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 symbol: FXYD4
• Ensembl ID: ENSCAFG00000024923
• Aliases: None
• Description: FXYD domain containing ion transport regulator 4 [Source:HGNC Symbol;Acc:4028]

Sequence

>retro_cfam_1820
GGCAGGCCTGCCTTGGAAGCCAGTGACCTGGTTGATAAAGACAGTCCCTTATACTATGACTGGGAAAGCCTGCAGCTGGG
TGGGATGATTTTTGGAGGACTCCTGTGCATCGCTGGAATCTTGATAGCCCTGAGTGGAAAATGCAAATGCAAATACCCTT
ACCGGAGAAAGCCACTCCACTCATCACTCCAGGCTCTGTCAGTACCT

Alignment

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:

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

Legend:

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

Expression

RNA-Seq

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

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1820 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1820 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1820 has 0 orthologous retrocopies within eutheria group .

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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,