RetrogeneDB ID: retro_cfam_1053

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:34495579..34496107(+)
• Located in intron of: None

Retrocopy information

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

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_1053
CTCCTTGGGACTACCATGCGCCAAGAAGGACTTCAGGCGTTCCTTGTGGAAGTTCACCAAGCCAATGCCTGTGGCCCTAC
TGCCCACTATCTTCAGCCCTAGGCAACAAGTTAGTCTTATTACAGTTTTGGAGATTCAGCTGCAACTCTGACTTCTAGGT
CCTACATGTTCAGAAGAAGGCTGGGTGTGGTGCTTCTGTGGTACACATTATGAATTCCAGTGAACTTTTTAAGATAGTAT
GAAATAGAGAAGAAATTCCACAGCAAATGTGAATTTCATTTGTAATTATTGGGAAGAGGAGCTCCAGGACAGACACTCTG
TCCACAAAAAGTGTTCAGATGCTTTTGGTTCCAGAAAATAGTTTCCCTTTGGGCTATTACCACATCCCCTTTCATAGGGA
CTGTGGGGCTAAGGGTTTTGGCCTTGGGAACAGTGACAGTAGTTTGTTGTACTTAGCCCTGTGTCTGGCCCCAGTTATAT
AGACTGACCAAAGAGCAAGTGAAACAGAATCCTACCCATAAGACCCAA

Alignment

ORF - retro_cfam_1053 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.75 %
• Parental protein coverage: 71.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LFGAALSQEGLQGFLVEAHPANACS-PIAPPPPAPVNGSVFIALLRRFDCNFDLKVLNAQK-AGYGAAVV
          L.G....QEGLQ.FLVE.H.ANAC..P..P...A..N..V.....R.F.CN.D..VL..QK.AG.GA.VV
Retrocopy LLGTTMRQEGLQAFLVEVHQANACG<PYCPLSSALGNKLVLLQFWR-FSCNSDF*VLHVQKKAGCGASVV

Parental  HNVNSNELLNMVWNSEEIQQQIWIPSVFIGERSSEYLRALFVYEKGARVLLVPDNSFPLGYYLI-PFTGI
          H..NS.EL...V.N.EEI.QQ..I..V.IG.RSS...R......K....LLVP.NSFPLGYY.I.PF.G.
Retrocopy HIMNSSELFKIV*NREEIPQQM*ISFVIIGKRSS---RTDTLSTKSVQMLLVPENSFPLGYYHI>PFIGT

Parental  VGLLVLAMGAVMVVRCIQHRKRLQRNRLSKEQLKQIPTHDYQ
          VGL.VLA.G.V.VV.C.......Q..RL.KEQ.KQ.PTH..Q
Retrocopy VGLRVLALGTVTVVCCT*PCVWPQLYRLTKEQVKQNPTHKTQ

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	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_1053 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1053 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1053 has 0 orthologous retrocopies within eutheria group .

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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,