RetrogeneDB - Retrocopy retro_dnov

						
>retro_dnov_1567
GTGACCATCATCTCCCTCTCCTCCCTCATGGGGGCCTGTGTGGTGCTCTTCATGAAGAAGATTTTTTACAAGAGGCTGCT

GCTCTACTTCCTAGCTCTAGTGATTGAAACCCTCTACTTCAATGCTGTCTTCCTGTTCATCCCCGAGACTTTAGGTTTCA

ACCCTCAGGAAGATTCTTATGTCTCGAAGTCTGCAGTGGTGTTTGGGGGATTTTATCTTTTCTTTTTCACAGAGAAGATT

TTGAGAGATGCTTCTTAAACACAAAAAAATGAGCATCATCATGGACATAACAATTTTGCCTCTGATGAGCCTTCCAAGAA

GGACCAGGAGGAGGGTATAACTGAGACACTGCAGAATGGGGATCTGGACCACATGATTCCTCAACCCCAGAACAGTGAGC

TAGATGGCAAGACCCCCAGAATTGATGAGAAGGTCTTCATGGGTTCACTGTCTGTCCAGGACCTCCAGGCTTCCAGAGTG

CATGCTCCTGGCTAAAAGGTGTCCACCACCCTCATATCAGCACTCTGGCCTGGCTGATCACTCTGAACGATGGCCTCCAC

AATTTCACTGATGACTTGGCAATTGGTGCCTCTTTTACCATCTCTGTTGTCCAAAGCATCAGCACTTCAGTGGCCATCCT

CTGTGAGGAGTTTCCCCAGGAGCTGGGAGACTTTGTCATCCTGCTCAATGCCGGGATGAGTATCCAGAAGGCCCTCTTCT

TCAATTTCCTTTCTGCCTGTTGCTGTTACCTTGGCCTGACCTTCAGGATCATAGCTGGCAGTCACTTTTCTGCCAACGGG

ATCTTTGCACTAGCTGGAGGAATGTTCTTGCATATTTCTCTGGCTGACATATTCCCTGAAATGAATGAAGTCTGTCAAGA

GAATCAAAGG

ORF - retro_dnov_1567 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	82.21 %
Parental protein coverage:	60.04 %
Number of stop codons detected:	1
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalVTIISLCALMGACVVPFMKKTFYKRLLLYFIALAIGTLYSNALFQLIPEAFGFNPKEDNYVSKSAVVFGG
		VTIISL..LMGACVV.FMKK.FYKRLLLYF.AL.I.TLY.NA.F..IPE..GFNP.ED.YVSKSAVVFGG
RetrocopyVTIISLSSLMGACVVLFMKKIFYKRLLLYFLALVIETLYFNAVFLFIPETLGFNPQEDSYVSKSAVVFGG
ParentalFYLFFFTEKILKMLL-KQKNEHHHGHNHFASDEPSKKDQEEGVTEKLQNGDLDHMIPQPRNSELDGKALR
		FYLFFFTEKIL......QKNEHHHGHN.FASDEPSKKDQEEG.TE.LQNGDLDHMIPQP.NSELDGK..R
RetrocopyFYLFFFTEKILRDAS*TQKNEHHHGHNNFASDEPSKKDQEEGITETLQNGDLDHMIPQPQNSELDGKTPR
ParentalVDEKVISGSLSVQDLQAS-QSACSWLKGVRYSDIGTLAWMITLSDGLHNFIDGLAIGASFTVSVFQGIST
		.DEKV..GSLSVQDLQAS.QSACSWLKGV....I.TLAW.ITL.DGLHNF.D.LAIGASFT.SV.Q.IST
RetrocopyIDEKVFMGSLSVQDLQAS<QSACSWLKGVHHPHISTLAWLITLNDGLHNFTDDLAIGASFTISVVQSIST
ParentalSVAILCEEFPHELGDFVILLNAGMSIQQALFFNFLSACCCYLGLAFGIVAGSHFSANWIFALAGGMFLYI
		SVAILCEEFP.ELGDFVILLNAGMSIQ.ALFFNFLSACCCYLGL.F.I.AGSHFSAN.IFALAGGMFL.I
RetrocopySVAILCEEFPQELGDFVILLNAGMSIQKALFFNFLSACCCYLGLTFRIIAGSHFSANGIFALAGGMFLHI
ParentalSLADMFPEMNEVCQEDER
		SLAD.FPEMNEVCQE..R
RetrocopySLADIFPEMNEVCQENQR

