RetrogeneDB - Retrocopy retro_cfam

						
>retro_cfam_84
ATGGCGCCCGCGGCCTCCGCGCTCGGGGTGCTGCGGGCCGCGCTGCTGGCCGCCGTGCTGGGGGGGCCGGGCCCCGCCCG

CGCGCTCGTCCGCGCCTCCTCCGCGCACCGCCGCCGCATGGACTTCGCCGACCTCCCGGCCCTGTTCGGGGCGGCGCTGA

GCCGCGAGGGGCTGGAGGGCTTCCTGGTGGAGGCGCGGCCGCCCGACGCCTGCAGCGCCGTGGCCCCGCCGCCCCCGGGC

GCCGTGAACGGGTCGGTGTTCATCGCGCTGCTGCGGAGGTTCGGCTGCGACTTCGACCTGAAGGTCCTGAACGCCCAGCG

CGCGGGGTTCGGCGCCGCCGTGGTGCACAACGTGCACTCGGACGCGCTGCTGAGCATGGTGCGGGGCGGCGCCGAGGCGC

AGCAGCAGATCGCCATCCCGTCGGTGTTCGTGGGCGAGAGGAGCGCCGACTACCTGCGGGCCCTGTTCGTCTACGACAAG

GGGGCGCAGGTGCTGCTGGTGCCCGACGACAACCTGCTGCTGGGCTACTGCCTCATCCCCTTCACGGGGGTCGTGGGGCT

GCTGCTCGTGGCCTCGGGCGCGGGGCTGGTCGTGCGCTTCGTGCGGCACCAGGGGCGGCTCCGGCGCAGTCGGCTGACCC

GCGAGCAGCTGGAGCGGATCCCCACGCGCGACTACCAGCGGGGAGCCCCGGACGACGTGTGCGCCATCTGCCTGGACGCC

TACGAGGTCGGCGAGCGGCTGCGGGTGCTGCCCTGCGCTCACGCCTACCACAGCCGCTGCGTGGACCCCTGGCTCACGCA

GACGCGCAGGACCTGCCCCGTGTGCAAGCAGCCCGTCCGCCGGAGCCCCGGGGCGGGGGGCCCGGGCCAGGAGACCCGGG

GGCAGGAGGAGGAGGGGGACGAGGCCGGGGCGCCGAGGGCACCCCCCGCCACCGAGCGGACGCCCCTCCTGGCCTCCAGC

CTCCCGCTTCCCGCCTCCTTCGGCTCCCTAGCCCCAGCCCCGGGTGGCGTTCCCGGGTCTGCAGGTGATCCGGCGCCCTC

CCCATCCTCCTCTTCCTCTTCTGCTGGTGTCCTGGTCTGA

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:

									ParentalMRPAAFPLPVV----VAAVLWGASPARALIRATSDHNASMDFADLPALFGAALSQEGLQGFLVEAHPANA
		M.PAA..L.V......AAVL.G..PARAL.RA.S.H...MDFADLPALFGAALS.EGL.GFLVEA.P..A
RetrocopyMAPAASALGVLRAALLAAVLGGPGPARALVRASSAHRRRMDFADLPALFGAALSREGLEGFLVEARPPDA
ParentalCSPIAPPPPAPVNGSVFIALLRRFDCNFDLKVLNAQKAGYGAAVVHNVNSNELLNMVWNSEEIQQQIWIP
		CS..APPPP..VNGSVFIALLRRF.C.FDLKVLNAQ.AG.GAAVVHNV.S..LL.MV....E.QQQI.IP
RetrocopyCSAVAPPPPGAVNGSVFIALLRRFGCDFDLKVLNAQRAGFGAAVVHNVHSDALLSMVRGGAEAQQQIAIP
ParentalSVFIGERSSEYLRALFVYEKGARVLLVPDNSFPLGYYLIPFTGIVGLLVLAMGAVMVVRCIQHRKRLQRN
		SVF.GERS..YLRALFVY.KGA.VLLVPD....LGY.LIPFTG.VGLL..A.GA..VVR...H..RL.R.
RetrocopySVFVGERSADYLRALFVYDKGAQVLLVPDDNLLLGYCLIPFTGVVGLLLVASGAGLVVRFVRHQGRLRRS
ParentalRLSKEQLKQIPTHDYQKG
		RL..EQL..IPT.DYQ.G
RetrocopyRLTREQLERIPTRDYQRG

							

							Legend:
							
								*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide

						

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_84 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_84 was not experimentally validated.

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

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,

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

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

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_cfam_84