RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_1818
CCTCCCGTGGAAGGTGCTCTTGTCTTCCGGGCGCTGGGTCCCATCGGGCCCTCCTCACCTGGGCTCACCCTCGGGGGCCT

GGCCGTGAGCGAGCACCGGCTCAGCAACAGGCTGCTGGCCTGGAGCGGCGTCCTCGAGTGACAGGAGAAGCGCAGACCCT

ACTGTGACTCCACTGTAAAGTTGAGGCGGACCCTGCCCTGCCAAGCCTACGTGAACCAAGGCGAGAACCTGGAGACCAAC

CAGTGGCAGCAGAAGCTGATCATGCAGCTGATCCCGCAGCAGCTGATGACCACCCTGGGACCCCTGTTCCGCAACTCCCA

GCTGGCACAGTTCCACTTCACCAACCGAGACTGCTGCTTGCTCAGTGGGCTCTGCCGCATCATGGGCAACGGCTTGGCGG

GCTGCACGCTGTTTCCCCACATCTCCCCCTGCGAGATGTGCGTGCGCATGCTCCTGTACTCTTCCAAGAGGCAGATCTTC

ATGGGCTTCATCCCCTACGACCAGAGCGGCTTCATCAGCGCCATCCGGCAGGTCATCACTACCCGCAAGCAAGCAGTGGG

ACCTGGTAGTGTCAACTCAGGCCCAGTCCAGATCTTCAACAACAAGTTCCTGGCGTGGAGAGGCGTCATGGAGTGGCAGG

AACCCAGGCCTGAGCCCAAAAGTCGATCCAAAAGGTGGCTGCCGTCCCACGTCTACGTGAACCAGGGGGAGATCATGAGG

ACCGAGCAGTGGCCGAGGAAGCTGTACATGCAGCTCATCCCACAGCAGCTGCTGACCACCCTGTGCTGCTGTTGCGGAAC

TCGTGCCTGGTACAGTTCCACTTCACCAAGGACCTGGAGACGCTGAAGAGCCTGTGCCAGATCATGGACAATGGCTTCGC

CGGCTGAGTGCATTTGTCCTACAAAGCGTTGTGCGAGATCCGCGTGCTC

ORF - retro_ptro_1818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	88.1 %
Parental protein coverage:	87.82 %
Number of stop codons detected:	2
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalPQTEGARVFGALGPIGPSSPGLTLGGLAVSEHRLSNKLLAWSGVLEWQEKRRPYSDSTAKLKRTLPCQAY
		P..EGA.VF.ALGPIGPSSPGLTLGGLAVSEHRLSN.LLAWSGVLE.QEKRRPY.DST.KL.RTLPCQAY
RetrocopyPPVEGALVFRALGPIGPSSPGLTLGGLAVSEHRLSNRLLAWSGVLE*QEKRRPYCDSTVKLRRTLPCQAY
ParentalVNQGENLETDQWPQKLIMQLIPQQLLTTLGPLFRNSQLAQFHFTNRDCDSLKGLCRIMGNGFAGCMLFPH
		VNQGENLET.QW.QKLIMQLIPQQL.TTLGPLFRNSQLAQFHFTNRDC..L.GLCRIMGNG.AGC.LFPH
RetrocopyVNQGENLETNQWQQKLIMQLIPQQLMTTLGPLFRNSQLAQFHFTNRDCCLLSGLCRIMGNGLAGCTLFPH
ParentalISPCEVRVLMLLYSSKKKIFMGLIPYDQSGFVSAIRQVITTRKQAVGPGGVNSGPVQIVNNKFLAWSGVM
		ISPCE..V.MLLYSSK..IFMG.IPYDQSGF.SAIRQVITTRKQAVGPG.VNSGPVQI.NNKFLAW.GVM
RetrocopyISPCEMCVRMLLYSSKRQIFMGFIPYDQSGFISAIRQVITTRKQAVGPGSVNSGPVQIFNNKFLAWRGVM
ParentalEWQEPRPEPNSRSKRWLPSHVYVNQGEILRTEQWPRKLYMQLIPQQLLTTL-VPLFRNSRLVQFHFTKDL
		EWQEPRPEP.SRSKRWLPSHVYVNQGEI.RTEQWPRKLYMQLIPQQLLTTL.V.L.RNS.LVQFHFTKDL
RetrocopyEWQEPRPEPKSRSKRWLPSHVYVNQGEIMRTEQWPRKLYMQLIPQQLLTTL<VLLLRNSCLVQFHFTKDL
ParentalETLKSLCRIMDNGFAGCVHFSYKASCEIRVL
		ETLKSLC.IMDNGFAG.VH.SYKA.CEIRVL
RetrocopyETLKSLCQIMDNGFAG*VHLSYKALCEIRVL

