RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_86
ATGTTGAAAGCCCTTTTCCTAACTATGCTGACTCTGGCGCTGGTCAAGTCACAGGACACCGAAGAAACCATCACGTACAC

GCAATGCACTGACGGATATGAGTGGGATCCTGTGAGACAGCAATGCAAAGATATTGATGAATGTGACATTGTCCCAGACG

CTTGTAAAGGTGGAATGAAGTGCGTCAACCACTATGGAGGATACCTCTGCCTTCCGAAAACAGCCCAGATTATTGTCAAT

AATGAACAGCCTCAGCAGGAAACACAACCAGCAGAAGGAACCTCAGGGGCAACCACCGGGGTTGTAGCTGCCAGCAGCAT

GGCAACCAGTGGAGTGTTGCCCGGGGGTGGTTTTGTGGCCAGTGCTGCTGCAGTCGCAGGCCCTGAAATGCAGACTGGCC

GAAATAACTTTGTCATCCGGCGGAACCCAGCTGACCCTCAGCGCATTCCCTCCAACCCTTCCCACCGTATCCAGTGTGCA

GCAGGCTACGAGCAAAGTGAACACAACGTGTGCCAAGACATAGACGAGTGCACTGCAGGGACGCACAACTGTAGAGCAGA

CCAAGTGTGCATCAATTTACGGGGATCCTTTGCATGTCAGTGCCCTCCTGGATATCAGAAGCGAGGGGAGCAGTGCGTAG

ACATAGATGAATGTACCATCCCTCCATATTGCCACCAAAGATGCGTGAATACACCAGGCTCATTTTATTGCCAGTGCAGT

CCTGGGTTTCAATTGGCAGCAAACAACTATACCTGCGTAGATATAAATGAATGTGATGCCAGCAATCAATGTGCTCAGCA

GTGCTACAACATTCTTGGTTCATTCATCTGTCAGTGCAATCAAGGATATGAGCTAAGCAGTGACAGGCTCAACTGTGAAG

ACATTGATGAATGCAGAACCTCAAGCTACCTGTGTCAATATCAATGTGTCAATGAACCTGGGAAATTCTCATGTATGTGC

CCCCAGGGATACCAAGTGGTGAGAAGTAGAACATGTCAAGATATAAATGAGTGTGAGACCACAAATGAATGCCGGGAGGA

TGAAATGTGTTGGAATTATCATGGCGGCTTCCGTTGTTATCCACGAAATCCTTGTCAAGATCCCTACATTCTAACACCAG

AGAACCGATGTGTTTGCCCAGTCTCAAATGCCATGTGCCGAGAACTGCCCCAGTCAATAGTCTACAAATACATGAGCATC

CGATCTGATAGGTCTGTGCCATCAGACATCTTCCAGATACAGGCCACAACTATTTATGCCAACACCATCAATACTTTTCG

GATTAAATCTGGAAATGAAAATGGAGAGTTCTACCTACGACAAACAAGTCCTGTAAGTGCAATGCTTGTGCTCGTGAAGT

CATTATCAGGACCAAGAGAACATATCGTGGACCTGGAGATGCTGACAGTCAGCAGTATAGGGACCTTCCGCACAAGCTCT

GTGTTAAGATTGACAATAATAGTGGGGCCATTTTCATTTTAG

ORF - retro_ptro_86 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	56.76 %
Parental protein coverage:	76.52 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalHPNPCPPGYEPDNQESCVDVDECAQALHDCRPSQDCHNLPGSYQCTCPDGYRKIGPECVDIDECRYR-YC
		H...C..GYE......C.D.DEC....H.CR..Q.C.NL.GS..C.CP.GY.K.G..CVDIDEC....YC
RetrocopyHRIQCAAGYEQSEHNVCQDIDECTAGTHNCRADQVCINLRGSFACQCPPGYQKRGEQCVDIDECTIPPYC
ParentalQHRCVNLPGSFRCQCEPGFQLGPNNRSCVDVNECDMGAPCEQRCFNSYGTFLCRCHQGYELHRDGFSCSD
		..RCVN.PGSF.CQC.PGFQL..NN..CVD.NECD....C.Q.C.N..G.F.C.C.QGYEL..D...C.D
RetrocopyHQRCVNTPGSFYCQCSPGFQLAANNYTCVDINECDASNQCAQQCYNILGSFICQCNQGYELSSDRLNCED
ParentalIDECSYSSYLCQYRCVNEPGRFSCHCPQGYQLLATRLCQDIDECESGAHQCSEAQTCVNFHGGYRCVDTN
		IDEC..SSYLCQY.CVNEPG.FSC.CPQGYQ....R.CQDI.ECE.....C.E...C.N.HGG.RC...N
RetrocopyIDECRTSSYLCQYQCVNEPGKFSCMCPQGYQVVRSRTCQDINECET-TNECREDEMCWNYHGGFRCYPRN
ParentalRCVEPYIQVSENRCLCPASNPLCREQPSSIVHRYMTITSERSVPADVFQIQATSVYPGAYNAFQIRAGNS
		.C..PYI...ENRC.CP.SN..CRE.P.SIV..YM.I.S.RSVP.D.FQIQAT..Y....N.F.I..GN.
RetrocopyPCQDPYILTPENRCVCPVSNAMCRELPQSIVYKYMSIRSDRSVPSDIFQIQATTIYANTINTFRIKSGNE
ParentalQGDFYIRQINNVSAMLVLARPVTGPREYVLDLEMVTMNSLMSYRASSVLRLTVFVGAYTF
		.G.FY.RQ...VSAMLVL.....GPRE...DLEM.T..S....R.SSVLRLT..VG...F
RetrocopyNGEFYLRQTSPVSAMLVLVKSLSGPREHIVDLEMLTVSSIGTFRTSSVLRLTIIVGPFSF

