RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_488
ATAAGTCTGCTAAACTGTGAAAACAGCTGTGGATCCAGCCAGTCTCAAAGTGACTACTGTGTGGCCATGGCCAGCTCCTG

TAGCGCAGCAACAAAAAATGATAGTGTGGGCAGAACTGCCAGCACGGGGAACCTCTCCAGCTCCTTTATGGAGGAGATCC

AGGGATATGATGTAGAGTTTGGCCCACCCCTGGAAAGCAAGTATGAATGCCCCATCTGCTTGATGGCATTACGAGAAGCA

GTGCAAACTCCATGCAGCCATAGGTTCTGCAAAGCCTGCATCATAAAATCAATAAGGGATGCAGGTCACAAATATCCAGT

TGACAATGAAATACTGCTGGAAAATAAACTATTTCCAGACAATTTTGCAAAACGTGAGATTATTTCTCTGATAGTGAAGT

GTCCAAATGAAGGTTGTTTGCACAAGACGGAACTGAGACATCTTGAGGATCATCAAACACATTGTGAGTTTGCTCTTATG

GATTGTCCCCAATGCCAGCCTCCCTTCCAAAAATTCCATATTAATATTCACATTATGAAGGGTTGTCCAAGGAGGCAGGT

ATCTTGTGACAACTGTACTGCATCAATGGCATTTGAAGATAAAAAGATCCATGACCAGAACTGCCCTTTGGCAAATGTCA

TCTGTGAGTACTGCAATACTATACTCATCAGAGAACAGATGCCTAACTTTATGACCTAGACCGCCCTACAGCCCCAATTC

CATGCACATTCCGTACTTTTCGTAGCCATGAAAAGATGCAGAGGAATCACTTGGCACGCCACCTACAAGAGAACACCCAA

TCAAACATGAGAATGTTGGCCCAGGCTGTTCATAGTTTGAGCCTTATACCCTACTCTGGGTATATCTCAGAGGTCCGGAA

TTTCCAGGAAAGTATTCACCAGTTAGAGGGTCGCCTTGTAAGACAATGTCATCAAATCCGGGAGCTGACTGATAAAATGG

AAACTCAGAGTATGTATGTAAGTGAGCTCAAATGAACCATTCGAACCCTTGAGGACAAAGTTGCTGAAATTGAAGCACAG

CAGTGCAATGGAATTTACATTTGGAAGATTGGGAAT

ORF - retro_ptro_488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	91.67 %
Parental protein coverage:	68.77 %
Number of stop codons detected:	1
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalMSLLNCENSCGSSQSESDCCVAMASSCSAATKDDSVGGTASTGNLSSSFMEEIQGYDVEFDPPLESKYEC
		.SLLNCENSCGSSQS.SD.CVAMASSCSAATK.DSVG.TASTGNLSSSFMEEIQGYDVEF.PPLESKYEC
RetrocopyISLLNCENSCGSSQSQSDYCVAMASSCSAATKNDSVGRTASTGNLSSSFMEEIQGYDVEFGPPLESKYEC
ParentalPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREILSLMVKCPNEGCL
		PICLMALREAVQTPC.HRFCKACIIKSIRDAGHK.PVDNEILLEN.LFPDNFAKREI.SL.VKCPNEGCL
RetrocopyPICLMALREAVQTPCSHRFCKACIIKSIRDAGHKYPVDNEILLENKLFPDNFAKREIISLIVKCPNEGCL
ParentalHKMELRHLEDHQAHCEFALMDCPQCQRPFQKFHINIHILKDCPRRQVSCDNCAASMAFEDKEIHDQNCPL
		HK.ELRHLEDHQ.HCEFALMDCPQCQ.PFQKFHINIHI.K.CPRRQVSCDNC.ASMAFEDK.IHDQNCPL
RetrocopyHKTELRHLEDHQTHCEFALMDCPQCQPPFQKFHINIHIMKGCPRRQVSCDNCTASMAFEDKKIHDQNCPL
ParentalANVICEYCNTILIREQMPNH-YDLDCPTAPIPCTFSTFGCHEKMQRNHLARHLQENTQSHMRMLAQAVHS
		ANVICEYCNTILIREQMPN..YDLD.PTAPIPCTF.TF..HEKMQRNHLARHLQENTQS.MRMLAQAVHS
RetrocopyANVICEYCNTILIREQMPNF<YDLDRPTAPIPCTFRTFRSHEKMQRNHLARHLQENTQSNMRMLAQAVHS
ParentalLSLIPDSGYISEVRNFQETIHQLEGRLVRQDHQIRELTAKMETQSMYVSELKRTIRTLEDKVAEIEAQQC
		LSLIP.SGYISEVRNFQE.IHQLEGRLVRQ.HQIRELT.KMETQSMYVSELK.TIRTLEDKVAEIEAQQC
RetrocopyLSLIPYSGYISEVRNFQESIHQLEGRLVRQCHQIRELTDKMETQSMYVSELK*TIRTLEDKVAEIEAQQC
ParentalNGIYIWKIGN
		NGIYIWKIGN
RetrocopyNGIYIWKIGN

