RetrogeneDB ID: retro_cfam_1197

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 26:22740810..22741057(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHCHD7
• Ensembl ID: ENSCAFG00000007055
• Aliases: None
• Description: coiled-coil-helix-coiled-coil-helix domain containing 7 [Source:HGNC Symbol;Acc:28314]

Sequence

>retro_cfam_1197
ATGCCCAAGGTAGCATGGAGGCTGAGAGAACATGACACAAATCCTTGCTTGTTGGAATCTGATGTTTCTACCAGAGGTAG
GGATGAAAATAACTATGACAGGGAGAGGTGGTCCACTTACTTCTTAAACTACAAAAGCTGCCAGAAATTCTGGAATTCTA
TCATGGGTCCAGAGAAGACAGAATGGAGTAAAGTCATCTATGCCTACAGCAGGAGAAAGAGATGAGATTCTTGGGGGTAA
CGGGAAA

Alignment

ORF - retro_cfam_1197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.11 %
• Parental protein coverage: 96.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPMVARRLRDPDINPCLLESDASTRCMDENNYDRERCSTYFLKYKNCRKFWNSVM-VQRRQKGVKPSMPT
          MP.VA.RLR..D.NPCLLESD.STR..DENNYDRER.STYFL.YK.C.KFWNS.M.VQRRQ.GVK.SMPT
Retrocopy MPKVAWRLREHDTNPCLLESDVSTRGRDENNYDRERWSTYFLNYKSCQKFWNSIM>VQRRQNGVKSSMPT

Parental  AAERDEILGAMGK
          A.ERDEILG..GK
Retrocopy AGERDEILGGNGK

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	15.50 RPM
SRP017611_brain	0.00 RPM	11.04 RPM
SRP017611_kidney	0.00 RPM	17.83 RPM
SRP017611_liver	0.00 RPM	4.28 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1197 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1197 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1197 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007055	1 retrocopy	retro_cfam_1197 ,
Echinops telfairi	ENSETEG00000020301	2 retrocopies	retro_etel_1330, retro_etel_888,
Monodelphis domestica	ENSMODG00000024930	1 retrocopy	retro_mdom_1124,
Ictidomys tridecemlineatus	ENSSTOG00000002724	1 retrocopy	retro_itri_278,