RetrogeneDB - Retrocopy retro_dnov

						
>retro_dnov_1573
CTCGTAGCAGTAATATTAGCTGTTTTTGCACCTTTATTGTATGAAAAAGATTGAACTGGATGACAGCATCAGTGCCAGCA

GTGTTCCCACGGGCTGTCTCAGCCATCCACCCAGATGACTCGTATCTGAGAGCTGACACGCCCAACAATGCAACTCCCGT

TACCAGCTCCCCACGTTATCCTACTTTGTGGATCGAGAAGAACCTGAGAAGTGTCACTCTTTTGGAGGCCAAGGCCAAGG

TGAAAGATATAGCAATAACCAGAGAGAGGATGACTCTAAAAGATGTACTCCAAGAAGGTACTTTTGGGCATATTTTCCAT

GAGACTTTAATAGATGAAAAGATCCAAATAAAGAAAAACAAGCATTTGTAAAAACAGTTAAAGATCAAGCTTCTTGAAAT

TCAGGTGACAATGATGCTCACTGAAGTTGTAAGCTACGATGTCTTCATCACAGAAATCTTCCTATTACTGGTGTGTGTAT

AGAAGAAGGAGAAAAGCCCATGCCTTACATGAATTGGCGGAATCTTAAATTGTTCTTAAGGCAGTGCAAATTAGTAGAGG

CCAACAGTCCTCAGGCAATTTCTCAATAGGACCTGGAACACATGGCCATTCAGAATGCCTGCAGAATGAGCTATCTGGCC

AGAAGGGAAGTCACCCCCAAAGATCTAGCTGCTAGGAATTGTGTAATTGATGATACGCTTCAAGTGCAGATCACAGACGC

CGCCCTCTCAAGAGACTTGTTCCCCGTGGACTATCACTGTCAAGGGGACAGTGAAAACAGGCCAGTTTGATGGATGGCTC

TTGAAAGTCTAGTTAATAATGCGTTTTCCAGCACCAGTGATGTGTGGGCCTTGGGAGTGACGCTGTGGGAGCTCATGACT

CTGGGCCAAACGCCATATGTGGATCCCTTTGAGATGGCCGCATACCTGAGAGATGGTTACTGGATAGCC

ORF - retro_dnov_1573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	84.55 %
Parental protein coverage:	60.83 %
Number of stop codons detected:	2
Number of frameshifts detected	6

Retrocopy - Parental Gene Alignment:

									ParentalLVAIILAG-LHLRSMKRIELDDSISASS-SSQGLSQPSTQTTQ-YLRADTPNNATPITSSSGYPTLRIEK
		LVA.ILA..LHL..MK.IELDDSISASS..S.GLSQPSTQ.T..YLRADTPNNATP.TSS..YPTL.IEK
RetrocopyLVAVILAV>LHLYCMKKIELDDSISASS<CSHGLSQPSTQMTR<YLRADTPNNATPVTSSPRYPTLWIEK
ParentalNDLRSVTLLEAKAKVKDIAITRERITLKDVLQEGTFGRIFHGTL-DEK-DPNKEKQAFVKTVKDQAS-EI
		N.LRSVTLLEAKAKVKDIAITRER.TLKDVLQEGTFG.IFH.TL.DEK.DPNKEKQAFVKTVKDQAS.EI
RetrocopyN-LRSVTLLEAKAKVKDIAITRERMTLKDVLQEGTFGHIFHETLIDEK<DPNKEKQAFVKTVKDQAS>EI
ParentalQVTMMLTE-SCKLRGLHHRNLLPITHVCIEEGEKPMVILPYMNWGNLKLFLRQCKLVEANNPQAISQQDL
		QVTMMLTE.SCKLR.LHHRNL.PIT.VCIEEGEKPM...PYMNW.NLKLFLRQCKLVEAN.PQAISQ.DL
RetrocopyQVTMMLTE<SCKLRCLHHRNL-PITGVCIEEGEKPM---PYMNWRNLKLFLRQCKLVEANSPQAISQ*DL
ParentalVHMAIQIACGMSYLARREVIHKDLAARNCVIDDTLQVKITDNALSRDLFPMDYHCLGDNENRPVRWMALE
		.HMAIQ.AC.MSYLARREV..KDLAARNCVIDDTLQV.ITD.ALSRDLFP.DYHC.GD.ENRPV.WMALE
RetrocopyEHMAIQNACRMSYLARREVTPKDLAARNCVIDDTLQVQITDAALSRDLFPVDYHCQGDSENRPV*WMALE
ParentalSLVNNEFSSASDVWAFGVTLWELMTLGQTPYVDIDPFEMAAYLKDGYRIA
		SLVNN.FSS.SDVWA.GVTLWELMTLGQTPYVD..PFEMAAYL.DGY.IA
RetrocopySLVNNAFSSTSDVWALGVTLWELMTLGQTPYVD--PFEMAAYLRDGYWIA

