RetrogeneDB - Retrocopy retro_pabe

						
>retro_pabe_467
ATGAGGGAAATTGTGCATATCCAGGCCTGTCAGTGTGGCAACCAGACGGGTGCCAAGTGCTGGGATGTGATCAGTGATGA

ACGTGAAATCGACCCCACCAGCACCTAACATGGGGACAGCGACCTGCAGCTGGACTGTGTCTCCATGTACTACAGTGAAG

CCACAGATGGCAAATATGTTCCTTGTGCTATCCTGGTGGATCTAGAACCTGGGACCATGGACTCTGCTAGCTCAGGCCCT

TTTGGCCAGGTGTTTAAACCAGACAACTTTGTTTTTGGTCAATCTGGGGCATGCAACAACTGGGCCAAAGGCCACTACAT

AGAGGGGGCCAAGCTGGTTGATTCAGTTGTAGATGTGGTACAGGAGGAGTAAGAGAGCTGTGACTGCCTGCAGGGTTTCC

AGCTGACCCACTCAATGGGCTTTGGAATGGGTACTCTCTTTATCAGCAAGATCCAAGAAGAGTGCCCTGATTGCATCATG

AACACCTTCAGTGTGGTGCCTCCACCCAAAGTGTCTGACACTGTGGTCGGGCCCTATAACATCACCCTTTCCGTCCATCA

GTCGTTAGAGAACACGGATGAGACCTACTGCATTGACAATGAGGCCCTCTATGACATCTGCTTCCGCACTTTGAAGCTGA

CCACACCAAACTATGGGGACTTGAACCACCTTGTCTCAGCCACCATAAGCAGTGTTACCATCTGTCTCCGCTTCCCTGGC

CAGCTCAATGCTGACCTCCACAAGTTGGCAGTCAAACTGGTGCCCTTACCACGTCTCCACTACTTCATGGCTGGCTTTGC

CCTCTCACCAGCTGTGGAAGCCAGCAGCATCGAGCTTTCACGGTGCCCGAACTCATCTGGCAGGATTTCAATGCCATGAA

CATAATG

ORF - retro_pabe_467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	80.07 %
Parental protein coverage:	67.57 %
Number of stop codons detected:	2
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalMREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEP
		MREIVHIQA.QCGNQ.GAK.W.VISDE..IDPT.T.HGDSDLQLD..S.YY.EAT.GKYVP.AILVDLEP
RetrocopyMREIVHIQACQCGNQTGAKCWDVISDEREIDPTST*HGDSDLQLDCVSMYYSEATDGKYVPCAILVDLEP
ParentalGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG
		GTMDS..SGPFGQ.F.PDNFVFGQSGA.NNWAKGHY.EGA.LVDSV.DVV..E.ESCDCLQGFQLTHS.G
RetrocopyGTMDSASSGPFGQVFKPDNFVFGQSGACNNWAKGHYIEGAKLVDSVVDVVQEE*ESCDCLQGFQLTHSMG
ParentalGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDI
		.G....MGTL.ISKI.EE.PD.IMNTFSVVP.PKVSDTVV.PYN.TLSVHQ..ENTDETYCIDNEALYDI
RetrocopyFG----MGTLFISKIQEECPDCIMNTFSVVPPPKVSDTVVGPYNITLSVHQSLENTDETYCIDNEALYDI
ParentalCFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFA-PLTSRGSQ
		CFRTLKLTTP.YGDLNHLVSAT.S.VT.CLRFPGQLNADL.KLAV..VP.PRLH.FM.GFA.PLTS.GSQ
RetrocopyCFRTLKLTTPNYGDLNHLVSATISSVTICLRFPGQLNADLHKLAVKLVPLPRLHYFMAGFA<PLTSCGSQ
ParentalQYRALTVPELTQQVFDAKNMM
		Q.RA.TVPEL..Q.F.A.N.M
RetrocopyQHRAFTVPELIWQDFNAMNIM

							

							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 .06 RPM	297 .35 RPM
SRP007412_cerebellum	0 .49 RPM	155 .53 RPM
SRP007412_heart	0 .12 RPM	108 .46 RPM
SRP007412_kidney	0 .23 RPM	127 .75 RPM
SRP007412_liver	2 .02 RPM	135 .81 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_467 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_467 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_pabe_467 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_155
Pan troglodytes	retro_ptro_151
Gorilla gorilla	retro_ggor_244
Macaca mulatta	retro_mmul_375

Parental genes homology:

Parental genes homology involve 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006969	2 retrocopies	retro_btau_471, retro_btau_55,
Canis familiaris	ENSCAFG00000000443	1 retrocopy	retro_cfam_1860,
Macaca mulatta	ENSMMUG00000023684	2 retrocopies	retro_mmul_2501, retro_mmul_375,
Nomascus leucogenys	ENSNLEG00000005348	1 retrocopy	retro_nleu_498,
Otolemur garnettii	ENSOGAG00000032213	1 retrocopy	retro_ogar_2391,
Ochotona princeps	ENSOPRG00000014770	4 retrocopies	retro_opri_1106, retro_opri_237, retro_opri_46, retro_opri_656,
Pongo abelii	ENSPPYG00000011180	1 retrocopy	retro_pabe_3250,
Pongo abelii	ENSPPYG00000016419	4 retrocopies	retro_pabe_2920, retro_pabe_3210, retro_pabe_3698, retro_pabe_467 ,

	RetrogeneDB ID:	retro_pabe_467
Retrocopy location	Organism:	*Orangutan (Pongo abelii)*
	Coordinates:	1:176727201..176728088(-)
	Located in intron of:	ENSPPYG00000001340
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	TUBB
	Ensembl ID:	ENSPPYG00000016419
	Aliases:	TUBB2A, TUBB, TUBB5
	Description:	Tubulin beta chain [Source:UniProtKB/Swiss-Prot;Acc:Q5R943]

Parental	MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEP
	MREIVHIQA.QCGNQ.GAK.W.VISDE..IDPT.T.HGDSDLQLD..S.YY.EAT.GKYVP.AILVDLEP
Retrocopy	MREIVHIQACQCGNQTGAKCWDVISDEREIDPTST*HGDSDLQLDCVSMYYSEATDGKYVPCAILVDLEP

Parental	GTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG
	GTMDS..SGPFGQ.F.PDNFVFGQSGA.NNWAKGHY.EGA.LVDSV.DVV..E.ESCDCLQGFQLTHS.G
Retrocopy	GTMDSASSGPFGQVFKPDNFVFGQSGACNNWAKGHYIEGAKLVDSVVDVVQEE*ESCDCLQGFQLTHSMG

Parental	GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDI
	.G....MGTL.ISKI.EE.PD.IMNTFSVVP.PKVSDTVV.PYN.TLSVHQ..ENTDETYCIDNEALYDI
Retrocopy	FG----MGTLFISKIQEECPDCIMNTFSVVPPPKVSDTVVGPYNITLSVHQSLENTDETYCIDNEALYDI

Parental	CFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFA-PLTSRGSQ
	CFRTLKLTTP.YGDLNHLVSAT.S.VT.CLRFPGQLNADL.KLAV..VP.PRLH.FM.GFA.PLTS.GSQ
Retrocopy	CFRTLKLTTPNYGDLNHLVSATISSVTICLRFPGQLNADLHKLAVKLVPLPRLHYFMAGFA<PLTSCGSQ

Parental	QYRALTVPELTQQVFDAKNMM
	Q.RA.TVPEL..Q.F.A.N.M
Retrocopy	QHRAFTVPELIWQDFNAMNIM

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

RetrogeneDB ID:

retro_pabe_467