RetrogeneDB - Retrocopy retro_cfam

                        
>retro_cfam_916
GCGCCCGCGGGGATCCCGGGGAACCCGCGGGAGGTCTCCAACCCCGCCAAGCCTGGCCGCAAGACCAAGCAGCTGCAGTA

CGCGCAGAACGTGGTGGTAAAGACGCCCTGGAATCACCAGCTCGCCTGGCCCTTCTACCAGCCCGTGGATGCAATCAAGC

TAAACCTGCCCGATTACCATAAAATCATAAACACCCGATGGCTATGGGGACTATTCAGAAGAGACTAGAAAATAATTATT

ACTGGAGCGCCAGCGAATGCGTGCAGGACTTCCACACCATGTTTACAAATTGTTACATTTACAACAAGCCCACAGATGAC

ACAGTGCTAACGGCCCAAGCCTTAGAGAAAATTTTTCTGCAGAGAGTGGCCCAGGTGCCCCAGGACGAAGTTGAATTATT

ACCCCCTGCTCCGAAGGGCAAAGGCCGGAACGCGGCGCAGGAACCCGGAGTGCAGGTGGGCAGCAAGTGGTGGCCGTGTC

CTCTGTCTCCCCAGCAACCCCCTTCCAGAGCGTCCCCCCACTGTCTCCAGACGCCTGTCATTGCTGCCCCCCCTCTGCCA

ACCATTACCGCAAACATCACGTCGGTCCCTGCGCCCCGGCCGCCGCCCCACCCCCTCCCTCGACGCCCATCATCCATCCC

TGTGGTCCCTCCCACAGCGCCTGTCGTCAAGGAAAAGGGTGCAAAGCGGAAAGCAGCCACCACGACGCCCACTCCATCCG

CGAGCCGGAGCGAATCGCCGCCGCCATCGTCAGACCCCAAGCAGGCCGAGGTGGGGGCTCGGCGAGAGAGTGGGGGCCGC

CCCATCGCACCGCCCTGGAAGGGTCTAGAGGACGGCGAGGTGCCTCAGCATGCGGGCCGGAAGGGCGAGCTGCCGAGCAC

TCGCGGCACTGTGACAGCGTCCTCGAGGACATGCCGTGCAAGAAGCGTGCGGCCTGCGCCTGGCCCTTCTCCAGCCGGTG

GACGCCGAGGCCCTGGAGCTGCACGACTACCACGACGTCACCGAGCACCCGATGGACCTCAGCACTGTCAAGAAGACGGA

CAGTCGCGAGTGCCCAGACGCGCAGGGCTTCGCTGCTGACACCCGGTTCATGTTCTCCAGCTGTTACCAGTACAACCCCC

AGGCCACAAGGTGGTG

ORF - retro_cfam_916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	79.7 %
Parental protein coverage:	52.75 %
Number of stop codons detected:	0
Number of frameshifts detected:	9

Retrocopy - Parental Gene Alignment:

                                ParentalAPGPVNPPPPEVSNPAKPGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKII-KNPMDM
AP......P.EVSNPAKPGRKT.QLQY.QNVVVKT.W.HQ.AWPFYQPVDAIKLNLPDYHKII.K.PM.M
RetrocopyAPAGIPGNPREVSNPAKPGRKTKQLQYAQNVVVKTPWNHQLAWPFYQPVDAIKLNLPDYHKII<KHPMAM
ParentalGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQEEVELLPPAPK
GTI.KRLENNYYWSASEC.QDF.TMFTNCYIYNKPTDD.VL.AQALEKIFLQ.VAQ.PQ.EVELLPPAPK
RetrocopyGTIQKRLENNYYWSASECVQDFHTMFTNCYIYNKPTDDTVLTAQALEKIFLQRVAQVPQDEVELLPPAPK
ParentalGKGRKPA-AGTQSAGTQQVVAVSSVSPATPFQSV-PPTVS-QTPVIAATPVPTITANITSVPVP-PAAAP
GKGR..A.AGT.SAG.QQVVAVSSVSPATPFQSV.PPTVS.QTPVIAA.P.PTITANITSVP.P.PAAAP
RetrocopyGKGRNAA<AGTRSAGGQQVVAVSSVSPATPFQSV<PPTVS<QTPVIAAPPLPTITANITSVPAP<PAAAP
ParentalPPPSTPII-PVVP-PTPPVVKKKGVKRKADTTTPTTSAITASRSESPPPLSDPKQAKVVARRESGGRPIK
PPPSTPII.P..P.PT.PVVK.KG.KRKA.TTTPT.SA...SRSESPPP.SDPKQA.V.ARRESGGRPI.
RetrocopyPPPSTPIIHPCGP>PTAPVVKEKGAKRKAATTTPTPSA---SRSESPPPSSDPKQAEVGARRESGGRPIA
ParentalPPKKDLEDGEVPQHAGKKGKL-SEHLRHCDSILKEMLSKKHAAYAWPF-YKPVDAEALELHDYHDIIKHP
PP.K.LEDGEVPQHAG.KG.L..EH.RHCDS.L..M..KK.AA.AWPF...PVDAEALELHDYHD...HP
RetrocopyPPWKGLEDGEVPQHAGRKGEL<AEHSRHCDSVLEDMPCKKRAACAWPF<LQPVDAEALELHDYHDVTEHP
ParentalMDLSTVKKKMDSREYPDAQGFAADIRLMFSNCYKYN-PPDHEVV
MDLSTV.KK.DSRE.PDAQGFAAD.R.MFS.CY.YN.PP.H.VV
RetrocopyMDLSTV-KKTDSRECPDAQGFAADTRFMFSSCYQYN<PPGHKVV

