RetrogeneDB ID: retro_cfam_1243

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:20300740..20300995(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: FRZB
• Ensembl ID: ENSCAFG00000024988
• Aliases: None
• Description: frizzled-related protein [Source:HGNC Symbol;Acc:3959]

Sequence

>retro_cfam_1243
AATTTTCCTATGGATCCTAGTAATGGAAACCGTAGAGGAGCCAGCAGTGAATGCTGCAAACGTAAACCTCTTAGGGCCAT
GCAGAAGACCTAGTTCCAAAACAACTATGTCATTCAGGCAGGCTGAAGTTAAGAGCTAAAGGCCAGATGCCATGGCATGG
CTGCAGTAGTGGAGGTGAAGGAGATTCTAAAGGCTTCTAGTAAACATTCCAAGCACACCATTAATCTTTACACCAAGTCT
GGCTGCCTACGTCCT

Alignment

ORF - retro_cfam_1243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.23 %
• Parental protein coverage: 52.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFPMDSSNGNCRGTSSERCKCKPVRATQKTYFRNNYNYVIRAKVK-EIKTKCHDVTVVIEVKEILKASLV
          .FPMD.SNGN.RG.SSE.CK.KP.RA.QKT.F.NN..YVI.A....E.K..CH....V.EVKEILKAS..
Retrocopy NFPMDPSNGNRRGASSECCKRKPLRAMQKT*FQNN--YVIQAG*S*ELKARCHGMAAVVEVKEILKASSK

Parental  NIPRDTVNLYTSSGCLCP
          .....T.NLYT.SGCL.P
Retrocopy H-SKHTINLYTKSGCLRP

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	50.52 RPM
SRP017611_brain	0.00 RPM	32.71 RPM
SRP017611_kidney	0.00 RPM	16.51 RPM
SRP017611_liver	0.00 RPM	5.66 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1243 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1243 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1243 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009717	1 retrocopy	retro_amel_596,
Canis familiaris	ENSCAFG00000024988	1 retrocopy	retro_cfam_1243 ,