							

							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	9 .28 RPM	16 .46 RPM
SRP007412_cerebellum	14 .41 RPM	11 .54 RPM
SRP007412_heart	7 .99 RPM	34 .22 RPM
SRP007412_kidney	15 .46 RPM	30 .34 RPM
SRP007412_liver	1 .34 RPM	9 .20 RPM
SRP007412_testis	0 .53 RPM	2 .53 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_86 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_86 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_86 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000003897	1 retrocopy	retro_ptro_86 ,

	RetrogeneDB ID:	retro_ptro_86
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	18:46074929..46076411(+)
	Located in intron of:	ENSPTRG00000010019
Retrocopy information	Ensembl ID:	ENSPTRG00000040728
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	EFEMP2
	Ensembl ID:	ENSPTRG00000003897
	Aliases:	None
	Description:	None

Parental	HPNPCPPGYEPDNQESCVDVDECAQALHDCRPSQDCHNLPGSYQCTCPDGYRKIGPECVDIDECRYR-YC
	H...C..GYE......C.D.DEC....H.CR..Q.C.NL.GS..C.CP.GY.K.G..CVDIDEC....YC
Retrocopy	HRIQCAAGYEQSEHNVCQDIDECTAGTHNCRADQVCINLRGSFACQCPPGYQKRGEQCVDIDECTIPPYC

Parental	QHRCVNLPGSFRCQCEPGFQLGPNNRSCVDVNECDMGAPCEQRCFNSYGTFLCRCHQGYELHRDGFSCSD
	..RCVN.PGSF.CQC.PGFQL..NN..CVD.NECD....C.Q.C.N..G.F.C.C.QGYEL..D...C.D
Retrocopy	HQRCVNTPGSFYCQCSPGFQLAANNYTCVDINECDASNQCAQQCYNILGSFICQCNQGYELSSDRLNCED

Parental	IDECSYSSYLCQYRCVNEPGRFSCHCPQGYQLLATRLCQDIDECESGAHQCSEAQTCVNFHGGYRCVDTN
	IDEC..SSYLCQY.CVNEPG.FSC.CPQGYQ....R.CQDI.ECE.....C.E...C.N.HGG.RC...N
Retrocopy	IDECRTSSYLCQYQCVNEPGKFSCMCPQGYQVVRSRTCQDINECET-TNECREDEMCWNYHGGFRCYPRN

Parental	RCVEPYIQVSENRCLCPASNPLCREQPSSIVHRYMTITSERSVPADVFQIQATSVYPGAYNAFQIRAGNS
	.C..PYI...ENRC.CP.SN..CRE.P.SIV..YM.I.S.RSVP.D.FQIQAT..Y....N.F.I..GN.
Retrocopy	PCQDPYILTPENRCVCPVSNAMCRELPQSIVYKYMSIRSDRSVPSDIFQIQATTIYANTINTFRIKSGNE

Parental	QGDFYIRQINNVSAMLVLARPVTGPREYVLDLEMVTMNSLMSYRASSVLRLTVFVGAYTF
	.G.FY.RQ...VSAMLVL.....GPRE...DLEM.T..S....R.SSVLRLT..VG...F
Retrocopy	NGEFYLRQTSPVSAMLVLVKSLSGPREHIVDLEMLTVSSIGTFRTSSVLRLTIIVGPFSF

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

RetrogeneDB ID:

retro_ptro_86