							

							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	0 .19 RPM	46 .09 RPM
SRP012922_cerebellum	0 .14 RPM	26 .39 RPM
SRP012922_heart	0 .00 RPM	19 .95 RPM
SRP012922_kidney	0 .00 RPM	23 .82 RPM
SRP012922_liver	0 .00 RPM	23 .22 RPM
SRP012922_lung	0 .15 RPM	63 .23 RPM
SRP012922_quadricep_muscle	0 .17 RPM	26 .48 RPM
SRP012922_spleen	0 .23 RPM	57 .23 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_1573 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010657	1 retrocopy	retro_dnov_1573 ,

	RetrogeneDB ID:	retro_dnov_1573
Retrocopy location	Organism:	*Armadillo (Dasypus novemcinctus)*
	Coordinates:	scaffold_23813:10538..11487(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	RYK
	Ensembl ID:	ENSDNOG00000010657
	Aliases:	None
	Description:	receptor-like tyrosine kinase [Source:HGNC Symbol;Acc:10481]

Parental	LVAIILAG-LHLRSMKRIELDDSISASS-SSQGLSQPSTQTTQ-YLRADTPNNATPITSSSGYPTLRIEK
	LVA.ILA..LHL..MK.IELDDSISASS..S.GLSQPSTQ.T..YLRADTPNNATP.TSS..YPTL.IEK
Retrocopy	LVAVILAV>LHLYCMKKIELDDSISASS<CSHGLSQPSTQMTR<YLRADTPNNATPVTSSPRYPTLWIEK

Parental	NDLRSVTLLEAKAKVKDIAITRERITLKDVLQEGTFGRIFHGTL-DEK-DPNKEKQAFVKTVKDQAS-EI
	N.LRSVTLLEAKAKVKDIAITRER.TLKDVLQEGTFG.IFH.TL.DEK.DPNKEKQAFVKTVKDQAS.EI
Retrocopy	N-LRSVTLLEAKAKVKDIAITRERMTLKDVLQEGTFGHIFHETLIDEK<DPNKEKQAFVKTVKDQAS>EI

Parental	QVTMMLTE-SCKLRGLHHRNLLPITHVCIEEGEKPMVILPYMNWGNLKLFLRQCKLVEANNPQAISQQDL
	QVTMMLTE.SCKLR.LHHRNL.PIT.VCIEEGEKPM...PYMNW.NLKLFLRQCKLVEAN.PQAISQ.DL
Retrocopy	QVTMMLTE<SCKLRCLHHRNL-PITGVCIEEGEKPM---PYMNWRNLKLFLRQCKLVEANSPQAISQ*DL

Parental	VHMAIQIACGMSYLARREVIHKDLAARNCVIDDTLQVKITDNALSRDLFPMDYHCLGDNENRPVRWMALE
	.HMAIQ.AC.MSYLARREV..KDLAARNCVIDDTLQV.ITD.ALSRDLFP.DYHC.GD.ENRPV.WMALE
Retrocopy	EHMAIQNACRMSYLARREVTPKDLAARNCVIDDTLQVQITDAALSRDLFPVDYHCQGDSENRPV*WMALE

Parental	SLVNNEFSSASDVWAFGVTLWELMTLGQTPYVDIDPFEMAAYLKDGYRIA
	SLVNN.FSS.SDVWA.GVTLWELMTLGQTPYVD..PFEMAAYL.DGY.IA
Retrocopy	SLVNNAFSSTSDVWALGVTLWELMTLGQTPYVD--PFEMAAYLRDGYWIA

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

RetrogeneDB ID:

retro_dnov_1573