RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_2103
ATGCCAGAAGGGCTGTTGGTGAGGACATTTCACCATTCGGTCTCTCCTTTTGTGGGCAAGCAGGTGGTAAAGACAGGGAG

CAACAGTAAGAAGTATAGCCCACCAGCCTCCAGTCTCTGTGGCTCCAGGACACCCAGGTCCATGGAAAGAAATTATTCCT

TAGATTTGATCCAGATGAAGAAATGGGGCCCGCTGGCAACAGCTCACCGCCAGAGCCTCCACAAAAAGAAGCGCAGATGG

AAGGGACTGTGGACTCAAAGCAGGCCCGGGAGCCAGTGGGCAGAAGACCCTTGACGCCTCCTCACGGTCCGCAGAGCTTG

TCCCCCAGGGAGAGGATGATTAGGAATGTTTGAAGGGAGACACCCCTACAGGAGATGCTGGGAGGCGGCTGCGTGTCAGC

TCTTGTTTGTTTGGCAGCGTTTGGGTGAACGACTTCTCCAGAGCCAAGAAAGCCAACAAGAGGGGGGACTGGAGGGACCC

TGCCCCGAGGTTGGTCCTGTACTTTGGTGGTGGTAGCTTCCTGGCACTTTATAATTGTCAGATGCCTTGGAGCTCTTCCC

CAGAGGTCACACCCACCTGTGACATCCTGTCTGAGAAGTTCCATTGAGGACAAGCCTTGGAAGCTCTAGGCCAGGCTCAG

CCTGTCTCTTATACACCATTGAACCAGAAATACTTCTCAGGGCTAGGGAACGTCATTAAGAATGAAGTCTTGTACAGAAC

TGGCATCCATCCCCTTTCTCTTGGTTCAGTCCTGAGTGCCTCCATGTTAGGAGGCCCTGGTGGATCACGTGGTGGAGTTC

AGTACAGCCTGGCTGCAGGGCAAGTTCCAGGGCAAACCGCAGCACATGCAGGTCTACCAGAAAGAACAGTGCCCAGCTGG

CCACCAGGTCATGAAGAAGCCCTTTGGGCCCTCAGGTGGGTTCCAGAGGCTCACCTGGTGGTGCCCACAGTGCCAGTCTC

AGTTGTTAGAGGAGCCGGAGCAGTGCCAGTTCTTCTAAGGGACTCAGGGTGCTCTTCATGGAACCTTGCCCCTTGGGGAA

CCTGATGTC

ORF - retro_ptro_2103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	80.17 %
Parental protein coverage:	100. %
Number of stop codons detected:	3
Number of frameshifts detected	3

Retrocopy - Parental Gene Alignment:

									ParentalMPEGPLVRKFHRLVSPFVGQQVVKTGGSSKKLQP-ASLQSLWLQDTQVHGKKLFLRFDLDEEMGPPGSSP
		MPEG.LVR.FH..VSPFVG.QVVKTG..SKK..P..SLQSLWLQDTQVHGKKLFLRFD.DEEMGP.G.S.
RetrocopyMPEGLLVRTFHHSVSPFVGKQVVKTGSNSKKYSP<TSLQSLWLQDTQVHGKKLFLRFDPDEEMGPAGNSS
ParentalTPEPPQKEVQKEGAADPKQVGEP-SGQKTLDGSSQSAELVPQGEDDSEYLERDAPAGDAGRWLRVSFGLF
		.PEPPQKE.Q.EG..D.KQ..EP.SGQKTLD.SS.SAELVPQGEDD.E.L..D.P.GDAGR.LRVS..LF
RetrocopyPPEPPQKEAQMEGTVDSKQAREP<SGQKTLDASSRSAELVPQGEDD*ECLKGDTPTGDAGRRLRVSSCLF
ParentalGSIWVNDFSRAKKANKRGDWRDPSPRLVLHFSGGGFLAFYNCQLSWSSSPVVTPTCDILSEKFHRGQALE
		GS.WVNDFSRAKKANKRGDWRDP.PRLVL.F.GG.FLA.YNCQ..WSSSP.VTPTCDILSEKFH.GQALE
RetrocopyGSVWVNDFSRAKKANKRGDWRDPAPRLVLYFGGGSFLALYNCQMPWSSSPEVTPTCDILSEKFH*GQALE
ParentalALGQAQPVCYTLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRR-EVLVDHVVEFSTAWLQGKFQ
		ALGQAQPV.YT.L.Q.YFSGLGN.IKNE.LYR.GIHPLSLGSVLSAS...E.LVDHVVEFSTAWLQGKFQ
RetrocopyALGQAQPVSYTPLNQKYFSGLGNVIKNEVLYRTGIHPLSLGSVLSASML>EALVDHVVEFSTAWLQGKFQ
ParentalGRPQHTQVYQKEQCPAGHQVMKEAFGPEDGLQRLTWWCPQCQPQLSEEPEQCQFSEGAGGAPHGTLPLGE
		G.PQH.QVYQKEQCPAGHQVMK..FGP..G.QRLTWWCPQCQ.QL.EEPEQCQF..G..GA.HGTLPLGE
RetrocopyGKPQHMQVYQKEQCPAGHQVMKKPFGPSGGFQRLTWWCPQCQSQLLEEPEQCQFF*GTQGALHGTLPLGE
ParentalPDV
		PDV
RetrocopyPDV

