RetrogeneDB - Retrocopy retro_pabe

                        
>retro_pabe_1272
ACAGAAGCACCCGAAGTAGTGACAAAGGAGGAGGATGACGATGAAGAGACTGCCCCTCCCGTTATTGCCCCACCACTGGA

TCATACCAAATCAATTTACACACGGTCTGTAATTGACCCTGTTCCTGCACCAGTTGGTGATTCAAATGTTGATGGTGGTG

GCAAGTCTTTAGACAAACAGAAAAAGAAGACTAAGATGACAGATGAAGAGATTATGGAGAAATTAAGAACTATTGTGAGC

ATAGGTGACCCGAAGAAAAAATTATACAAGATATGAAAAAACTGGACAAGGGGCTTCTGGTACAGTTTTCACTGCTACTG

ACGTTGCACTGGGACAGAAGGTTGCTATCAAACAAATTAATTTACAGAAACAGCCAAAGAAGGAATTGATCATTAATGAG

ATTCTGGTGATGAAAGAATTAAAAAATCCCAACATAGTTAACTTCTTGGACAGTTACCTGGTAGGAGATGAATTGTTTGT

GGTCATGGAATACCTTGCTGGGGGGTCACTCACTGATGTGGTAACAGAAACCTGCATGGATGAAGCACAGATCGCTGCTG

TATGCAGAGAGAGTTTACAGGCATTGGAGTTTTTACATGCTAATCAAGTGATCCACAGAGACATCAAAAGTGACAGTGTA

CTTTTGGGAATGGAAGGATCGGTTAAGCTCACTGACTTTGGTTTCTGTGCCCAGATCACCCCTGAGCAGAGCAAACGCAG

TACCATGGTCAGAACGCCATACTGGATGGCACCAGAGGTGGTTACATGGAAGGCTTATGGCCCTAAAGTCAACGTATGGT

CTCTGGGTATCATGGCTACTGAGATGGTAGAAGGAGAGCCTCCATACCTCGATGAAAATCCCTTGAGGGCCTTGTGCCTA

ATAGCAACTAATGGAATCCCAGAACTTCAGAATCCAGAGAAACTTTCCCCAATATTTCGGGATTTCTTAAATCGATGTTT

GGAAACGGATGTGGAAAGAAGGGGCTCAGCCAAAGAATTATTACAGCATCTTTTCCTGAAACTAGCCAAACTGTTATCTA

GCTTGACGCCACTGATCATGGCAGCTAAAGAAGCAATGAAGAGTAACCAC

ORF - retro_pabe_1272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	75.34 %
Parental protein coverage:	66.12 %
Number of stop codons detected:	0
Number of frameshifts detected:	1

Retrocopy - Parental Gene Alignment:

                                ParentalTPPPVIAPRPEHTKSVYTRSVIEPLPVTPTRDVATSPIS---PTENNTTPPDALTRNTEKQKKKPKMSDE
T..P......E.........VI.P.P...T....T.......P........D.......KQKKK.KM.DE
RetrocopyTEAPEVVTKEEDDDEETAPPVIAP-PLDHTKSIYTRSVIDPVPAPVGDSNVDGGGKSLDKQKKKTKMTDE
ParentalEILEKLRSIVSVGDPKKK-YTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMR
EI.EKLR.IVS.GDPKKK.YTR.EK.GQGASGTV.TA.DVA.GQ.VAIKQ.NLQ.QPKKELIINEILVM.
RetrocopyEIMEKLRTIVSIGDPKKK>YTRYEKTGQGASGTVFTATDVALGQKVAIKQINLQKQPKKELIINEILVMK
ParentalENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRDI
E.KNPNIVN.LDSYLVGDEL.VVMEYLAGGSLTDVVTETCMDE.QIAAVCRE.LQALEFLH.NQVIHRDI
RetrocopyELKNPNIVNFLDSYLVGDELFVVMEYLAGGSLTDVVTETCMDEAQIAAVCRESLQALEFLHANQVIHRDI
ParentalKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEG
KSD..LLGM.GSVKLTDFGFCAQITPEQSKRSTMV.TPYWMAPEVVT.KAYGPKV..WSLGIMA.EM.EG
RetrocopyKSDSVLLGMEGSVKLTDFGFCAQITPEQSKRSTMVRTPYWMAPEVVTWKAYGPKVNVWSLGIMATEMVEG
ParentalEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSL
EPPYL.ENPLRAL.LIATNG.PELQNPEKLS.IFRDFLNRCLE.DVE.RGSAKELLQH.FLK.AK.LSSL
RetrocopyEPPYLDENPLRALCLIATNGIPELQNPEKLSPIFRDFLNRCLETDVERRGSAKELLQHLFLKLAKLLSSL
ParentalTPLIAAAKEATKNNH
TPLI.AAKEA.K.NH
RetrocopyTPLIMAAKEAMKSNH

