RetrogeneDB ID: retro_cfam_884

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 2:11518182..11518433(+)
• Located in intron of: ENSCAFG00000004145

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000029413
• Aliases: None
• Description: None

Sequence

>retro_cfam_884
ATGATCTCTCTGCTTTATACCTGGTGTATTCCCAGAGCTTCCATTTCCATGTGGCACGTCTTTGTTTGTTTTGGGTATCG
CACTTCCCAGCTTATTATTGTCAGAGATTACCAAAAGAAGCCGATGTGACAAAGGATAAAGAGATGACAATACACTGGTT
TAGACAAGCCTCCAAGCAGGACCATCCCTGCGCATTCTTTAACCTTGCAGTGGGAAAACTGAAAAACATAACTGGGTCCA
CTGAACTAGGC

Alignment

ORF - retro_cfam_884 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.98 %
• Parental protein coverage: 67.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MISLLYIWLYSQSFHFHVAHLYARFGYPSAQLIVG-QRYLKGAGVVKDEEMAMYWFRQASKQDHPYASF-
          MISLLY.W...........H....FGY...QLI...QR..K.A.V.KD.EM...WFRQASKQDHP.A.F.
Retrocopy MISLLYTWCIPRA-SISMWHVFVCFGYRTSQLIIV<QRLPKEADVTKDKEMTIHWFRQASKQDHPCAFFN

Parental  LAVGKLKNMTGSMEVG
          LAVGKLKN.TGS.E.G
Retrocopy LAVGKLKNITGSTELG

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	0.08 RPM
SRP017611_brain	0.00 RPM	0.08 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.07 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_884 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_884 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_884 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029413	1 retrocopy	retro_cfam_884 ,