							

							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 .00 RPM	12 .74 RPM
SRP007412_cerebellum	0 .04 RPM	23 .88 RPM
SRP007412_heart	0 .06 RPM	3 .21 RPM
SRP007412_kidney	0 .08 RPM	5 .05 RPM
SRP007412_liver	0 .00 RPM	5 .04 RPM
SRP007412_testis	0 .00 RPM	15 .60 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_2103 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_2103 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_2103 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3111
Pongo abelii	retro_pabe_2569
Macaca mulatta	retro_mmul_1982

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000154328	1 retrocopy	retro_hsap_3111,
Macaca mulatta	ENSMMUG00000019209	1 retrocopy	retro_mmul_1982,
Nomascus leucogenys	ENSNLEG00000015054	1 retrocopy	retro_nleu_766,
Pongo abelii	ENSPPYG00000018348	1 retrocopy	retro_pabe_2569,
Pan troglodytes	ENSPTRG00000019995	1 retrocopy	retro_ptro_2103 ,

	RetrogeneDB ID:	retro_ptro_2103
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	4:153432415..153433464(-)
	Located in intron of:	ENSPTRG00000023095
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	NEIL2
	Ensembl ID:	ENSPTRG00000019995
	Aliases:	None
	Description:	None

Parental	MPEGPLVRKFHRLVSPFVGQQVVKTGGSSKKLQP-ASLQSLWLQDTQVHGKKLFLRFDLDEEMGPPGSSP
	MPEG.LVR.FH..VSPFVG.QVVKTG..SKK..P..SLQSLWLQDTQVHGKKLFLRFD.DEEMGP.G.S.
Retrocopy	MPEGLLVRTFHHSVSPFVGKQVVKTGSNSKKYSP<TSLQSLWLQDTQVHGKKLFLRFDPDEEMGPAGNSS

Parental	TPEPPQKEVQKEGAADPKQVGEP-SGQKTLDGSSQSAELVPQGEDDSEYLERDAPAGDAGRWLRVSFGLF
	.PEPPQKE.Q.EG..D.KQ..EP.SGQKTLD.SS.SAELVPQGEDD.E.L..D.P.GDAGR.LRVS..LF
Retrocopy	PPEPPQKEAQMEGTVDSKQAREP<SGQKTLDASSRSAELVPQGEDD*ECLKGDTPTGDAGRRLRVSSCLF

Parental	GSIWVNDFSRAKKANKRGDWRDPSPRLVLHFSGGGFLAFYNCQLSWSSSPVVTPTCDILSEKFHRGQALE
	GS.WVNDFSRAKKANKRGDWRDP.PRLVL.F.GG.FLA.YNCQ..WSSSP.VTPTCDILSEKFH.GQALE
Retrocopy	GSVWVNDFSRAKKANKRGDWRDPAPRLVLYFGGGSFLALYNCQMPWSSSPEVTPTCDILSEKFH*GQALE

Parental	ALGQAQPVCYTLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRR-EVLVDHVVEFSTAWLQGKFQ
	ALGQAQPV.YT.L.Q.YFSGLGN.IKNE.LYR.GIHPLSLGSVLSAS...E.LVDHVVEFSTAWLQGKFQ
Retrocopy	ALGQAQPVSYTPLNQKYFSGLGNVIKNEVLYRTGIHPLSLGSVLSASML>EALVDHVVEFSTAWLQGKFQ

Parental	GRPQHTQVYQKEQCPAGHQVMKEAFGPEDGLQRLTWWCPQCQPQLSEEPEQCQFSEGAGGAPHGTLPLGE
	G.PQH.QVYQKEQCPAGHQVMK..FGP..G.QRLTWWCPQCQ.QL.EEPEQCQF..G..GA.HGTLPLGE
Retrocopy	GKPQHMQVYQKEQCPAGHQVMKKPFGPSGGFQRLTWWCPQCQSQLLEEPEQCQFF*GTQGALHGTLPLGE

Parental	PDV
	PDV
Retrocopy	PDV

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

RetrogeneDB ID:

retro_ptro_2103