RetrogeneDB ID: retro_cfam_1001

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 21:3965810..3966056(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFV3
• Ensembl ID: ENSCAFG00000010508
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa [Source:HGNC Symbol;Acc:7719]

Sequence

>retro_cfam_1001
ATGACAGTGTCACTTCTGCTGCGGCAAGGAGGGTCTGGGGCACTGAAAACTATGCTCCTAGAAGCATGAGTATTTCGAGG
ACTTGCTCCTACAGTTTCTCTCTGTGCAGAATTAGGGAAGAGCGAAAAGGGATTGCCACCGAATCCCAAGAAACAAAGTC
CACCAGAAGAGCCTGCTCAAGCTGAGCCGTTTGACAACACCACGTACAGGAACCTCCAGCACCACGACTACACCCTGCAC
ACCTTC

Alignment

ORF - retro_cfam_1001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.9 %
• Parental protein coverage: 74.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASLLLREGRSAALKIMLLEARVFRGLASTVSLCAESGKSEKGLPPNPKKQSPPKIPKSAAHEPAQAEP
          M..SLLLR.G.S.ALK.MLLEA.VFRGLA.TVSLCAE.GKSEKGLPPNPKKQSPP..P..A..EP.....
Retrocopy MTVSLLLRQGGSGALKTMLLEA*VFRGLAPTVSLCAELGKSEKGLPPNPKKQSPPEEPAQA--EPFDNTT

Parental  FDNTTYRNLQHHDY
          ..N........H..
Retrocopy YRNLQHHDYTLHTF

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	35.78 RPM
SRP017611_brain	0.00 RPM	30.65 RPM
SRP017611_kidney	0.00 RPM	104.87 RPM
SRP017611_liver	0.00 RPM	21.75 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1001 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1001 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1001 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021491	10 retrocopies	retro_btau_445, retro_btau_769, retro_btau_770, retro_btau_772, retro_btau_773, retro_btau_774, retro_btau_803, retro_btau_804, retro_btau_805, retro_btau_806,
Canis familiaris	ENSCAFG00000010508	1 retrocopy	retro_cfam_1001 ,
Callithrix jacchus	ENSCJAG00000015786	1 retrocopy	retro_cjac_1498,