RetrogeneDB - Retrocopy retro_ptro

                        
>retro_ptro_2215
ATGTCCGGCCTGCGGGCGCTGCCGGGCTCGGGCTGCTGGCTGCGGCTCGCGCCTGCGCGAATCAAAAGCCAGACCAGCGC

CTGCCGCTCGGGACCCACCTAGTGGGGACCGCAGCGGCTGAACTCGGGTGGCCGCTGGGACTCAGCGGTCATGGCGAGCA

TAGCGGTGAAGCACCTGAGCCAGGAGGAAGCCCAGGCCGTGGACCAGGAGCTATTCAACGAGTACTAGTTCAGCGTGGAC

CGACTTGTGGAGCTGGCCGGGCTGAGCTGTGCCGCAGCCATCGCCGAGGCATATTCCCCCACGTCCATGTCCAGGAGCTC

CACTACTGTCCTGGTCATCTGTGGCCCGGGGAATAATGGAGGAGATGGTCTGGTCTGTGCTCCGCACCTCAAACTCTTTG

GCTAACCAGCCAACCCTCTATTACCCCAAAAGGCCTAACAAGCCCCTCTTCATTGCGTTGGTGACCCCGCGTCAGAAAAT

GGACATCCCTTTCCTTGGGGAAATGCGCTCAGAGCCCGTGATGATTGAGCTGTATGAGCTGGTGGTGGATGCCATCTTCG

GCTTCAGCTTCGAGGGTGATGTTCGGGAACGTTCCACAGCATCCTGAGGGTCCTGAAGGGATTCACCGTGCCCACTGCCG

GCATCAACATTCCCTCAGGATGGGATGTGGAGAAGGGAAACTCTGGAGGGATCCAGCCAGACTTGCTCATCTCCCTCACA

GCACCCAAAAAGTCTGCAACCCAGGTTACCCGGTCGCCACCATTACCTGGGGGGTCGTTTTGTGCCACCTGCTCTGGAAA

AGAAGTAGCAGCTGAACCTGCCCCCTACCCTGACACCAAGTGTGTGTAT

ORF - retro_ptro_2215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	83.22 %
Parental protein coverage:	98.96 %
Number of stop codons detected:	3
Number of frameshifts detected:	7

Retrocopy - Parental Gene Alignment:

                                ParentalMSRLRAL-LGLGLLVA-GSRL-PRIKSQTVACRSGPTWWGPQRLNSGGRWDSEVMASTVVKYLSQEEAQA
MS.LRAL..GLGLL.A.GSRL..RIKSQT.ACRSGPT.WGPQRLNSGGRWDS.VMAS..VK.LSQEEAQA
RetrocopyMSGLRAL<AGLGLLAA<GSRL<ARIKSQTSACRSGPT*WGPQRLNSGGRWDSAVMASIAVKHLSQEEAQA
ParentalVDQELFNEYQFSVDQLMELAGLSCATAIAKAYPPTSMSRSPPTVLVICGPGNNGGDGLVCARHLKLFG-Y
VDQELFNEY.FSVD.L.ELAGLSCA.AIA.AY.PTSMSRS..TVLVICGPGNNGGDGLVCA.HLKLFG..
RetrocopyVDQELFNEY*FSVDRLVELAGLSCAAAIAEAYSPTSMSRSSTTVLVICGPGNNGGDGLVCAPHLKLFG>N
ParentalEPTIYYPKRPNKPLFTALVTQCQKMDIPFLGEMPAEPMTIDELYELVVDAIFGFSFKGDVRE-PFHSILS
.PT.YYPKRPNKPLF.ALVT..QKMDIPFLGEM..EP..I.ELYELVVDAIFGFSF.GDVRE..FHSIL.
RetrocopyQPTLYYPKRPNKPLFIALVTPRQKMDIPFLGEMRSEPVMI-ELYELVVDAIFGFSFEGDVRE<TFHSILR
ParentalVLKGLTVPIASIDIPSGWDVEKGNAGGIQPDLLISLTAPKKSATQFT-GRYHYLGGRFVPPALEKKYQLN
VLKG.TVP.A.I.IPSGWDVEKGN.GGIQPDLLISLTAPKKSATQ.T.GR.HYLGGRFVPPALEKK.QLN
RetrocopyVLKGFTVPTAGINIPSGWDVEKGNSGGIQPDLLISLTAPKKSATQVT>GRHHYLGGRFVPPALEKK*QLN
ParentalLP-PYPDTECVY
LP.PYPDT.CVY
RetrocopyLP<PYPDTKCVY

