RetrogeneDB ID: retro_cfam_57

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:72394745..72395105(+)
• Located in intron of: ENSCAFG00000015929

Retrocopy information

• Ensembl ID: ENSCAFG00000015933
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ACYP2
• Ensembl ID: ENSCAFG00000023070
• Aliases: None
• Description: acylphosphatase 2, muscle type [Source:HGNC Symbol;Acc:180]

Sequence

>retro_cfam_57
CTGGTCGGCCGTGCTGTCCCGAACGCCCGAGAGGAGGCCGAGGAGGGTGTGGGCATGAACATGGCAGAAGGGGACACCCT
GATATCAGTGGATTATGAAATTTTTGGGAAGGTCCAAGGGGTGTTTTTCCACAAGTACACTCAGGCTGAGGGTAAAAAGC
TGGGATTGGTTGGCTGGGTCCAGAACACTGACCAGGGCACAGTGCAAGGACAATTGCAAGGTCCCATCTCCAAAGTGCAT
CTTATGCAGGAATGGCTTGAAACAAAAGGAAGTCCCAAATCACACATCGACAGAGCAAACTTCAGGAATGAGAAGGTCAT
CTTAAAGTTGGATTACTCAGATTTCCAAATTGTGAAATAA

Alignment

ORF - retro_cfam_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.86 %
• Parental protein coverage: 79.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLAAAMSAARPLKSVDYEVFGRVQGVCFRMYTEDEAKKIGVVGWVKNTSKGTVTGQVQGPEDKVNSMMSW
          G....M.....L.SVDYE.FG.VQGV.F..YT..E.KK.G.VGWV.NT..GTV.GQ.QGP..KV..M..W
Retrocopy GVGMNMAEGDTLISVDYEIFGKVQGVFFHKYTQAEGKKLGLVGWVQNTDQGTVQGQLQGPISKVHLMQEW

Parental  LSKVGSPSSRIDRTNFSNEKTISKVEYSNFSI
          L...GSP.S.IDR.NF.NEK.I.K..YS.F.I
Retrocopy LETKGSPKSHIDRANFRNEKVILKLDYSDFQI

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	1.64 RPM	15.75 RPM
SRP017611_brain	1.11 RPM	14.61 RPM
SRP017611_kidney	0.40 RPM	12.55 RPM
SRP017611_liver	0.07 RPM	11.46 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_57 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_57 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_57 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000023070	1 retrocopy	retro_cfam_57 ,
Echinops telfairi	ENSETEG00000017888	1 retrocopy	retro_etel_1505,
Oryctolagus cuniculus	ENSOCUG00000015408	1 retrocopy	retro_ocun_1372,
Tupaia belangeri	ENSTBEG00000013671	1 retrocopy	retro_tbel_935,