							

							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 .39 RPM	91 .79 RPM
SRP012922_cerebellum	0 .00 RPM	11 .82 RPM
SRP012922_heart	0 .00 RPM	15 .31 RPM
SRP012922_kidney	0 .27 RPM	7 .12 RPM
SRP012922_liver	0 .00 RPM	157 .59 RPM
SRP012922_lung	0 .00 RPM	7 .94 RPM
SRP012922_quadricep_muscle	0 .00 RPM	4 .67 RPM
SRP012922_spleen	0 .00 RPM	11 .22 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_1567 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013599	1 retrocopy	retro_dnov_1964,
Dasypus novemcinctus	ENSDNOG00000018834	1 retrocopy	retro_dnov_1567 ,
Homo sapiens	ENSG00000104635	1 retrocopy	retro_hsap_322,
Gorilla gorilla	ENSGGOG00000003765	1 retrocopy	retro_ggor_348,
Nomascus leucogenys	ENSNLEG00000015557	1 retrocopy	retro_nleu_1765,

	RetrogeneDB ID:	retro_dnov_1567
Retrocopy location	Organism:	*Armadillo (Dasypus novemcinctus)*
	Coordinates:	scaffold_235989:544..1434(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	SLC39A14
	Ensembl ID:	ENSDNOG00000018834
	Aliases:	None
	Description:	solute carrier family 39 (zinc transporter), member 14 [Source:HGNC Symbol;Acc:20858]

Parental	VTIISLCALMGACVVPFMKKTFYKRLLLYFIALAIGTLYSNALFQLIPEAFGFNPKEDNYVSKSAVVFGG
	VTIISL..LMGACVV.FMKK.FYKRLLLYF.AL.I.TLY.NA.F..IPE..GFNP.ED.YVSKSAVVFGG
Retrocopy	VTIISLSSLMGACVVLFMKKIFYKRLLLYFLALVIETLYFNAVFLFIPETLGFNPQEDSYVSKSAVVFGG

Parental	FYLFFFTEKILKMLL-KQKNEHHHGHNHFASDEPSKKDQEEGVTEKLQNGDLDHMIPQPRNSELDGKALR
	FYLFFFTEKIL......QKNEHHHGHN.FASDEPSKKDQEEG.TE.LQNGDLDHMIPQP.NSELDGK..R
Retrocopy	FYLFFFTEKILRDAS*TQKNEHHHGHNNFASDEPSKKDQEEGITETLQNGDLDHMIPQPQNSELDGKTPR

Parental	VDEKVISGSLSVQDLQAS-QSACSWLKGVRYSDIGTLAWMITLSDGLHNFIDGLAIGASFTVSVFQGIST
	.DEKV..GSLSVQDLQAS.QSACSWLKGV....I.TLAW.ITL.DGLHNF.D.LAIGASFT.SV.Q.IST
Retrocopy	IDEKVFMGSLSVQDLQAS<QSACSWLKGVHHPHISTLAWLITLNDGLHNFTDDLAIGASFTISVVQSIST

Parental	SVAILCEEFPHELGDFVILLNAGMSIQQALFFNFLSACCCYLGLAFGIVAGSHFSANWIFALAGGMFLYI
	SVAILCEEFP.ELGDFVILLNAGMSIQ.ALFFNFLSACCCYLGL.F.I.AGSHFSAN.IFALAGGMFL.I
Retrocopy	SVAILCEEFPQELGDFVILLNAGMSIQKALFFNFLSACCCYLGLTFRIIAGSHFSANGIFALAGGMFLHI

Parental	SLADMFPEMNEVCQEDER
	SLAD.FPEMNEVCQE..R
Retrocopy	SLADIFPEMNEVCQENQR

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

RetrogeneDB ID:

retro_dnov_1567