RetrogeneDB ID: retro_cfam_108

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:35783103..35783520(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000029456
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000029910
• Aliases: None
• Description: None

Sequence

>retro_cfam_108
ATGTTTTCAAGCTTCTTTCTTCCTCCTTCCCTCCCTCTCCCACCTCTCTCTCTCTTTCTTTCTTTCTTTCTCTTTCTCTT
TTTTCTTTTCTTTTCTTTTCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTCTTCTTTCTTCTTTCTTCTTTTCTTTCTT
TCTTTCCTCCCTCTCCCACCTCTCTCCCTCCCTCTCCCTTTCCCTCCCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTT
TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTTCCTTCCTTCCT
TCCTTCCTTCCTTCCTTCCTTCCTTCCTCAACCATGTTTCATAAGTAAGGACCAAAGAGACTGTCTACAGGTAAGAGCAT
TAAGGTCTATATTCTGA

Alignment

ORF - retro_cfam_108 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPSFSFFLFFLSFSFFL--SFFLSFFLSFFLFFFLSFLSFFLSFFLSFLTFFP--FFLSFFLSFFLSFFL
          LP..S.FL.F..F.FFL..SF.LSFFLSFFLFFFL..LS.FLSFF....T..P...F.S.FLSFFLSFFL
Retrocopy LPPLSLFLSFFLFLFFLFFSFLLSFFLSFFLFFFL--LSSFLSFFPPSPTSLPPSPFPSLFLSFFLSFFL

Parental  SFFLLFF--FF--LSLSLSLSFLPSFLPSFL
          SFFL.FF..FF..LSLSLSLS.LPSFLPSFL
Retrocopy SFFLSFFLSFFLSLSLSLSLSLLPSFLPSFL

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	0.04 RPM	0.00 RPM
SRP017611_brain	0.40 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_108 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_108 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	ENSCAFG00000029910	1 retrocopy	retro_cfam_108 ,