RetrogeneDB - Retrocopy retro_cfam

                        
>retro_cfam_322
TTCCATCTTTTACCCAGTAGAATAATTAACCCAAATGTTACTGCATTCATTGGAAATGCTGTGATAATTCATCTTCCCAG

ATTGAGGAAGCAGAGGAAAATGTCCAAAAAGGGAAAAGTCTAGAAGGCTAGGGAAAAAAAGGCCTATCATATCTGACAGT

GCTAACACTGTATTCAATTATCATCAAGCAACTGATGGTCTCCAGGAGCAACAGAGACAAGAATAAGCAAGGAAAAATGT

GAGTACCACAAAAAAGCACATTGGCCTAGTTTATTCTTCCAAAGCTACTGGGAGTGGACTGCAGATATATGATCTTGTTT

CTGACTCTGATGGCTTCTCTGAGAGGTTCAAAGTTCTGGCCAACCAATACAAATCATATACCCCACCCTGGAAATCAAGA

TTGAAAGTGAATTACAAAACCTCAAGAGCTATATGAAAAGGATTAAACCAATGGTGAGAGATAGAGTTTATTTCCTCAAG

GGGGCCCTACAGGGACCACCAAAGAAAATCTTGGTAGAAGATGTGAATGCAGCAGTACTAGATACAGATTTTGGAACTTA

TCCTTTTATAGCCTCTCTGAATCGTACAGTTGGAGGTGTCTATACCCAGTTGGCTATGCCCCCTCAAATACTGGAGATGT

GATGGGGTTGTGAAAGGTTACACAACTCAAGTTGGCATTGGTGCCTTCCCTACTTAGCAAAACAATGAAATTGGAGAATT

ATTACAAACACAAGGTGGAGAGTTTGGGGTAATCACTGAAAGGAAAAGAAAGTGTAGCTAGTTGGACCTCATTTTGCTCA

AATATGCTCCTATGATTAGTGAATTTCCTGCATTGGCACTTACCAAATTAAATATTTTGGACATGTTTATGGAAATCAAA

GTTGGAGTTGTTTACAAGTTAGATGGTGAAATCATACCTCATTTCCTAGCAAACCAAGAAGTCTTAAATAAAATTGAAGT

TCAATGTAAGACTCTCCTAGATTGGAGCACAGATATATCAATGCAAGGACATTTAAAGAACTACCTGTTAATGCACAAAA

TTACATTCAATTTATTGAAGATGAGCTTTAAATTCCAGGTAAATGGATCAGTGTAAGGAAATCCAGA

ORF - retro_cfam_322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	74.2 %
Parental protein coverage:	81.36 %
Number of stop codons detected:	4
Number of frameshifts detected:	5

Retrocopy - Parental Gene Alignment:

                                ParentalFHLLPSGIINPNVTAFIGNGVVIHLPGLFEEAEKNVQKG-KGLRGWEKRLIISDRAHIVFDFHQAADGIQ
FHLLPS.IINPNVTAFIGN.V.IHLP.L.....K...KG.K..R...KR.IISD.A..VF..HQA.DG.Q
RetrocopyFHLLPSRIINPNVTAFIGNAVIIHLPRL-RKQRKMSKKG>KSRRLGKKRPIISDSANTVFNYHQATDGLQ
ParentalEQQRQEQAGKNLGTTKKGIGPVYSSKAARSGLRMCDLVSDFDGFSERFKVLANQYKS-IYPTLEIDIEGE
EQQRQE.A.KN..TTKK.IG.VYSSKA..SGL...DLVSD.DGFSERFKVLANQYKS.IYPTLEI.IE.E
RetrocopyEQQRQE*ARKNVSTTKKHIGLVYSSKATGSGLQIYDLVSDSDGFSERFKVLANQYKS<IYPTLEIKIESE
ParentalLQKLKGYMERIKPMVRDGVYFLYEALHGPPKKILVEGANAALLDIDFGTYPFVTSSNCTVGGVCTGLGMP
LQ.LK.YM.RIKPMVRD.VYFL..AL.GPPKKILVE..NAA.LD.DFGTYPF..S.N.TVGGV.T.L.MP
RetrocopyLQNLKSYMKRIKPMVRDRVYFLKGALQGPPKKILVEDVNAAVLDTDFGTYPFIASLNRTVGGVYTQLAMP
ParentalPQ-NVGEVY-GVVKAYTTRVGIGAFPTEQDNEIGELLQTRGREFGVTTGRKRRCGWLDLVLLKYAHMING
PQ.N.G.V..GVVK.YTT.VGIGAFPT.Q.NEIGELLQT.G.EFGV.T.RKR.C..LDL.LLKYA.MI..
RetrocopyPQ<NTGDVM<GVVKGYTTQVGIGAFPT*QNNEIGELLQTQGGEFGVITERKRKCS*LDLILLKYAPMISE
ParentalFTALALTKLDILDMFTEIKVGVAYKLDGEIIPHFPANQEVLNKVEVQYKTLPGWNTDIS-NARTFKELPI
F.ALALTKL.ILDMF.EIKVGV.YKLDGEIIPHF.ANQEVLNK.EVQ.KTL..W.TDIS.NARTFKELP.
RetrocopyFPALALTKLNILDMFMEIKVGVVYKLDGEIIPHFLANQEVLNKIEVQCKTLLDWSTDIS<NARTFKELPV
ParentalNAQNYVRFIEDELQIPVKWIGVGKSR
NAQNY..FIEDEL.IP.KWI.V.KSR
RetrocopyNAQNYIQFIEDEL*IPGKWISVRKSR