							

							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
SRP007412_brain_prefrontal_cortex	0 .02 RPM	6 .08 RPM
SRP007412_cerebellum	0 .00 RPM	7 .99 RPM
SRP007412_heart	0 .00 RPM	7 .75 RPM
SRP007412_kidney	0 .08 RPM	10 .43 RPM
SRP007412_liver	0 .00 RPM	6 .51 RPM
SRP007412_testis	0 .11 RPM	12 .54 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_488 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_488 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_488 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_680
Gorilla gorilla	retro_ggor_586

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000036009	1 retrocopy	retro_btau_391,
Homo sapiens	ENSG00000175104	1 retrocopy	retro_hsap_680,
Gorilla gorilla	ENSGGOG00000005854	1 retrocopy	retro_ggor_586,
Nomascus leucogenys	ENSNLEG00000017949	1 retrocopy	retro_nleu_782,
Pan troglodytes	ENSPTRG00000003510	1 retrocopy	retro_ptro_488 ,

	RetrogeneDB ID:	retro_ptro_488
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	10:57475647..57476723(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	TRAF6
	Ensembl ID:	ENSPTRG00000003510
	Aliases:	None
	Description:	None

Parental	MSLLNCENSCGSSQSESDCCVAMASSCSAATKDDSVGGTASTGNLSSSFMEEIQGYDVEFDPPLESKYEC
	.SLLNCENSCGSSQS.SD.CVAMASSCSAATK.DSVG.TASTGNLSSSFMEEIQGYDVEF.PPLESKYEC
Retrocopy	ISLLNCENSCGSSQSQSDYCVAMASSCSAATKNDSVGRTASTGNLSSSFMEEIQGYDVEFGPPLESKYEC

Parental	PICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKREILSLMVKCPNEGCL
	PICLMALREAVQTPC.HRFCKACIIKSIRDAGHK.PVDNEILLEN.LFPDNFAKREI.SL.VKCPNEGCL
Retrocopy	PICLMALREAVQTPCSHRFCKACIIKSIRDAGHKYPVDNEILLENKLFPDNFAKREIISLIVKCPNEGCL

Parental	HKMELRHLEDHQAHCEFALMDCPQCQRPFQKFHINIHILKDCPRRQVSCDNCAASMAFEDKEIHDQNCPL
	HK.ELRHLEDHQ.HCEFALMDCPQCQ.PFQKFHINIHI.K.CPRRQVSCDNC.ASMAFEDK.IHDQNCPL
Retrocopy	HKTELRHLEDHQTHCEFALMDCPQCQPPFQKFHINIHIMKGCPRRQVSCDNCTASMAFEDKKIHDQNCPL

Parental	ANVICEYCNTILIREQMPNH-YDLDCPTAPIPCTFSTFGCHEKMQRNHLARHLQENTQSHMRMLAQAVHS
	ANVICEYCNTILIREQMPN..YDLD.PTAPIPCTF.TF..HEKMQRNHLARHLQENTQS.MRMLAQAVHS
Retrocopy	ANVICEYCNTILIREQMPNF<YDLDRPTAPIPCTFRTFRSHEKMQRNHLARHLQENTQSNMRMLAQAVHS

Parental	LSLIPDSGYISEVRNFQETIHQLEGRLVRQDHQIRELTAKMETQSMYVSELKRTIRTLEDKVAEIEAQQC
	LSLIP.SGYISEVRNFQE.IHQLEGRLVRQ.HQIRELT.KMETQSMYVSELK.TIRTLEDKVAEIEAQQC
Retrocopy	LSLIPYSGYISEVRNFQESIHQLEGRLVRQCHQIRELTDKMETQSMYVSELK*TIRTLEDKVAEIEAQQC

Parental	NGIYIWKIGN
	NGIYIWKIGN
Retrocopy	NGIYIWKIGN

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

RetrogeneDB ID:

retro_ptro_488