RetrogeneDB ID: retro_cfam_24

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 18:53341357..53341552(-)
• Located in intron of: ENSCAFG00000015073

Retrocopy information

• Ensembl ID: ENSCAFG00000005186
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000005180
• Aliases: None
• Description: None

Sequence

>retro_cfam_24
ATGTTCCTGTCCACGGTCACCTTTGCCAAGAGCAAGTCAAAAACCATTCTGGTCAAAATGCTGAGCCAAGCTGGAACAGG
TTACTCCTTCAACACTAAGAGAAGCCGACTACGGGAGAAACTCACTCTCTTACATTATGACCCAATTGTGAAAACAAAAG
TCCTCTTTGTGGAACAGAAGAAAATACGCTCCCTC

Alignment

ORF - retro_cfam_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFLSAVTFAKSKSKTILVKMLSQAGTGYSFNTKRSRLREKLTLLHYDPIVKTKVLFVEQKKIRSL
          MFLS.VTFAKSKSKTILVKMLSQAGTGYSFNTKRSRLREKLTLLHYDPIVKTKVLFVEQKKIRSL
Retrocopy MFLSTVTFAKSKSKTILVKMLSQAGTGYSFNTKRSRLREKLTLLHYDPIVKTKVLFVEQKKIRSL

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	0.63 RPM	24.61 RPM
SRP017611_brain	0.32 RPM	24.29 RPM
SRP017611_kidney	1.25 RPM	24.76 RPM
SRP017611_liver	0.15 RPM	11.31 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_24 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_24 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_24 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
Canis familiaris	ENSCAFG00000005180	1 retrocopy	retro_cfam_24 ,
Canis familiaris	ENSCAFG00000012023	1 retrocopy	retro_cfam_334,