RetrogeneDB - Retrocopy retro_pabe

						
>retro_pabe_746
ATGCTCTGGTTTCAAGGAAATAGCATGCAACTTGCCAGATCCTCCCTTGGACTCTTCTTGATAAACTGCTCCGCCTCTAA

GACAACTCTGCCTGTGCTGACCTTATTCACAAAGGACCCATGTCCCCTCTGTGGCAAAGCCAAGGAAGTACTCAAGCCTT

ATAAAAACAGGGTTTATTTTACAGGAGGTGAACGTCACACTTCCAGAAAACTCTGCCTGGTATGAAAGGTATAAATTTGA

CATTCCTGTCTTTCACTTGTGTGGCCAGTTTCCTGATGATGCATCGAGAAAACACCTCAAAACTTGAAAAACAGCTCCTG

AAACTTGAGCAGCAAAGTACCGGA

ORF - retro_pabe_746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	88.79 %
Parental protein coverage:	100. %
Number of stop codons detected:	0
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalMLWFQGNSMQLARSSFGLFLRNCSASKTTLPVLTLFTKDSCPLCDEAKEVLKPYKNR-FIFQEVNITLPE
		MLWFQGNSMQLARSS.GLFL.NCSASKTTLPVLTLFTKD.CPLC..AKEVLKPYKNR.FI.QEVN.TLPE
RetrocopyMLWFQGNSMQLARSSLGLFLINCSASKTTLPVLTLFTKDPCPLCGKAKEVLKPYKNR>FILQEVNVTLPE
ParentalNSVWYERYKFDIPVFHLNGQ-FLMMHRVNTSKLEKQLRKLEQQSTG
		NS.WYERYKFDIPVFHL.GQ.FLMMHR.NTSKLEKQL.KLEQQSTG
RetrocopyNSAWYERYKFDIPVFHLCGQ>FLMMHRENTSKLEKQLLKLEQQSTG

							

							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	1 .27 RPM
SRP007412_cerebellum	0 .00 RPM	3 .28 RPM
SRP007412_heart	0 .00 RPM	1 .96 RPM
SRP007412_kidney	0 .00 RPM	3 .68 RPM
SRP007412_liver	0 .00 RPM	2 .57 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_746 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_746 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_pabe_746 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_788
Gorilla gorilla	retro_ggor_653
Macaca mulatta	retro_mmul_1091

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000164241	1 retrocopy	retro_hsap_788,
Gorilla gorilla	ENSGGOG00000006111	1 retrocopy	retro_ggor_653,
Macaca mulatta	ENSMMUG00000009523	1 retrocopy	retro_mmul_1091,
Pongo abelii	ENSPPYG00000015732	1 retrocopy	retro_pabe_746 ,

	RetrogeneDB ID:	retro_pabe_746
Retrocopy location	Organism:	*Orangutan (Pongo abelii)*
	Coordinates:	11:9486219..9486563(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	C5orf63
	Ensembl ID:	ENSPPYG00000015732
	Aliases:	None
	Description:	chromosome 5 open reading frame 63 [Source:HGNC Symbol;Acc:40051]

Parental	MLWFQGNSMQLARSSFGLFLRNCSASKTTLPVLTLFTKDSCPLCDEAKEVLKPYKNR-FIFQEVNITLPE
	MLWFQGNSMQLARSS.GLFL.NCSASKTTLPVLTLFTKD.CPLC..AKEVLKPYKNR.FI.QEVN.TLPE
Retrocopy	MLWFQGNSMQLARSSLGLFLINCSASKTTLPVLTLFTKDPCPLCGKAKEVLKPYKNR>FILQEVNVTLPE

Parental	NSVWYERYKFDIPVFHLNGQ-FLMMHRVNTSKLEKQLRKLEQQSTG
	NS.WYERYKFDIPVFHL.GQ.FLMMHR.NTSKLEKQL.KLEQQSTG
Retrocopy	NSAWYERYKFDIPVFHLCGQ>FLMMHRENTSKLEKQLLKLEQQSTG

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

RetrogeneDB ID:

retro_pabe_746