RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_1993
ATGGTGACCCTGCGGAAGAGGACCCTGAAAGTGCTCACCTTCCTCATGCTCTTCATCTTCCTCACCTCCTTCCTGAACTA

CTCCCACGCCATGGTGGCCACCACCTGGTTCCCCAAGAAGATGGTCCTGGAGCTCTTGGAGAACCTGAAGAGACTGATCA

AGCACAGGCCCTGCACTTGCCCCCACTGCATCAGGCAGCGTGGGCTCTCAGCCTGGTTCGACAAGAGGTTCAACTAGATC

GTGCAGCTGCTGCTGACTGCCCAGAATGCGCTCTTGGAGGACAACACCTACCAATGGTGGCTGAGGCTCCAGCAGGAGAA

GAAGCCCAATATCTTGAACAATACCATCAAGGAATTCAGAGCAGTACCTGGGAATGTGGACCCAATGCTGGAGAAGAGGT

CGGTGGGCTGCTGGCACTGTGCTGTCATGGGCAACTCGGGCAACCTGAGGCAATTGTCGTATAGGCCTGAGATAAACAGT

CACAATTTTATGCTCAGGATGAACAAGGCACCCACGGCAGGGTTTAAAGCTGATGCTGGGAGCAAAACCGCCCACCATCT

GGTGTACCCTGAGAGCTTCCGGGAGCTGGGGGACAATGTCAGCATGGTCCTGGTGCCCTTAAAGACCATGAACTTGGAGT

GGGTGGTGAGCACCACCACCACGGGTGCCATTTCCCACACCTACACCCCGGTCCTTGTGAAGATCAGAGTGAAACAGGAT

AAGATCCTGATCTACCACCCAGCCTTCATCAAGTATGTCTTCGACAACTGGCTGCAGAGCCACAGGCGGTACCCACTCAC

CAGCATCGTCTCGGTCATCTTCTCAATGCATGTCTGCGATTAGGTAGACTTGTATAGCTTCTGAGCAGACAGCAAAGGGA

ACTGACACCACTACTGAGAGAAAAACCTGTCCGCGGGGTCTTTTCACAAGACGGGGGTGCACGATGCAGGCTTTGAGTCT

AACCTGACGGCCACCTTGGCTTCATCAATAAAATCCGGATCTTCAAGGGGAGA

ORF - retro_ptro_1993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	82.7 %
Parental protein coverage:	100. %
Number of stop codons detected:	5
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalMVTLRKRTLKVLTFLVLFIFLTSFFLNYSHTMVATTWFPKQMVLELSENLKRLIKHRPCTCTHCIGQRKL
		MVTLRKRTLKVLTFL.LFIFLTSF.LNYSH.MVATTWFPK.MVLEL.ENLKRLIKHRPCTC.HCI.QR.L
RetrocopyMVTLRKRTLKVLTFLMLFIFLTSF-LNYSHAMVATTWFPKKMVLELLENLKRLIKHRPCTCPHCIRQRGL
ParentalSAWFDERFNQTVQPLLTAQNALLEDDTYRWWLRLQREKKPNNLNDTIKELFRVVPGNVDPMLEKRSVGCR
		SAWFD.RFN..VQ.LLTAQNALLED.TY.WWLRLQ.EKKPN.LN.TIKE.FR.VPGNVDPMLEKRSVGC.
RetrocopySAWFDKRFN*IVQLLLTAQNALLEDNTYQWWLRLQQEKKPNILNNTIKE-FRAVPGNVDPMLEKRSVGCW
ParentalRCAVVGNSGNLRESSYGPEIDSHDFVLRMNKAPTAGFEADVGTKTTHHLVYPESFRELGDNVSMILVPFK
		.CAV.GNSGNLR..SY.PEI.SH.F.LRMNKAPTAGF.AD.G.KT.HHLVYPESFRELGDNVSM.LVP.K
RetrocopyHCAVMGNSGNLRQLSYRPEINSHNFMLRMNKAPTAGFKADAGSKTAHHLVYPESFRELGDNVSMVLVPLK
ParentalTIDLEWVVSAITTGTISHTYVPVPAKIRVKQDKILIYHPAFIKYVFDNWLQGHGRYPSTGILSVIFSMHV
		T..LEWVVS..TTG.ISHTY.PV..KIRVKQDKILIYHPAFIKYVFDNWLQ.H.RYP.T.I.SVIFSMHV
RetrocopyTMNLEWVVSTTTTGAISHTYTPVLVKIRVKQDKILIYHPAFIKYVFDNWLQSHRRYPLTSIVSVIFSMHV
ParentalCDEVDLYGFGADSKGNWHHYWENNPSAGAFRKTGVHDADFESNVTATLAS-INKIRIFKGR
		CD.VDLY.F.ADSKGN.HHY.E.N.SAG.F.KTGVHDA.FESN.TATLAS.INKIRIFKGR
RetrocopyCD*VDLYSF*ADSKGN*HHY*EKNLSAGSFHKTGVHDAGFESNLTATLAS<INKIRIFKGR

