RetrogeneDB - Retrocopy retro_dnov

						
>retro_dnov_3
GCACCATACTGGACATTCCTTTTATGTGCCCTGGGACTCTTTTTCTACCAGTCACTGGATGCAATTGATGGGAAACAAGC

CAGAAGAACAAATTCTTGTTCTCCTTTAGGGGAACTTTTTGACCGTGGTGGTGACTCTCTTTCCACAGTGTTAATGGCAG

TTGGAGCATCAATTGCTGTTCGCTTAGGAACCCATCCTGACTGGTTGTTTTTCTGCTCTTTTATTGGAATGTTCATGTTT

TATTGTGCTCACGGGCAGACTTATGTTTCAGGCGTATTGAGGTTTGGAAAAGTGGATGTAACTGAAATCCAGGTAGGTTT

AATAATCGTCTTTGTGTTGTCTACATTTGGAGGAGCAACAATGTGGGACTATACGATACCCATTCTAGAAATAAAATTGA

AGATTGTTCCAGTTCTTGGAGTAGTAGGTGGAGCAGTTTTTTCCTGTTCAAATTATTTCCATGTTATCCTTCATGGTAGT

GTTGGCAAGAATGGATCTACTATAGCAGGCACCAGTGTCTTGTCACCTGGACTCCACATTGGACTAATTATCATACTGGC

AATAATGATCTATAAAAAGTCAGCAACTAATGTGTTTGAAAAACATCCTTGTCTTTATACCTTAATGTTTGGATGTGTCT

TTGCTAAAGTTGCACAAAAACTAGTGGTAGCTCACATGATGAAAAGTGAACTATACCTTCAAGACACTGTGTTCATTGGG

CCAGCTCTTTTATTTTTAGATCAATACTTTAATAATTTTGTAGATGAATATATTGTTCTCTGGATAGCAATGGTCATTGC

TTCATTTGATATGACGGCATACTTTAGTGCTTTGTGCCTGCAAATTTCAAGACACCTTCATATAAATATCTTCAAGACTT

CATGTCATCAAGCACCTGAACAGGTTCAAGTTCTTGCTTCAAAGAATCATCAGAATAATATGGACTGA

ORF - retro_dnov_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	66.44 %
Parental protein coverage:	74.87 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalAPLWAYIACACGLFIYQSLDAIDGKQARRTNSSSPLGELFDHGCDSLSTVFVVLGTCIAVQLGTNPDWMF
		AP.W....CA.GLF.YQSLDAIDGKQARRTNS.SPLGELFD.G.DSLSTV....G..IAV.LGT.PDW.F
RetrocopyAPYWTFLLCALGLFFYQSLDAIDGKQARRTNSCSPLGELFDRGGDSLSTVLMAVGASIAVRLGTHPDWLF
ParentalFCCFAGTFMFYCAHWQTYVSGTLRFGIIDVTEVQIFIIIMHLLAVIGGPPFWQSMIPVLNIQMKIFPALC
		FC.F.G.FMFYCAH.QTYVSG.LRFG..DVTE.Q...II...L...GG...W...IP.L.I..KI.P.L.
RetrocopyFCSFIGMFMFYCAHGQTYVSGVLRFGKVDVTEIQVGLIIVFVLSTFGGATMWDYTIPILEIKLKIVPVLG
ParentalTVAGTIFSCTNYFRVIFTGGVGKNGSTIAGTSVLSPFLHIGSVITLAAVIYKKSAVQLFEKHPCLYILTF
		.V.G..FSC.NYF.VI..G.VGKNGSTIAGTSVLSP.LHIG..I.LA..IYKKSA...FEKHPCLY.L.F
RetrocopyVVGGAVFSCSNYFHVILHGSVGKNGSTIAGTSVLSPGLHIGLIIILAIMIYKKSATNVFEKHPCLYTLMF
ParentalGFVSAKITNKLVVAHMTKSEMHLHDTAFIGPALLFLDQYFNSFIDEYIVLWIALVFSFFDLIRYCVSVCN
		G.V.AK...KLVVAHM.KSE..L.DT.FIGPALLFLDQYFN.F.DEYIVLWIA.V...FD...Y....C.
RetrocopyGCVFAKVAQKLVVAHMMKSELYLQDTVFIGPALLFLDQYFNNFVDEYIVLWIAMVIASFDMTAYFSALCL
ParentalQIASHLHIHVFR
		QI..HLHI..F.
RetrocopyQISRHLHINIFK

