYGDA<FPDQNFKLTYY*PGWGRSMPSAD>DSDGSWFFITT

Parental	VKTA-WLDGKHVVFG-VLEGMEVVRKVESTKTDSRDKPLK
	.....W.DGKH..FG.VLEGMEVV.KVEST.TD....P.K
Retrocopy	TRSP<WKDGKHALFGKVLEGMEVVWKVESTRTDWGQTPEK

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

RetrogeneDB ID:

retro_ocun_413