RetrogeneDB ID: retro_cfam_1279

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 28:15703821..15704007(-)
• Located in intron of: ENSCAFG00000010380

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM7
• Ensembl ID: ENSCAFG00000000736
• Aliases: None
• Description: LYR motif containing 7 [Source:HGNC Symbol;Acc:28072]

Sequence

>retro_cfam_1279
CAGGTTTTTAAAAATGATACCAGAGCATTAGAAGCAGCCAGAATAAAGATAAATGAAGAATTCAAAAGTAATAAAAGTGA
AACTTCTCCCAAGAAAATAGAAGAGCTAATAAAAATAGGTTCCGATGTTGAATTGTTACTCAGAACATCTGTTATACAAG
GTATTCACACAGACCACAATACACTA

Alignment

ORF - retro_cfam_1279 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 62.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVFKNDTRALEAARIKINEEFKSNKSETSPKKIEELIKIGSDVELLLRTSVIQGIHTDHNTL
          QVFKNDTRALEAARIKINEEFKSNKSETSPKKIEELIKIGSDVELLLRTSVIQGIHTDHNTL
Retrocopy QVFKNDTRALEAARIKINEEFKSNKSETSPKKIEELIKIGSDVELLLRTSVIQGIHTDHNTL

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	0.67 RPM	3.61 RPM
SRP017611_brain	0.32 RPM	3.18 RPM
SRP017611_kidney	2.58 RPM	11.42 RPM
SRP017611_liver	0.00 RPM	0.58 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1279 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1279 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1279 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017776	1 retrocopy	retro_amel_1472,
Canis familiaris	ENSCAFG00000000736	1 retrocopy	retro_cfam_1279 ,
Choloepus hoffmanni	ENSCHOG00000006766	6 retrocopies	retro_chof_1440, retro_chof_2015, retro_chof_2366, retro_chof_2681, retro_chof_488, retro_chof_688,
Echinops telfairi	ENSETEG00000010130	1 retrocopy	retro_etel_1126,
Oryctolagus cuniculus	ENSOCUG00000000166	1 retrocopy	retro_ocun_1740,
Ochotona princeps	ENSOPRG00000015568	4 retrocopies	retro_opri_1182, retro_opri_212, retro_opri_361, retro_opri_611,
Rattus norvegicus	ENSRNOG00000045961	1 retrocopy	retro_rnor_552,