                            

                            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 .09 RPM	46 .04 RPM
SRP007412_cerebellum	0 .00 RPM	38 .21 RPM
SRP007412_heart	0 .00 RPM	51 .85 RPM
SRP007412_kidney	0 .03 RPM	82 .93 RPM
SRP007412_liver	0 .10 RPM	47 .50 RPM
SRP007412_testis	0 .21 RPM	34 .04 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_2215 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_2215 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_2215 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3275
Gorilla gorilla	retro_ggor_2228
Pongo abelii	retro_pabe_2709
Macaca mulatta	retro_mmul_2060

Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000163382	2 retrocopies	retro_hsap_1973, retro_hsap_3275,
Gorilla gorilla	ENSGGOG00000000754	1 retrocopy	retro_ggor_2228,
Macaca mulatta	ENSMMUG00000002623	2 retrocopies	retro_mmul_1364, retro_mmul_2060,
Nomascus leucogenys	ENSNLEG00000012663	2 retrocopies	retro_nleu_2615, retro_nleu_2992,
Pongo abelii	ENSPPYG00000000713	2 retrocopies	retro_pabe_1692, retro_pabe_2709,
Pan troglodytes	ENSPTRG00000001463	2 retrocopies	retro_ptro_1315, retro_ptro_2215 ,

	RetrogeneDB ID:	retro_ptro_2215
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	5:179273172..179274021(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	APOA1BP
	Ensembl ID:	ENSPTRG00000001463
	Aliases:	None
	Description:	NAD(P)H-hydrate epimerase [Source:UniProtKB/TrEMBL;Acc:H2Q098]

Parental	MSRLRAL-LGLGLLVA-GSRL-PRIKSQTVACRSGPTWWGPQRLNSGGRWDSEVMASTVVKYLSQEEAQA
	MS.LRAL..GLGLL.A.GSRL..RIKSQT.ACRSGPT.WGPQRLNSGGRWDS.VMAS..VK.LSQEEAQA
Retrocopy	MSGLRAL<AGLGLLAA<GSRL<ARIKSQTSACRSGPT*WGPQRLNSGGRWDSAVMASIAVKHLSQEEAQA

Parental	VDQELFNEYQFSVDQLMELAGLSCATAIAKAYPPTSMSRSPPTVLVICGPGNNGGDGLVCARHLKLFG-Y
	VDQELFNEY.FSVD.L.ELAGLSCA.AIA.AY.PTSMSRS..TVLVICGPGNNGGDGLVCA.HLKLFG..
Retrocopy	VDQELFNEY*FSVDRLVELAGLSCAAAIAEAYSPTSMSRSSTTVLVICGPGNNGGDGLVCAPHLKLFG>N

Parental	EPTIYYPKRPNKPLFTALVTQCQKMDIPFLGEMPAEPMTIDELYELVVDAIFGFSFKGDVRE-PFHSILS
	.PT.YYPKRPNKPLF.ALVT..QKMDIPFLGEM..EP..I.ELYELVVDAIFGFSF.GDVRE..FHSIL.
Retrocopy	QPTLYYPKRPNKPLFIALVTPRQKMDIPFLGEMRSEPVMI-ELYELVVDAIFGFSFEGDVRE<TFHSILR

Parental	VLKGLTVPIASIDIPSGWDVEKGNAGGIQPDLLISLTAPKKSATQFT-GRYHYLGGRFVPPALEKKYQLN
	VLKG.TVP.A.I.IPSGWDVEKGN.GGIQPDLLISLTAPKKSATQ.T.GR.HYLGGRFVPPALEKK.QLN
Retrocopy	VLKGFTVPTAGINIPSGWDVEKGNSGGIQPDLLISLTAPKKSATQVT>GRHHYLGGRFVPPALEKK*QLN

Parental	LP-PYPDTECVY
	LP.PYPDT.CVY
Retrocopy	LP<PYPDTKCVY

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

RetrogeneDB ID:

retro_ptro_2215