RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_405
GGGAACCTGGGCCAAGGCGCCTGTGGCAAGGGGGTGAGTGCTTGGACCCTGCCAGAAGGACGTCTCGGGTTGCCGGAGGG

TCATCTGCAATGTAGGCAAGCACCGGGAGGCAGCACCGCCAAAAATCAACGCTCTCGAAAAAAATAAACGAGAAGGACTA

AGAGAACCAGCTCCTGTGCGTCTTGGGGTGTGACTGGTTCACCCTCCACGGTCCATGCATATCACCTTTGAGCTCCTGGG

CAGGAAAACCCTTGAGTTCCCGAAGGATAATAACATCCAGCCATTCCCCTCCCACATGTCTGGCACATGGCCCACCAGCT

CTGCCACACTCTTAGATTTCTGCACGAGAACCGGCTGACCCACGCACACCTGAAAACCGAGAACATCCTGCATGTGGATT

CTGAGTTAAAAACTGTCTACAGCAAGCACAGGAGCGATGAGAAGTCAGTGAGGAGCACCAGCGTCCGAGTGGCTGACTTC

CCCAATGCCACCTCTGACCGTGAGCATCACACCGCCATGGTGACCACGGTCACTGTCGCCTGCCTGAACTGATCCTTGAT

CTGGGCTGGACACGCCCCTGCCATGTCCAGGGCATGGGCTACCTTCTCTTTAAGTACTACCAGGTTTCACACTCTTCCAG

ACCTGTGAAAACCAAGAGCGCCTGGTGATGTTGAAGACCCTACGGCCCATCCCATTATGCGTGATCTCCTGTACCAAGAA

GCAGAAATATTTCTACAAATGGGGCCTAGTTTGGGATGAGAACAGCTCTGACAGCCCATATGTGAAGAACTGCAAACGTC

TGAAGAGTGACATGCTCCAAGACTCTCTGGAGCACGTGCAGCTGTTTGAGCTGATGCGGAGGGTGGTAAAATTGGACGCT

GCCCAGCACATCACTCTGGCTGAGACTCTTCTGCACCCCGTCTTTGCTGGCCTGGCAACCTCAGTCGTGATCCTTCCACA

CAAGCCACAACCCAAGCAGA

ORF - retro_ptro_405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	65.19 %
Parental protein coverage:	55.72 %
Number of stop codons detected:	2
Number of frameshifts detected	8

Retrocopy - Parental Gene Alignment:

									ParentalGNLGEGTFGKVV-ECLDHARGKSQVA-LKIIRNVGKYREAARLEINVL-KKIKEKDKENKFLCVLMSDWF
		GNLG.G..GK.V.ECLD.AR..S.VA....I.NVGK.REAA...IN.L.KKI.EKD.EN..LCVL..DWF
RetrocopyGNLGQGACGKGV<ECLDPARRTSRVA<RRVICNVGKHREAAPPKINAL>KKINEKD*ENQLLCVLGCDWF
ParentalNFHG-HMCIAFELLGKNTFEFLKENNFQPYP-LPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNS
		..HG..M.I.FELLG..T.EF.K.NN.QP.P.LPHV.HMA.QLCH.LRFLHEN.LTH..LK.ENIL.V.S
RetrocopyTLHG<SMHITFELLGRKTLEFPKDNNIQPFP<LPHVWHMAHQLCHTLRFLHENRLTHAHLKTENILHVDS
ParentalEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVAT-RHYRPPEVILELGWAQPCDVWSIGCI
		E..T.Y..H.S..EKSV..TS.RVADF..AT.D.EHHT..V.T..H.R.PE.IL.LGW..PC.V...G..
RetrocopyELKTVYSKHRS-DEKSVRSTSVRVADFPNATSDREHHTAMVTT<GHCRLPELILDLGWTRPCHVQGMGYL
ParentalLFEYYR-GFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLK
		LF.YY..GFTLFQT.EN.E.LVM..K.L.PIP...I..T.KQKYFYK.GLVWDENSSD..YVK.NCK.LK
RetrocopyLFKYYQ<GFTLFQTCENQERLVML-KTLRPIPLCVISCTKKQKYFYKWGLVWDENSSDSPYVK-NCKRLK
ParentalSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLT-PEERSFHTSRNPSR
		S.MLQDSLEHVQLF.LMRR....D.AQ.ITLAE.LLHP.FAGL..P...SFHTS.NPSR
RetrocopySDMLQDSLEHVQLFELMRRVVKLDAAQHITLAETLLHPVFAGLA>PQS*SFHTSHNPSR