                            

                            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	36 .62 RPM
SRP017611_brain	0 .00 RPM	66 .93 RPM
SRP017611_kidney	0 .00 RPM	78 .32 RPM
SRP017611_liver	0 .00 RPM	32 .34 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_322 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_322 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cfam_322 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015815	1 retrocopy	retro_cfam_322 ,
Myotis lucifugus	ENSMLUG00000017320	1 retrocopy	retro_mluc_1435,
Monodelphis domestica	ENSMODG00000006559	1 retrocopy	retro_mdom_1431,
Mustela putorius furo	ENSMPUG00000015741	1 retrocopy	retro_mputfur_1286,

	RetrogeneDB ID:	retro_cfam_322
Retrocopy location	Organism:	*Dog (Canis familiaris)*
	Coordinates:	1:81579424..81580531(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	ADSS
	Ensembl ID:	ENSCAFG00000015815
	Aliases:	None
	Description:	adenylosuccinate synthase [Source:HGNC Symbol;Acc:292]

Parental	FHLLPSGIINPNVTAFIGNGVVIHLPGLFEEAEKNVQKG-KGLRGWEKRLIISDRAHIVFDFHQAADGIQ
	FHLLPS.IINPNVTAFIGN.V.IHLP.L.....K...KG.K..R...KR.IISD.A..VF..HQA.DG.Q
Retrocopy	FHLLPSRIINPNVTAFIGNAVIIHLPRL-RKQRKMSKKG>KSRRLGKKRPIISDSANTVFNYHQATDGLQ

Parental	EQQRQEQAGKNLGTTKKGIGPVYSSKAARSGLRMCDLVSDFDGFSERFKVLANQYKS-IYPTLEIDIEGE
	EQQRQE.A.KN..TTKK.IG.VYSSKA..SGL...DLVSD.DGFSERFKVLANQYKS.IYPTLEI.IE.E
Retrocopy	EQQRQE*ARKNVSTTKKHIGLVYSSKATGSGLQIYDLVSDSDGFSERFKVLANQYKS<IYPTLEIKIESE

Parental	LQKLKGYMERIKPMVRDGVYFLYEALHGPPKKILVEGANAALLDIDFGTYPFVTSSNCTVGGVCTGLGMP
	LQ.LK.YM.RIKPMVRD.VYFL..AL.GPPKKILVE..NAA.LD.DFGTYPF..S.N.TVGGV.T.L.MP
Retrocopy	LQNLKSYMKRIKPMVRDRVYFLKGALQGPPKKILVEDVNAAVLDTDFGTYPFIASLNRTVGGVYTQLAMP

Parental	PQ-NVGEVY-GVVKAYTTRVGIGAFPTEQDNEIGELLQTRGREFGVTTGRKRRCGWLDLVLLKYAHMING
	PQ.N.G.V..GVVK.YTT.VGIGAFPT.Q.NEIGELLQT.G.EFGV.T.RKR.C..LDL.LLKYA.MI..
Retrocopy	PQ<NTGDVM<GVVKGYTTQVGIGAFPTQNNEIGELLQTQGGEFGVITERKRKCSLDLILLKYAPMISE

Parental	FTALALTKLDILDMFTEIKVGVAYKLDGEIIPHFPANQEVLNKVEVQYKTLPGWNTDIS-NARTFKELPI
	F.ALALTKL.ILDMF.EIKVGV.YKLDGEIIPHF.ANQEVLNK.EVQ.KTL..W.TDIS.NARTFKELP.
Retrocopy	FPALALTKLNILDMFMEIKVGVVYKLDGEIIPHFLANQEVLNKIEVQCKTLLDWSTDIS<NARTFKELPV

Parental	NAQNYVRFIEDELQIPVKWIGVGKSR
	NAQNY..FIEDEL.IP.KWI.V.KSR
Retrocopy	NAQNYIQFIEDEL*IPGKWISVRKSR

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

RetrogeneDB ID:

retro_cfam_322