RetrogeneDB ID: retro_cfam_1834

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 7:9275065..9275526(+)
• Located in intron of: ENSCAFG00000012077

Retrocopy information

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

Parental gene information

• Parental gene symbol: C16orf13
• Ensembl ID: ENSCAFG00000019655
• Aliases: None
• Description: chromosome 16 open reading frame 13 [Source:HGNC Symbol;Acc:14141]

Sequence

>retro_cfam_1834
CCCCGTGCCAAAAAACCAGCTGTGGACGTGGACTAGCGCTTCATGGATAGCATCTCAGTCACCAGTCAGGCTCAGGGACT
GTCCAATGCGAAGGCCCCATTGTAGCTGGACATGATCTGGGATTGGAAGCAGTGGGGCAGGATCCTGCCACGGTCGCTGG
ACTTGCTGCTCATCATCAACATGATCTGCATCAACCCCCTGAAATGCACGGAGAGGCTCTAGAGAGCAGAAGGGCACCTG
CTCTCACCCAAGGCATCGCTGATCACTGCTGGGCCCTATAAAATCAATGGGAGATCACTCCACAGAGTAATATAGATTTT
GACCTAACCCTTAGAAGTAGTCTCTGGAAGTGGGGGCTGTGGGAAAGAGCGCTCCTAGAGGACCTGAGCCAAGCCAGTGG
CCTGCTCCTGGAGAGAAGGATGGATATGCCAGCCAACAAGTACTTCATATTCCGGAAAGAC

Alignment

ORF - retro_cfam_1834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.59 %
• Parental protein coverage: 81.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPAEWQPSDVDQRCLDSISATTRAQGLSNVKAPLYLDVTWDWEHWGGILPQSLDLLLCINMIHISPLSCT
          P.A.....DVD.R..DSIS.T..AQGLSN.KAPL.LD..WDW..WG.ILP.SLDLLL.INMI.I.PL.CT
Retrocopy PRAKKPAVDVD*RFMDSISVTSQAQGLSNAKAPL*LDMIWDWKQWGRILPRSLDLLLIINMICINPLKCT

Parental  EGLFRAAGHLLKPKALLITYGPYAVNGR-ITPQSNVDFDLTLRCRNPEWGLRDTALLEDLGQASGLLLER
          E.L.RA.GHLL.PKA.LIT.GPY..NGR.ITPQSN.DFDLTLR.....WGL...ALLEDL.QASGLLLER
Retrocopy ERL*RAEGHLLSPKASLITAGPYKINGR<ITPQSNIDFDLTLRSSLWKWGLWERALLEDLSQASGLLLER

Parental  MVDMPANNKCLIFRKE
          ..DMPA.NK..IFRK.
Retrocopy RMDMPA-NKYFIFRKD

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	0.13 RPM	30.91 RPM
SRP017611_brain	0.08 RPM	33.19 RPM
SRP017611_kidney	0.07 RPM	44.91 RPM
SRP017611_liver	0.07 RPM	13.56 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1834 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1834 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1834 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019655	1 retrocopy	retro_cfam_1834 ,
Felis catus	ENSFCAG00000024937	1 retrocopy	retro_fcat_1783,
Tursiops truncatus	ENSTTRG00000009231	1 retrocopy	retro_ttru_184,