RetrogeneDB ID: retro_cfam_84

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:86137669..86138749(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000019051
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RNF167
• Ensembl ID: ENSCAFG00000015830
• Aliases: None
• Description: ring finger protein 167 [Source:HGNC Symbol;Acc:24544]

Sequence

>retro_cfam_84
ATGGCGCCCGCGGCCTCCGCGCTCGGGGTGCTGCGGGCCGCGCTGCTGGCCGCCGTGCTGGGGGGGCCGGGCCCCGCCCG
CGCGCTCGTCCGCGCCTCCTCCGCGCACCGCCGCCGCATGGACTTCGCCGACCTCCCGGCCCTGTTCGGGGCGGCGCTGA
GCCGCGAGGGGCTGGAGGGCTTCCTGGTGGAGGCGCGGCCGCCCGACGCCTGCAGCGCCGTGGCCCCGCCGCCCCCGGGC
GCCGTGAACGGGTCGGTGTTCATCGCGCTGCTGCGGAGGTTCGGCTGCGACTTCGACCTGAAGGTCCTGAACGCCCAGCG
CGCGGGGTTCGGCGCCGCCGTGGTGCACAACGTGCACTCGGACGCGCTGCTGAGCATGGTGCGGGGCGGCGCCGAGGCGC
AGCAGCAGATCGCCATCCCGTCGGTGTTCGTGGGCGAGAGGAGCGCCGACTACCTGCGGGCCCTGTTCGTCTACGACAAG
GGGGCGCAGGTGCTGCTGGTGCCCGACGACAACCTGCTGCTGGGCTACTGCCTCATCCCCTTCACGGGGGTCGTGGGGCT
GCTGCTCGTGGCCTCGGGCGCGGGGCTGGTCGTGCGCTTCGTGCGGCACCAGGGGCGGCTCCGGCGCAGTCGGCTGACCC
GCGAGCAGCTGGAGCGGATCCCCACGCGCGACTACCAGCGGGGAGCCCCGGACGACGTGTGCGCCATCTGCCTGGACGCC
TACGAGGTCGGCGAGCGGCTGCGGGTGCTGCCCTGCGCTCACGCCTACCACAGCCGCTGCGTGGACCCCTGGCTCACGCA
GACGCGCAGGACCTGCCCCGTGTGCAAGCAGCCCGTCCGCCGGAGCCCCGGGGCGGGGGGCCCGGGCCAGGAGACCCGGG
GGCAGGAGGAGGAGGGGGACGAGGCCGGGGCGCCGAGGGCACCCCCCGCCACCGAGCGGACGCCCCTCCTGGCCTCCAGC
CTCCCGCTTCCCGCCTCCTTCGGCTCCCTAGCCCCAGCCCCGGGTGGCGTTCCCGGGTCTGCAGGTGATCCGGCGCCCTC
CCCATCCTCCTCTTCCTCTTCTGCTGGTGTCCTGGTCTGA

Alignment

ORF - retro_cfam_84 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.86 %
• Parental protein coverage: 89.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRPAAFPLPVV----VAAVLWGASPARALIRATSDHNASMDFADLPALFGAALSQEGLQGFLVEAHPANA
          M.PAA..L.V......AAVL.G..PARAL.RA.S.H...MDFADLPALFGAALS.EGL.GFLVEA.P..A
Retrocopy MAPAASALGVLRAALLAAVLGGPGPARALVRASSAHRRRMDFADLPALFGAALSREGLEGFLVEARPPDA

Parental  CSPIAPPPPAPVNGSVFIALLRRFDCNFDLKVLNAQKAGYGAAVVHNVNSNELLNMVWNSEEIQQQIWIP
          CS..APPPP..VNGSVFIALLRRF.C.FDLKVLNAQ.AG.GAAVVHNV.S..LL.MV....E.QQQI.IP
Retrocopy CSAVAPPPPGAVNGSVFIALLRRFGCDFDLKVLNAQRAGFGAAVVHNVHSDALLSMVRGGAEAQQQIAIP

Parental  SVFIGERSSEYLRALFVYEKGARVLLVPDNSFPLGYYLIPFTGIVGLLVLAMGAVMVVRCIQHRKRLQRN
          SVF.GERS..YLRALFVY.KGA.VLLVPD....LGY.LIPFTG.VGLL..A.GA..VVR...H..RL.R.
Retrocopy SVFVGERSADYLRALFVYDKGAQVLLVPDDNLLLGYCLIPFTGVVGLLLVASGAGLVVRFVRHQGRLRRS

Parental  RLSKEQLKQIPTHDYQKG
          RL..EQL..IPT.DYQ.G
Retrocopy RLTREQLERIPTRDYQRG

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	30.37 RPM
SRP017611_brain	0.00 RPM	20.96 RPM
SRP017611_kidney	0.00 RPM	34.87 RPM
SRP017611_liver	0.00 RPM	18.56 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_84 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_84 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_84 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_583
Sus scrofa	retro_sscr_518

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006392	1 retrocopy	retro_amel_43,
Bos taurus	ENSBTAG00000004913	1 retrocopy	retro_btau_217,
Canis familiaris	ENSCAFG00000008370	1 retrocopy	retro_cfam_815,
Canis familiaris	ENSCAFG00000015830	2 retrocopies	retro_cfam_1053, retro_cfam_84 ,
Dipodomys ordii	ENSDORG00000011757	2 retrocopies	retro_dord_277, retro_dord_432,
Equus caballus	ENSECAG00000021567	1 retrocopy	retro_ecab_583,
Felis catus	ENSFCAG00000011173	1 retrocopy	retro_fcat_99,
Mustela putorius furo	ENSMPUG00000010940	1 retrocopy	retro_mputfur_95,
Pteropus vampyrus	ENSPVAG00000003781	1 retrocopy	retro_pvam_1206,
Sorex araneus	ENSSARG00000011216	1 retrocopy	retro_sara_517,
Sus scrofa	ENSSSCG00000017906	1 retrocopy	retro_sscr_518,
Tursiops truncatus	ENSTTRG00000001298	1 retrocopy	retro_ttru_1062,