                            

                            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 .00 RPM	128 .98 RPM
SRP017611_brain	0 .00 RPM	36 .68 RPM
SRP017611_kidney	0 .00 RPM	34 .08 RPM
SRP017611_liver	0 .00 RPM	21 .39 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_916 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_916 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cfam_916 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019817	2 retrocopies	retro_cfam_915, retro_cfam_916 ,

	RetrogeneDB ID:	retro_cfam_916
Retrocopy location	Organism:	*Dog (Canis familiaris)*
	Coordinates:	2:5388415..5389551(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	None
	Ensembl ID:	ENSCAFG00000019817
	Aliases:	None
	Description:	None

Parental	APGPVNPPPPEVSNPAKPGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKII-KNPMDM
	AP......P.EVSNPAKPGRKT.QLQY.QNVVVKT.W.HQ.AWPFYQPVDAIKLNLPDYHKII.K.PM.M
Retrocopy	APAGIPGNPREVSNPAKPGRKTKQLQYAQNVVVKTPWNHQLAWPFYQPVDAIKLNLPDYHKII<KHPMAM

Parental	GTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQEEVELLPPAPK
	GTI.KRLENNYYWSASEC.QDF.TMFTNCYIYNKPTDD.VL.AQALEKIFLQ.VAQ.PQ.EVELLPPAPK
Retrocopy	GTIQKRLENNYYWSASECVQDFHTMFTNCYIYNKPTDDTVLTAQALEKIFLQRVAQVPQDEVELLPPAPK

Parental	GKGRKPA-AGTQSAGTQQVVAVSSVSPATPFQSV-PPTVS-QTPVIAATPVPTITANITSVPVP-PAAAP
	GKGR..A.AGT.SAG.QQVVAVSSVSPATPFQSV.PPTVS.QTPVIAA.P.PTITANITSVP.P.PAAAP
Retrocopy	GKGRNAA<AGTRSAGGQQVVAVSSVSPATPFQSV<PPTVS<QTPVIAAPPLPTITANITSVPAP<PAAAP

Parental	PPPSTPII-PVVP-PTPPVVKKKGVKRKADTTTPTTSAITASRSESPPPLSDPKQAKVVARRESGGRPIK
	PPPSTPII.P..P.PT.PVVK.KG.KRKA.TTTPT.SA...SRSESPPP.SDPKQA.V.ARRESGGRPI.
Retrocopy	PPPSTPIIHPCGP>PTAPVVKEKGAKRKAATTTPTPSA---SRSESPPPSSDPKQAEVGARRESGGRPIA

Parental	PPKKDLEDGEVPQHAGKKGKL-SEHLRHCDSILKEMLSKKHAAYAWPF-YKPVDAEALELHDYHDIIKHP
	PP.K.LEDGEVPQHAG.KG.L..EH.RHCDS.L..M..KK.AA.AWPF...PVDAEALELHDYHD...HP
Retrocopy	PPWKGLEDGEVPQHAGRKGEL<AEHSRHCDSVLEDMPCKKRAACAWPF<LQPVDAEALELHDYHDVTEHP

Parental	MDLSTVKKKMDSREYPDAQGFAADIRLMFSNCYKYN-PPDHEVV
	MDLSTV.KK.DSRE.PDAQGFAAD.R.MFS.CY.YN.PP.H.VV
Retrocopy	MDLSTV-KKTDSRECPDAQGFAADTRFMFSSCYQYN<PPGHKVV

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

RetrogeneDB ID:

retro_cfam_916