							

							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 .07 RPM	8 .35 RPM
SRP007412_cerebellum	0 .00 RPM	2 .51 RPM
SRP007412_heart	0 .06 RPM	34 .07 RPM
SRP007412_kidney	0 .13 RPM	53 .01 RPM
SRP007412_liver	0 .16 RPM	32 .21 RPM
SRP007412_testis	0 .00 RPM	3 .06 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_1993 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1993 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_1993 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
Homo sapiens	ENSG00000008513	1 retrocopy	retro_hsap_3046,
Macaca mulatta	ENSMMUG00000012531	1 retrocopy	retro_mmul_1888,
Pongo abelii	ENSPPYG00000018896	1 retrocopy	retro_pabe_2435,
Pan troglodytes	ENSPTRG00000020606	1 retrocopy	retro_ptro_1993 ,

	RetrogeneDB ID:	retro_ptro_1993
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	4:62196407..62197420(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	ST3GAL1
	Ensembl ID:	ENSPTRG00000020606
	Aliases:	None
	Description:	Pan troglodytes ST3 beta-galactoside alpha-2,3-sialyltransferase 1 (ST3GAL1), mRNA. [Source:RefSeq mRNA;Acc:NM_001009037]

Parental	MVTLRKRTLKVLTFLVLFIFLTSFFLNYSHTMVATTWFPKQMVLELSENLKRLIKHRPCTCTHCIGQRKL
	MVTLRKRTLKVLTFL.LFIFLTSF.LNYSH.MVATTWFPK.MVLEL.ENLKRLIKHRPCTC.HCI.QR.L
Retrocopy	MVTLRKRTLKVLTFLMLFIFLTSF-LNYSHAMVATTWFPKKMVLELLENLKRLIKHRPCTCPHCIRQRGL

Parental	SAWFDERFNQTVQPLLTAQNALLEDDTYRWWLRLQREKKPNNLNDTIKELFRVVPGNVDPMLEKRSVGCR
	SAWFD.RFN..VQ.LLTAQNALLED.TY.WWLRLQ.EKKPN.LN.TIKE.FR.VPGNVDPMLEKRSVGC.
Retrocopy	SAWFDKRFN*IVQLLLTAQNALLEDNTYQWWLRLQQEKKPNILNNTIKE-FRAVPGNVDPMLEKRSVGCW

Parental	RCAVVGNSGNLRESSYGPEIDSHDFVLRMNKAPTAGFEADVGTKTTHHLVYPESFRELGDNVSMILVPFK
	.CAV.GNSGNLR..SY.PEI.SH.F.LRMNKAPTAGF.AD.G.KT.HHLVYPESFRELGDNVSM.LVP.K
Retrocopy	HCAVMGNSGNLRQLSYRPEINSHNFMLRMNKAPTAGFKADAGSKTAHHLVYPESFRELGDNVSMVLVPLK

Parental	TIDLEWVVSAITTGTISHTYVPVPAKIRVKQDKILIYHPAFIKYVFDNWLQGHGRYPSTGILSVIFSMHV
	T..LEWVVS..TTG.ISHTY.PV..KIRVKQDKILIYHPAFIKYVFDNWLQ.H.RYP.T.I.SVIFSMHV
Retrocopy	TMNLEWVVSTTTTGAISHTYTPVLVKIRVKQDKILIYHPAFIKYVFDNWLQSHRRYPLTSIVSVIFSMHV

Parental	CDEVDLYGFGADSKGNWHHYWENNPSAGAFRKTGVHDADFESNVTATLAS-INKIRIFKGR
	CD.VDLY.F.ADSKGN.HHY.E.N.SAG.F.KTGVHDA.FESN.TATLAS.INKIRIFKGR
Retrocopy	CDVDLYSFADSKGNHHYEKNLSAGSFHKTGVHDAGFESNLTATLAS<INKIRIFKGR

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

RetrogeneDB ID:

retro_ptro_1993