RetrogeneDB ID: retro_cfam_1758

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:26462295..26462593(-)
• Located in intron of: ENSCAFG00000014838

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBP7
• Ensembl ID: ENSCAFG00000019753
• Aliases: None
• Description: retinol binding protein 7, cellular [Source:HGNC Symbol;Acc:30316]

Sequence

>retro_cfam_1758
TTATTTAAGGAAGAACATACATTATCCACAGAAAAAAACATGTTCTCATGCCAGCAAGCTAATAAATCTCATAATATCAT
TAAAGTCACTCTAGTTCAGTTCAGGAAACATTTGTGGGGAAATAAAGACCTGGATAACAGAAAAATGCAAGAGCTTAGTC
ACTTGGGACAATGACAGACTCACCTGCGTCCAGAAGGGGGAGAAGAACAGAGGCTGGACCCACTGGATGGAAGGAGACAA
ACTCCACTTGGAAATGTTCTATGAAGGCCAAGTGTGCAAACAGACGTTCCAGAGAGCC

Alignment

ORF - retro_cfam_1758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.39 %
• Parental protein coverage: 70.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLKPQKVIEQNEDSFTIHTYSSLRNYL-VTFKVGEEFDEDNKGLDNRK-CKSLVTWDNDRLTCIQKGEKK
          L.K...........F.........N...VT..........NK.LDNRK.CKSLVTWDNDRLTC.QKGE.K
Retrocopy LFKEEHTLSTEKNMFSCQQANKSHNIIKVTLVQFRKHLWGNKDLDNRK>CKSLVTWDNDRLTCVQKGE-K

Parental  NRGWTHWMEGDKLHLEMFCEGQVCKQTFQRA
          NRGWTHWMEGDKLHLEMF.EGQVCKQTFQRA
Retrocopy NRGWTHWMEGDKLHLEMFYEGQVCKQTFQRA

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	33.56 RPM
SRP017611_brain	0.00 RPM	0.08 RPM
SRP017611_kidney	0.00 RPM	0.86 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_1758 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1758 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1758 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019753	1 retrocopy	retro_cfam_1758 ,
Canis familiaris	ENSCAFG00000025410	3 retrocopies	retro_cfam_132, retro_cfam_137, retro_cfam_228,
Loxodonta africana	ENSLAFG00000028419	1 retrocopy	retro_lafr_910,