RetrogeneDB ID: retro_cfam_1706

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:62270904..62271218(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19ORF70
• Ensembl ID: ENSCAFG00000018796
• Aliases: None
• Description: None

Sequence

>retro_cfam_1706
GGCATTGTGGCTGGGGCCACCATCCACTTGGTGTATGACTAGAAGTTCCTGGGGCCTAGCGAAAGAGCCAGACTGTCCTT
CAGAAGTCTAAGGAGGTAGCCCCACCCCAGTCATGAGCCAATTCACCCAGTACAGGCGTGAGCAGACCAGTCTCAAGACA
CCCCAAACCCCAGTCCCTCCGAAGTTTAACTCTCACATCTAATAAGTCTTAGAATTCAGGCATCATTCTGCTGATGTTGG
CTTTCTCGGTAGCCCCCTCCAAGGCCCCTAAGTACTCCAAGGAGGGCTGAGAATACCTGAAGGAGCAAATCAAG

Alignment

ORF - retro_cfam_1706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.41 %
• Parental protein coverage: 88.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GSVAGGAVYLVYDQELLGPSD-KSQAVLQRA-EEVVP-PAMYQLSQYVCEQTGLKMPQLPAPPKFNFHF-
          G.VAG....LVYD...LGPS..KSQ.VLQ...E...P.P.M.Q..QY..EQT.LK.PQ.P.PPKFN.H..
Retrocopy GIVAGATIHLVYD*KFLGPSE<KSQTVLQKSKEVAPP<PVMSQFTQYRREQTSLKTPQTPVPPKFNSHI>

Parental  RDTWNSGILTVMSALSVAPSKAREYSRDGWEYLKERIK
          ....NSGI...M.A.SVAPSKA..YS..G.EYLKE.IK
Retrocopy NKS*NSGIILLMLAFSVAPSKAPKYSKEG*EYLKEQIK

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	36.50 RPM
SRP017611_brain	0.00 RPM	20.01 RPM
SRP017611_kidney	0.00 RPM	102.62 RPM
SRP017611_liver	0.00 RPM	12.40 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1706 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1706 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1706 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018796	2 retrocopies	retro_cfam_1706 , retro_cfam_756,
Callithrix jacchus	ENSCJAG00000017076	2 retrocopies	retro_cjac_2329, retro_cjac_735,
Felis catus	ENSFCAG00000011836	1 retrocopy	retro_fcat_287,
Loxodonta africana	ENSLAFG00000026050	1 retrocopy	retro_lafr_1241,
Macaca mulatta	ENSMMUG00000028920	1 retrocopy	retro_mmul_251,
Monodelphis domestica	ENSMODG00000001268	1 retrocopy	retro_mdom_1960,
Mustela putorius furo	ENSMPUG00000006136	2 retrocopies	retro_mputfur_1001, retro_mputfur_217,
Procavia capensis	ENSPCAG00000006583	1 retrocopy	retro_pcap_106,
Tupaia belangeri	ENSTBEG00000013386	1 retrocopy	retro_tbel_1443,