RetrogeneDB ID: retro_cfam_1718

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:1023677..1024082(+)
• Located in intron of: ENSCAFG00000009799

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB7
• Ensembl ID: ENSCAFG00000016258
• Aliases: None
• Description: None

Sequence

>retro_cfam_1718
GGGGCGCGTCTGGGCCGGTGCTGTGTGAGCCATCCCTCAGGGAAGCCTGACCGCAAGCAGATGCCCACCTCCCGCCAGAC
TAAGGTTTCCGGGGCACAGGGAGCACGAGATGGTGGTCCCGCGGCAGCAGATGAACGCCATGCAGCTGGTACTCCAGCAG
CGACACTCTGTGCCCACCACCTCATCCGGCTGCTCAATGCAAGCGGGACAGCCTCCCCAACTCCCCGGCCTGCAAGCCTG
AGCAGCGCCACTGGGACTGCCGCGAGCACCTTGACTGCATGATGCACGTGAAGGAGTTTGAGTGGAACGGCAACTGCTCC
AGTGGAAGAAGCGGCAGAGCAGAGGGAGGCGACAGATGTGGCCAGAGGCCAGGGAGCTGGGGAGGTGGCCCCCGGGATAG
TCCTG

Alignment

ORF - retro_cfam_1718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.38 %
• Parental protein coverage: 99.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GAHPARRYVTDPSGEPDPK-RMPTFPADYGFPGRKEREMVATQQQMNDAQLVLQQRD-YCAHYLIRLL-K
          GA...R..V..PSG.PD.K.R.P..PA...FPG..E.EMV...QQMN..QLVLQQR...CAH.LIRLL..
Retrocopy GARLGRCCVSHPSGKPDRK>RCPP-PARLRFPGHREHEMVVPRQQMNAMQLVLQQRH<LCAHHLIRLL<Q

Parental  CKRDSFPNILACKHEQHDWDYCEHLDYVMRMKEFE-RERRLLQRKKRR-EQREA-DVARGQGAGEVAPEV
          CKRDS.PN..ACK.EQ..WD..EHLD..M..KEFE..ER.LLQ.KKR..EQREA.DVARGQGAGEVAP..
Retrocopy CKRDSLPNSPACKPEQRHWDCREHLDCMMHVKEFE<VERQLLQWKKRQ<EQREATDVARGQGAGEVAPGI

Parental  AL
          .L
Retrocopy VL

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	24.11 RPM
SRP017611_brain	0.08 RPM	14.77 RPM
SRP017611_kidney	0.00 RPM	59.37 RPM
SRP017611_liver	0.00 RPM	17.40 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1718 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1718 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1718 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011470	1 retrocopy	retro_amel_1288,
Canis familiaris	ENSCAFG00000016258	1 retrocopy	retro_cfam_1718 ,
Dipodomys ordii	ENSDORG00000015213	1 retrocopy	retro_dord_6,
Mus musculus	ENSMUSG00000033938	1 retrocopy	retro_mmus_2539,
Otolemur garnettii	ENSOGAG00000009615	1 retrocopy	retro_ogar_2154,