RetrogeneDB ID: retro_cfam_267

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:73361320..73361652(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5S
• Ensembl ID: ENSCAFG00000014285
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit s (factor B) [Source:HGNC Symbol;Acc:18799]

Sequence

>retro_cfam_267
ATTGATGCCACCAACCCTTGTATCACAGGCGTTGCATTTGATCACTTAAGCGCTTAGAGCATGTTGGAAAAATAAGGCTA
GGAGCGTGTCATTAAATCAAGGTCCATGGCTTGGAGAGACTTAGTAAACTTGAAATTTTACAAAAAAGCATGTTGGAAAT
GGAAACAATTTCATGTGGAAATATCTCAGACAAGGACATCATTGCTTTACATCGCTTAAGAAACCTCAACTATTTGTTGT
TAAGTGATCTTCCTGGAATGAGAGAAAAAGGAAACCTTATCCAAGCCTTTAAGACAACACTGCCTTCTCTGGAATCAAAA
TTGGACTTGAAA

Alignment

ORF - retro_cfam_267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.54 %
• Parental protein coverage: 53.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDATDSCIMSFGFDHLEG-LQHVEKIRLCKCHYIEDNCLERLGKLENLQKSILEMEIISCGNITDKGIMA
          IDAT..CI....FDHL...L.HV.KIRL..CH.I....LERL.KLE.LQKS.LEME.ISCGNI.DK.I.A
Retrocopy IDATNPCITGVAFDHLSA<LEHVGKIRLGACH*IKVHGLERLSKLEILQKSMLEMETISCGNISDKDIIA

Parental  LYHLRNLKYLLLSDLPGVREKENLIQIFKTALPSLELKLDLK
          L..LRNL.YLLLSDLPG.REK.NLIQ.FKT.LPSLE.KLDLK
Retrocopy LHRLRNLNYLLLSDLPGMREKGNLIQAFKTTLPSLESKLDLK

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	5.50 RPM
SRP017611_brain	0.00 RPM	6.75 RPM
SRP017611_kidney	0.00 RPM	13.54 RPM
SRP017611_liver	0.00 RPM	3.63 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_267 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_267 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_267 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009828	1 retrocopy	retro_amel_377,
Canis familiaris	ENSCAFG00000014285	1 retrocopy	retro_cfam_267 ,
Cavia porcellus	ENSCPOG00000014471	1 retrocopy	retro_cpor_740,
Felis catus	ENSFCAG00000029962	1 retrocopy	retro_fcat_72,
Loxodonta africana	ENSLAFG00000013773	1 retrocopy	retro_lafr_167,
Pteropus vampyrus	ENSPVAG00000006173	1 retrocopy	retro_pvam_539,
Sorex araneus	ENSSARG00000007707	1 retrocopy	retro_sara_694,