							

							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 .07 RPM	83 .26 RPM
SRP007412_cerebellum	0 .04 RPM	44 .63 RPM
SRP007412_heart	0 .00 RPM	9 .79 RPM
SRP007412_kidney	0 .03 RPM	73 .70 RPM
SRP007412_liver	0 .10 RPM	36 .70 RPM
SRP007412_testis	0 .21 RPM	23 .82 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_1818 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1818 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_1818 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2694
Gorilla gorilla	retro_ggor_1877
Pongo abelii	retro_pabe_2288
Macaca mulatta	retro_mmul_1426

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003495	1 retrocopy	retro_cfam_289,
Callithrix jacchus	ENSCJAG00000004105	1 retrocopy	retro_cjac_445,
Homo sapiens	ENSG00000104960	1 retrocopy	retro_hsap_2694,
Gorilla gorilla	ENSGGOG00000010182	1 retrocopy	retro_ggor_1877,
Macaca mulatta	ENSMMUG00000011618	1 retrocopy	retro_mmul_1426,
Nomascus leucogenys	ENSNLEG00000005374	1 retrocopy	retro_nleu_1191,
Pongo abelii	ENSPPYG00000010265	1 retrocopy	retro_pabe_2288,
Pan troglodytes	ENSPTRG00000011321	1 retrocopy	retro_ptro_1818 ,

	RetrogeneDB ID:	retro_ptro_1818
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	3:123678946..123679875(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSPTRG00000039922
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	PTOV1
	Ensembl ID:	ENSPTRG00000011321
	Aliases:	None
	Description:	prostate tumor overexpressed 1 [Source:HGNC Symbol;Acc:9632]

Parental	PQTEGARVFGALGPIGPSSPGLTLGGLAVSEHRLSNKLLAWSGVLEWQEKRRPYSDSTAKLKRTLPCQAY
	P..EGA.VF.ALGPIGPSSPGLTLGGLAVSEHRLSN.LLAWSGVLE.QEKRRPY.DST.KL.RTLPCQAY
Retrocopy	PPVEGALVFRALGPIGPSSPGLTLGGLAVSEHRLSNRLLAWSGVLE*QEKRRPYCDSTVKLRRTLPCQAY

Parental	VNQGENLETDQWPQKLIMQLIPQQLLTTLGPLFRNSQLAQFHFTNRDCDSLKGLCRIMGNGFAGCMLFPH
	VNQGENLET.QW.QKLIMQLIPQQL.TTLGPLFRNSQLAQFHFTNRDC..L.GLCRIMGNG.AGC.LFPH
Retrocopy	VNQGENLETNQWQQKLIMQLIPQQLMTTLGPLFRNSQLAQFHFTNRDCCLLSGLCRIMGNGLAGCTLFPH

Parental	ISPCEVRVLMLLYSSKKKIFMGLIPYDQSGFVSAIRQVITTRKQAVGPGGVNSGPVQIVNNKFLAWSGVM
	ISPCE..V.MLLYSSK..IFMG.IPYDQSGF.SAIRQVITTRKQAVGPG.VNSGPVQI.NNKFLAW.GVM
Retrocopy	ISPCEMCVRMLLYSSKRQIFMGFIPYDQSGFISAIRQVITTRKQAVGPGSVNSGPVQIFNNKFLAWRGVM

Parental	EWQEPRPEPNSRSKRWLPSHVYVNQGEILRTEQWPRKLYMQLIPQQLLTTL-VPLFRNSRLVQFHFTKDL
	EWQEPRPEP.SRSKRWLPSHVYVNQGEI.RTEQWPRKLYMQLIPQQLLTTL.V.L.RNS.LVQFHFTKDL
Retrocopy	EWQEPRPEPKSRSKRWLPSHVYVNQGEIMRTEQWPRKLYMQLIPQQLLTTL<VLLLRNSCLVQFHFTKDL

Parental	ETLKSLCRIMDNGFAGCVHFSYKASCEIRVL
	ETLKSLC.IMDNGFAG.VH.SYKA.CEIRVL
Retrocopy	ETLKSLCQIMDNGFAG*VHLSYKALCEIRVL

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

RetrogeneDB ID:

retro_ptro_1818