							

							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
SRP012922_ascending_colon	116 .10 RPM	39 .87 RPM
SRP012922_cerebellum	41 .65 RPM	28 .46 RPM
SRP012922_heart	73 .09 RPM	7 .43 RPM
SRP012922_kidney	127 .86 RPM	24 .09 RPM
SRP012922_liver	118 .27 RPM	34 .21 RPM
SRP012922_lung	92 .55 RPM	19 .09 RPM
SRP012922_quadricep_muscle	62 .31 RPM	7 .27 RPM
SRP012922_spleen	86 .19 RPM	38 .57 RPM

ChIP-Seq - click to see more details

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST - click to see more details

Dasypus novemcinctus was not studied using EST data.

TSS - click to see more details

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab - click to see more details

retro_dnov_3 was not experimentally validated.

Retrocopy orthology:

Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007908	3 retrocopies	retro_chof_1945, retro_chof_241, retro_chof_2710,
Dasypus novemcinctus	ENSDNOG00000017013	1 retrocopy	retro_dnov_3 ,
Otolemur garnettii	ENSOGAG00000010799	1 retrocopy	retro_ogar_2444,

	RetrogeneDB ID:	retro_dnov_3
Retrocopy location	Organism:	*Armadillo (Dasypus novemcinctus)*
	Coordinates:	scaffold_70711:7517..8465(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSDNOG00000008207
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	CEPT1
	Ensembl ID:	ENSDNOG00000017013
	Aliases:	None
	Description:	choline/ethanolamine phosphotransferase 1 [Source:HGNC Symbol;Acc:24289]

Parental	APLWAYIACACGLFIYQSLDAIDGKQARRTNSSSPLGELFDHGCDSLSTVFVVLGTCIAVQLGTNPDWMF
	AP.W....CA.GLF.YQSLDAIDGKQARRTNS.SPLGELFD.G.DSLSTV....G..IAV.LGT.PDW.F
Retrocopy	APYWTFLLCALGLFFYQSLDAIDGKQARRTNSCSPLGELFDRGGDSLSTVLMAVGASIAVRLGTHPDWLF

Parental	FCCFAGTFMFYCAHWQTYVSGTLRFGIIDVTEVQIFIIIMHLLAVIGGPPFWQSMIPVLNIQMKIFPALC
	FC.F.G.FMFYCAH.QTYVSG.LRFG..DVTE.Q...II...L...GG...W...IP.L.I..KI.P.L.
Retrocopy	FCSFIGMFMFYCAHGQTYVSGVLRFGKVDVTEIQVGLIIVFVLSTFGGATMWDYTIPILEIKLKIVPVLG

Parental	TVAGTIFSCTNYFRVIFTGGVGKNGSTIAGTSVLSPFLHIGSVITLAAVIYKKSAVQLFEKHPCLYILTF
	.V.G..FSC.NYF.VI..G.VGKNGSTIAGTSVLSP.LHIG..I.LA..IYKKSA...FEKHPCLY.L.F
Retrocopy	VVGGAVFSCSNYFHVILHGSVGKNGSTIAGTSVLSPGLHIGLIIILAIMIYKKSATNVFEKHPCLYTLMF

Parental	GFVSAKITNKLVVAHMTKSEMHLHDTAFIGPALLFLDQYFNSFIDEYIVLWIALVFSFFDLIRYCVSVCN
	G.V.AK...KLVVAHM.KSE..L.DT.FIGPALLFLDQYFN.F.DEYIVLWIA.V...FD...Y....C.
Retrocopy	GCVFAKVAQKLVVAHMMKSELYLQDTVFIGPALLFLDQYFNNFVDEYIVLWIAMVIASFDMTAYFSALCL

Parental	QIASHLHIHVFR
	QI..HLHI..F.
Retrocopy	QISRHLHINIFK

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

RetrogeneDB ID:

retro_dnov_3