RetrogeneDB - Retrocopy retro_ptro

                        
>retro_ptro_3168
ATGGCAACTGTGATGACCGTGACCAATGTTCCAGAGATCTATGATGTGAGGAGAACTGAGCATAGAGGTGTTCACTCCCA

CATCTGAGGACTGGGGCTGGATGATGCTTTGGAGGCTCAACAGGCTTCCCAGGGCATGGTGGGTCAGCTTTGCTGCACAG

CAGGCAGCTCGTGTGGGGCTGGAGATGATCCATAAAGGGAAGATTGTCAAGTGGGCAGTCCTCATTGCTGGTCAGCTGGG

CAGAGGGAAGACAGCCATCGCCCTAGACATGGCATAGGCCCTGGGACCTGACACCTTGTTCATAGCCATCACCGGCAGTG

AGATCTCCCTGGAGATGAGCAAGACCCAGGCACTGACACAGGCTTTCTGGCCATCTTTTGGCATTCACTTCAAGGAGGAG

ATGGAGATCATCGAAGGGGAAGTGGTTGAGACCCAGATTTATAGAACAGTGACAGGAATGGGCTCCAAGGTGGGCAAACT

GACTAACAAAACCAAGAAGATGGAGACCATCTATGACCTGGGCATGAAGATGATTGAGTCCCTGACCAAAGACAAGATCC

ACGCTGGTGACATGATCACTATTGACAAAGCAATGGGAAAGATCTCCAAGTTGGGCCACTCCTTTACATGGTCTGGTGAC

TACAACCCCATGGACTCCCAGACCAAATTCAGGCAGCCCCCATATGGGAAGCTCCAGAAATGCAAGGCGCATACTGTGTC

CCTTGCACAAGATCAACATCATCAACTCCCACACGCATGGCTTCCTGGCTCTCTTCTCATGTGACACAAGAGAGATCAAG

TCAGAAGTTGCCAAGCAGATCAATGTCAAAGTGGCCGAGTGGATGGAACAAAATAGA

ORF - retro_ptro_3168 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	71.38 %
Parental protein coverage:	62.2 %
Number of stop codons detected:	2
Number of frameshifts detected:	2

Retrocopy - Parental Gene Alignment:

                                ParentalMATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQL-AARRAAGVVLEMIREGKIA
MATV...T.VPEI.DV.R.E..G.HSHI.GLGLDDALE..QASQGMVGQL.AA..AA.V.LEMI..GKI.
RetrocopyMATVMTVTNVPEIYDVRRTEHRGVHSHI*GLGLDDALEAQQASQGMVGQL>AAQQAARVGLEMIHKGKIV
ParentalGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIE
..AVLIAGQ.G.GKTAIA..MA.ALGPDT.F.AI.GSEI.SLEMSKT.ALTQAF..S.G...KEE.EIIE
RetrocopyKWAVLIAGQLGRGKTAIALDMA*ALGPDTLFIAITGSEI-SLEMSKTQALTQAFWPSFGIHFKEEMEIIE
ParentalGEVVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRSF
GEVVE.QI.R..TG.GSKVGKLT.KT..METIYDLG.KMIESLTKDK..AGD.ITIDKA.GKISKLG.SF
RetrocopyGEVVETQIYRTVTGMGSKVGKLTNKTKKMETIYDLGMKMIESLTKDKIHAGDMITIDKAMGKISKLGHSF
ParentalTRARDYDAMGSQTKFVQCPDGELQKRKEVVHTVS-LHEIDVINSRTQGFLALFSGDTGEIKSEVREQINA
T...DY..M.SQTKF.Q.P.G.LQK.K...HTVS.LH.I..INS.T.GFLALFS.DT.EIKSEV..QIN.
RetrocopyTWSGDYNPMDSQTKFRQPPYGKLQKCK--AHTVS>LHKINIINSHTHGFLALFSCDTREIKSEVAKQINV
ParentalKVAEWREEGK
KVAEW.E...
RetrocopyKVAEWMEQNR

                            

                            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	31 .53 RPM
SRP007412_cerebellum	0 .00 RPM	26 .85 RPM
SRP007412_heart	0 .00 RPM	9 .53 RPM
SRP007412_kidney	0 .00 RPM	35 .67 RPM
SRP007412_liver	0 .00 RPM	32 .47 RPM
SRP007412_testis	0 .00 RPM	197 .38 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_3168 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_3168 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_3168 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4755
Gorilla gorilla	retro_ggor_2961
Pongo abelii	retro_pabe_3701
Macaca mulatta	retro_mmul_2536

Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000222	2 retrocopies	retro_cjac_329, retro_cjac_4119,
Homo sapiens	ENSG00000183207	1 retrocopy	retro_hsap_4755,
Gorilla gorilla	ENSGGOG00000009245	1 retrocopy	retro_ggor_2961,
Macropus eugenii	ENSMEUG00000000069	1 retrocopy	retro_meug_2099,
Macaca mulatta	ENSMMUG00000003915	1 retrocopy	retro_mmul_2536,
Nomascus leucogenys	ENSNLEG00000004769	1 retrocopy	retro_nleu_1251,
Otolemur garnettii	ENSOGAG00000007519	2 retrocopies	retro_ogar_2473, retro_ogar_3246,
Pongo abelii	ENSPPYG00000010225	1 retrocopy	retro_pabe_3701,
Pan troglodytes	ENSPTRG00000011270	1 retrocopy	retro_ptro_3168 ,

	RetrogeneDB ID:	retro_ptro_3168
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	X:129035096..129035953(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	RUVBL2
	Ensembl ID:	ENSPTRG00000011270
	Aliases:	None
	Description:	None

Parental	MATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQL-AARRAAGVVLEMIREGKIA
	MATV...T.VPEI.DV.R.E..G.HSHI.GLGLDDALE..QASQGMVGQL.AA..AA.V.LEMI..GKI.
Retrocopy	MATVMTVTNVPEIYDVRRTEHRGVHSHI*GLGLDDALEAQQASQGMVGQL>AAQQAARVGLEMIHKGKIV

Parental	GRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIE
	..AVLIAGQ.G.GKTAIA..MA.ALGPDT.F.AI.GSEI.SLEMSKT.ALTQAF..S.G...KEE.EIIE
Retrocopy	KWAVLIAGQLGRGKTAIALDMA*ALGPDTLFIAITGSEI-SLEMSKTQALTQAFWPSFGIHFKEEMEIIE

Parental	GEVVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRSF
	GEVVE.QI.R..TG.GSKVGKLT.KT..METIYDLG.KMIESLTKDK..AGD.ITIDKA.GKISKLG.SF
Retrocopy	GEVVETQIYRTVTGMGSKVGKLTNKTKKMETIYDLGMKMIESLTKDKIHAGDMITIDKAMGKISKLGHSF

Parental	TRARDYDAMGSQTKFVQCPDGELQKRKEVVHTVS-LHEIDVINSRTQGFLALFSGDTGEIKSEVREQINA
	T...DY..M.SQTKF.Q.P.G.LQK.K...HTVS.LH.I..INS.T.GFLALFS.DT.EIKSEV..QIN.
Retrocopy	TWSGDYNPMDSQTKFRQPPYGKLQKCK--AHTVS>LHKINIINSHTHGFLALFSCDTREIKSEVAKQINV

Parental	KVAEWREEGK
	KVAEW.E...
Retrocopy	KVAEWMEQNR

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

RetrogeneDB ID:

retro_ptro_3168