							

							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	27 .74 RPM
SRP007412_cerebellum	0 .00 RPM	28 .07 RPM
SRP007412_heart	0 .00 RPM	10 .99 RPM
SRP007412_kidney	0 .00 RPM	24 .45 RPM
SRP007412_liver	0 .00 RPM	16 .66 RPM
SRP007412_testis	0 .00 RPM	34 .25 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_405 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_405 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_405 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_540

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000179335	1 retrocopy	retro_hsap_540,
Macaca mulatta	ENSMMUG00000011069	1 retrocopy	retro_mmul_457,
Pan troglodytes	ENSPTRG00000001419	1 retrocopy	retro_ptro_2604,
Pan troglodytes	ENSPTRG00000007278	1 retrocopy	retro_ptro_405 ,
Pan troglodytes	ENSPTRG00000017683	1 retrocopy	retro_ptro_2859,

	RetrogeneDB ID:	retro_ptro_405
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	1:227425194..227426174(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	CLK3
	Ensembl ID:	ENSPTRG00000007278
	Aliases:	None
	Description:	Pan troglodytes CDC-like kinase 3 (CLK3), mRNA. [Source:RefSeq mRNA;Acc:NM_001246509]

Parental	GNLGEGTFGKVV-ECLDHARGKSQVA-LKIIRNVGKYREAARLEINVL-KKIKEKDKENKFLCVLMSDWF
	GNLG.G..GK.V.ECLD.AR..S.VA....I.NVGK.REAA...IN.L.KKI.EKD.EN..LCVL..DWF
Retrocopy	GNLGQGACGKGV<ECLDPARRTSRVA<RRVICNVGKHREAAPPKINAL>KKINEKD*ENQLLCVLGCDWF

Parental	NFHG-HMCIAFELLGKNTFEFLKENNFQPYP-LPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNS
	..HG..M.I.FELLG..T.EF.K.NN.QP.P.LPHV.HMA.QLCH.LRFLHEN.LTH..LK.ENIL.V.S
Retrocopy	TLHG<SMHITFELLGRKTLEFPKDNNIQPFP<LPHVWHMAHQLCHTLRFLHENRLTHAHLKTENILHVDS

Parental	EFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVAT-RHYRPPEVILELGWAQPCDVWSIGCI
	E..T.Y..H.S..EKSV..TS.RVADF..AT.D.EHHT..V.T..H.R.PE.IL.LGW..PC.V...G..
Retrocopy	ELKTVYSKHRS-DEKSVRSTSVRVADFPNATSDREHHTAMVTT<GHCRLPELILDLGWTRPCHVQGMGYL

Parental	LFEYYR-GFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLK
	LF.YY..GFTLFQT.EN.E.LVM..K.L.PIP...I..T.KQKYFYK.GLVWDENSSD..YVK.NCK.LK
Retrocopy	LFKYYQ<GFTLFQTCENQERLVML-KTLRPIPLCVISCTKKQKYFYKWGLVWDENSSDSPYVK-NCKRLK

Parental	SYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLT-PEERSFHTSRNPSR
	S.MLQDSLEHVQLF.LMRR....D.AQ.ITLAE.LLHP.FAGL..P...SFHTS.NPSR
Retrocopy	SDMLQDSLEHVQLFELMRRVVKLDAAQHITLAETLLHPVFAGLA>PQS*SFHTSHNPSR

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

RetrogeneDB ID:

retro_ptro_405