RetrogeneDB - Retrocopy retro_cfam

	RetrogeneDB ID:	retro_cfam_1820
Retrocopy location	Organism:	*Dog (Canis familiaris)*
	Coordinates:	6:41216191..41216398(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSCAFG00000019775
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	FXYD4
	Ensembl ID:	ENSCAFG00000024923
	Aliases:	None
	Description:	FXYD domain containing ion transport regulator 4 [Source:HGNC Symbol;Acc:4028]

Retrocopy-Parental alignment summary:

						
>retro_cfam_1820
GGCAGGCCTGCCTTGGAAGCCAGTGACCTGGTTGATAAAGACAGTCCCTTATACTATGACTGGGAAAGCCTGCAGCTGGG

TGGGATGATTTTTGGAGGACTCCTGTGCATCGCTGGAATCTTGATAGCCCTGAGTGGAAAATGCAAATGCAAATACCCTT

ACCGGAGAAAGCCACTCCACTCATCACTCCAGGCTCTGTCAGTACCT

ORF - retro_cfam_1820 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	76.81 %
Parental protein coverage:	78.41 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalGLPALEANDLVDKDSPFYYDWESLQLGGMIFGGLLCIAGILIALSGKCKCKYNQKHSPLPEKATPLITP
		G.PALEA.DLVDKDSP.YYDWESLQLGGMIFGGLLCIAGILIALSGKCKCKY.....PL......L..P
RetrocopyGRPALEASDLVDKDSPLYYDWESLQLGGMIFGGLLCIAGILIALSGKCKCKYPYRRKPLHSSLQALSVP

							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
SRP012049_cerebellum	0 .00 RPM	0 .34 RPM
SRP017611_brain	0 .00 RPM	0 .16 RPM
SRP017611_kidney	0 .00 RPM	13 .08 RPM
SRP017611_liver	0 .00 RPM	0 .00 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_1820 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1820 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cfam_1820 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000024923	1 retrocopy	retro_cfam_1820 ,
Dasypus novemcinctus	ENSDNOG00000017385	1 retrocopy	retro_dnov_643,
Erinaceus europaeus	ENSEEUG00000010030	4 retrocopies	retro_eeur_148, retro_eeur_264, retro_eeur_524, retro_eeur_559,
Felis catus	ENSFCAG00000022417	2 retrocopies	retro_fcat_284, retro_fcat_990,
Monodelphis domestica	ENSMODG00000027578	1 retrocopy	retro_mdom_976,
Oryctolagus cuniculus	ENSOCUG00000006722	1 retrocopy	retro_ocun_1050,
Tupaia belangeri	ENSTBEG00000016033	1 retrocopy	retro_tbel_1911,
Tarsius syrichta	ENSTSYG00000014460	3 retrocopies	retro_tsyr_1494, retro_tsyr_70, retro_tsyr_875,

Parental	GLPALEANDLVDKDSPFYYDWESLQLGGMIFGGLLCIAGILIALSGKCKCKYNQKHSPLPEKATPLITP
	G.PALEA.DLVDKDSP.YYDWESLQLGGMIFGGLLCIAGILIALSGKCKCKY.....PL......L..P
Retrocopy	GRPALEASDLVDKDSPLYYDWESLQLGGMIFGGLLCIAGILIALSGKCKCKYPYRRKPLHSSLQALSVP

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

RetrogeneDB ID:

retro_cfam_1820