RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_28
ATGGACGAGAAGGTGTTCACCAAGGAGCTGGACCAGTGGATCGAGCAGCTGAACGAGTGCAAGCAGCTATCCGAGTCCCA

GGTCAAGAGCCTCTGCGAGAAGGCTAAAGAAATCCTGACAAAAGAATCCAACGTGCAAGAGGTTCGATGTCCAGTTACTG

TCTGTGGAGATGTGCATGGGCAATTTCATGATCTCATGGAACTGTTTAGAATTGGTGGCAAATCACCAGATACAAATTAC

TTGTTTATGGGAGATTATGTTGACAGAGGATATTATTCAGTTGAAACAGTTACACTGCTTGTAGCTCTTAAGGTTCGTTA

CCGTGAACGCATCACCATTCTTCGAGGGAATCATGAGAGCAGACAGATCACACAAGTTTATGGTTTCTATGATGAATGTT

TAAGAAAATATGGAAATGCAAATGTTTGGAAATATTTTACAGATCTTTTTGACTATCTTCCTCTCACTGCCTTGGTGGAT

GGGCAGATCTTCTGTCTACATGGTGGTCTCTCGCCATCTATAGATACACTGGATCATATCAGAGTACTTGATCGCCTACA

AGAAGTTCCCCATGAGGGTCCAATGTGTGACTTGCTGTGGTCAGATCCAGATGACCGTGGTGGTTGGGGTATATCTCCTC

GAGTAGCTGGTTACACCTTTGGGCAAGATATTTCTGAGACATTTAATCATGCCAATGGCCTCACGTTGGTGTCTAGAGCT

CACCAGCTAGTGATGGAGGGATATAACTGGTGCCATGACCGGAATGTAGTAACGATTTTCAGTGCTCCAAACTATTGTTA

TCGTTGTGGTAACCAAGCTGCAATCATGGAACTTGACGATACTCTAAAATACTCTTTCTTGCAGTTTGACCCAGCACCTC

GTAGAGGCGAGCCACATGTTACTCGTCGTACCCCAGACTACTTC

ORF - retro_ptro_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	66.23 %
Parental protein coverage:	98.05 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalDLDRQIEQLRRCELIKESEVKALCAKAREILVEESNVQRVDSPVTVCGDIHGQFYDLKELFRVGGDVPET
		.LD..IEQL..C....ES.VK.LC.KA.EIL..ESNVQ.V..PVTVCGD.HGQF.DL.ELFR.GG..P.T
RetrocopyELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFRIGGKSPDT
ParentalNYLFMGDFVDRGFYSVETFLLLLALKVRYPDRITLIRGNHESRQITQVYGFYDECLRKYGSVTVWRYCTE
		NYLFMGD.VDRG.YSVET..LL.ALKVRY..RIT..RGNHESRQITQVYGFYDECLRKYG...VW.Y.T.
RetrocopyNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTD
ParentalIFDYLSLSAIIDGKIFCVHGGLSPSIQTLDQIRTIDRKQEVPHDGPMCDLLWSDPEDTTGWGVSPRGAGY
		.FDYL.L.A..DG.IFC.HGGLSPSI.TLD.IR..DR.QEVPH.GPMCDLLWSDP.D..GWG.SPR.AGY
RetrocopyLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRVLDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRVAGY
ParentalLFGSDVVAQFNAANDIDMICRAHQLVMEGYKWHFNETVLTVWSAPNYCYRCGNVAAILELDEHLQKDFII
		.FG.D....FN.AN......RAHQLVMEGY.W.....V.T..SAPNYCYRCGN.AAI.ELD..L...F..
RetrocopyTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQ
ParentalFEAAPQETRGIPS-KKPVADYF
		F..AP...RG.P.......DYF
RetrocopyFDPAPR--RGEPHVTRRTPDYF

							

							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	52 .59 RPM	29 .21 RPM
SRP007412_cerebellum	39 .76 RPM	29 .47 RPM
SRP007412_heart	21 .98 RPM	13 .55 RPM
SRP007412_kidney	21 .92 RPM	74 .87 RPM
SRP007412_liver	14 .83 RPM	114 .57 RPM
SRP007412_testis	15 .60 RPM	41 .63 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_28 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_28 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_28 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015223	1 retrocopy	retro_amel_286,
Canis familiaris	ENSCAFG00000017089	1 retrocopy	retro_cfam_16,
Ciona savignyi	ENSCSAVG00000004266	1 retrocopy	retro_csav_27,
Equus caballus	ENSECAG00000022179	1 retrocopy	retro_ecab_911,
Felis catus	ENSFCAG00000014171	1 retrocopy	retro_fcat_1043,
Macropus eugenii	ENSMEUG00000000397	5 retrocopies	retro_meug_1014, retro_meug_1188, retro_meug_1336, retro_meug_560, retro_meug_859,
Ornithorhynchus anatinus	ENSOANG00000008136	1 retrocopy	retro_oana_25,
Pan troglodytes	ENSPTRG00000007984	1 retrocopy	retro_ptro_28 ,
Tursiops truncatus	ENSTTRG00000005532	1 retrocopy	retro_ttru_1015,

	RetrogeneDB ID:	retro_ptro_28
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	X:117797681..117798605(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSPTRG00000017238
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	PPP4C
	Ensembl ID:	ENSPTRG00000007984
	Aliases:	None
	Description:	Serine/threonine-protein phosphatase [Source:UniProtKB/TrEMBL;Acc:H2RA87]

Parental	DLDRQIEQLRRCELIKESEVKALCAKAREILVEESNVQRVDSPVTVCGDIHGQFYDLKELFRVGGDVPET
	.LD..IEQL..C....ES.VK.LC.KA.EIL..ESNVQ.V..PVTVCGD.HGQF.DL.ELFR.GG..P.T
Retrocopy	ELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFRIGGKSPDT

Parental	NYLFMGDFVDRGFYSVETFLLLLALKVRYPDRITLIRGNHESRQITQVYGFYDECLRKYGSVTVWRYCTE
	NYLFMGD.VDRG.YSVET..LL.ALKVRY..RIT..RGNHESRQITQVYGFYDECLRKYG...VW.Y.T.
Retrocopy	NYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTD

Parental	IFDYLSLSAIIDGKIFCVHGGLSPSIQTLDQIRTIDRKQEVPHDGPMCDLLWSDPEDTTGWGVSPRGAGY
	.FDYL.L.A..DG.IFC.HGGLSPSI.TLD.IR..DR.QEVPH.GPMCDLLWSDP.D..GWG.SPR.AGY
Retrocopy	LFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRVLDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRVAGY

Parental	LFGSDVVAQFNAANDIDMICRAHQLVMEGYKWHFNETVLTVWSAPNYCYRCGNVAAILELDEHLQKDFII
	.FG.D....FN.AN......RAHQLVMEGY.W.....V.T..SAPNYCYRCGN.AAI.ELD..L...F..
Retrocopy	TFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQ

Parental	FEAAPQETRGIPS-KKPVADYF
	F..AP...RG.P.......DYF
Retrocopy	FDPAPR--RGEPHVTRRTPDYF

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

RetrogeneDB ID:

retro_ptro_28