                            

                            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 .17 RPM	427 .89 RPM
SRP007412_cerebellum	0 .24 RPM	266 .18 RPM
SRP007412_heart	0 .21 RPM	6 .23 RPM
SRP007412_kidney	0 .46 RPM	30 .06 RPM
SRP007412_liver	0 .24 RPM	6 .58 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_1272 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_1272 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_pabe_1272 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000164	1 retrocopy	retro_cpor_1301,
Pongo abelii	ENSPPYG00000003708	1 retrocopy	retro_pabe_1272 ,

	RetrogeneDB ID:	retro_pabe_1272
Retrocopy location	Organism:	*Orangutan (Pongo abelii)*
	Coordinates:	15:18476672..18477762(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSPPYG00000006250
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	PAK1
	Ensembl ID:	ENSPPYG00000003708
	Aliases:	None
	Description:	p21 protein (Cdc42/Rac)-activated kinase 1 [Source:HGNC Symbol;Acc:8590]

Parental	TPPPVIAPRPEHTKSVYTRSVIEPLPVTPTRDVATSPIS---PTENNTTPPDALTRNTEKQKKKPKMSDE
	T..P......E.........VI.P.P...T....T.......P........D.......KQKKK.KM.DE
Retrocopy	TEAPEVVTKEEDDDEETAPPVIAP-PLDHTKSIYTRSVIDPVPAPVGDSNVDGGGKSLDKQKKKTKMTDE

Parental	EILEKLRSIVSVGDPKKK-YTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMR
	EI.EKLR.IVS.GDPKKK.YTR.EK.GQGASGTV.TA.DVA.GQ.VAIKQ.NLQ.QPKKELIINEILVM.
Retrocopy	EIMEKLRTIVSIGDPKKK>YTRYEKTGQGASGTVFTATDVALGQKVAIKQINLQKQPKKELIINEILVMK

Parental	ENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRDI
	E.KNPNIVN.LDSYLVGDEL.VVMEYLAGGSLTDVVTETCMDE.QIAAVCRE.LQALEFLH.NQVIHRDI
Retrocopy	ELKNPNIVNFLDSYLVGDELFVVMEYLAGGSLTDVVTETCMDEAQIAAVCRESLQALEFLHANQVIHRDI

Parental	KSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEG
	KSD..LLGM.GSVKLTDFGFCAQITPEQSKRSTMV.TPYWMAPEVVT.KAYGPKV..WSLGIMA.EM.EG
Retrocopy	KSDSVLLGMEGSVKLTDFGFCAQITPEQSKRSTMVRTPYWMAPEVVTWKAYGPKVNVWSLGIMATEMVEG

Parental	EPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSL
	EPPYL.ENPLRAL.LIATNG.PELQNPEKLS.IFRDFLNRCLE.DVE.RGSAKELLQH.FLK.AK.LSSL
Retrocopy	EPPYLDENPLRALCLIATNGIPELQNPEKLSPIFRDFLNRCLETDVERRGSAKELLQHLFLKLAKLLSSL

Parental	TPLIAAAKEATKNNH
	TPLI.AAKEA.K.NH
Retrocopy	TPLIMAAKEAMKSNH

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

RetrogeneDB ID:

retro_pabe_1272