RetrogeneDB ID: retro_cfam_1052

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:33708874..33709339(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000029587
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDUFS3
• Ensembl ID: ENSCAFG00000008411
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7710]

Sequence

>retro_cfam_1052
CCCACTGTCAGACCACGGAATGATGTGGCTCACAAGCAGCTCTCAGCATTTGGAGAGTATGTGGCTGAAATCCTGCCCAA
GTATGTCCAACAAGTTCAGGTGTTCTGCTTCAATGAGTTAGAGATCTGTATCCATCCTGATGGGGTCATCCCAGTGCTGA
CTTTCCTCAGGGATCACACCAGTGCACCATTTCAATCCTTGGCTGACTTGACAGCAGTGGACATCCCCACCTGGCAGAAC
CATTTTGAGATTGTTTACAACCTGCTTTCTCTGCGTTTCAACTCTTGGATCTGTGTGAGGACTTATACAGATGAGCTGAC
ACCCATTGAGTTCACTGTTTCTGTGTATAAGGCAGCTAACTGGTATGTGAGAGAGATCTGGGACTTGTTTGGAGTCTTCT
TTGCTAACCACCCTGACCTAAGAAGGACCCTGACAGACTATGGCTTTGAAGGACATCCTTTCCGG

Alignment

ORF - retro_cfam_1052 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.61 %
• Parental protein coverage: 58.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PTVRPRNDVAHKQLSAFGEYVAEILPKYVQQVQVSCFNELEICIHPDGVIPVLTFLRDHTNAQFKSLADL
          PTVRPRNDVAHKQLSAFGEYVAEILPKYVQQVQV.CFNELEICIHPDGVIPVLTFLRDHT.A.F.SLADL
Retrocopy PTVRPRNDVAHKQLSAFGEYVAEILPKYVQQVQVFCFNELEICIHPDGVIPVLTFLRDHTSAPFQSLADL

Parental  TAVDIPTRQNRFEIVYNLLSLRFNSRIRVKTYTDELTPIESTVSVYKAANWYEREIWDMFGVFFANHPDL
          TAVDIPT.QN.FEIVYNLLSLRFNS.I.V.TYTDELTPIE.TVSVYKAANWY.REIWD.FGVFFANHPDL
Retrocopy TAVDIPTWQNHFEIVYNLLSLRFNSWICVRTYTDELTPIEFTVSVYKAANWYVREIWDLFGVFFANHPDL

Parental  RRILTDYGFEGHPFR
          RR.LTDYGFEGHPFR
Retrocopy RRTLTDYGFEGHPFR

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	50.99 RPM
SRP017611_brain	0.00 RPM	48.59 RPM
SRP017611_kidney	0.07 RPM	74.03 RPM
SRP017611_liver	0.00 RPM	27.48 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1052 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1052 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1052 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008411	1 retrocopy	retro_cfam_1052 ,
Callithrix jacchus	ENSCJAG00000020194	1 retrocopy	retro_cjac_4059,
Equus caballus	ENSECAG00000013454	1 retrocopy	retro_ecab_431,
Erinaceus europaeus	ENSEEUG00000007356	1 retrocopy	retro_eeur_52,
Mus musculus	ENSMUSG00000005510	2 retrocopies	retro_mmus_2338, retro_mmus_792,