RetrogeneDB - Retrocopy retro_pabe

						
>retro_pabe_61
ATGGGCAACGCCCCCGCCAAGAAGGACACCGAGCAGGAGAAGAGCGCGACGGAGTTCCTAGTCAAAGCCAGAGGAGATTT

CCTCTACAGATGGGGAAACCCCGCTCAAAACACCGCCAGCTCCGATCAGTTTGAACGGCTCAGGACGCTGGGCACCGGCT

CCTTCGGGCGGGTGATGCTGGTGAGGCACCGGGAGACCGGCGGCCACTACGCCATGAAGATCCTTCACAAGCAGAAGCTG

GTGAAGCTGAAGCAGGTCGAGCACACACTGAACGAGAAGCGCATCCTGCAGGCGATCGACTTTCCGTTCCTCGTCAAGCT

CCAGTTCTCCTTTAAGGACAACTCCTACCTGTACCTGGTGATGGAGTACGTGCCGGGTGGGGAGATGTTCTCCCACCTAC

GGCGCGTCGGAAGTTTCAGCGAGCCCCATGCCTGTTTCTATGCCGCCCAGGTCGTCCTGGCCTTCCAGTACCTACACTCG

CTTGACCTCATCCACCGCGACCTGAAGCCCGAGAATCTCCTCATCGACCAGCAGGGCTACCTGCGGGTGACGGACTTCGG

TTTCGCCAAGCGCGTGAAGGGCCGTACTTGGACCTTGTGCGGGACCCCACAGTACCTGGCCCCCGAGATCATCCTGAGCA

AAGGCTACAACAAGGCCGTGGACTGGTGGGCCCTAGGGGTGCTCATCTATGAGATGACTGTGGGCTTCCCACCCTTCTAC

GCCGACGAACCCATCCAGATCTACGAGAAGATCGTCTCTGGGAGGGTGCGGTTTCCCTCCAAACTCAGCTCTGACCTCAA

GGATCTGCTGCGGAGCCTGCTCCAGGTGGACCTCACCAAGCGCTTCGGAAACCTCAGGAACGGGGTTGGCGACATCAAGA

ACCACAAGTGGTTCGCCACAACCAGCTGGATCGCCATCTATGAGAAGAAGGTGGAAGCCCCCTTCATCCCGAAGTACACA

GGCCCTGGGGATGCCAGTAACTTTGACGACTACGAGGAGGAAGAGCTCCGGATCTCCATCAATGAGAAGTGTGCCAAGGA

GTTTTCTGAGTTT

ORF - retro_pabe_61 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	77.65 %
Parental protein coverage:	98.59 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalSSDASACSSSEISVKEFLAKAKEDFLKKWENPTQNNAGLEDFERKKTLGTGSFGRVMLVKHKATEQYYAM
		...A......E.S..EFL.KA..DFL..W.NP.QN.A....FER..TLGTGSFGRVMLV.H..T...YAM
RetrocopyNAPAKKDTEQEKSATEFLVKARGDFLYRWGNPAQNTASSDQFERLRTLGTGSFGRVMLVRHRETGGHYAM
ParentalKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVRLEYAFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEP
		KIL.KQK.VKLKQ.EHTLNEKRILQA..FPFLV.L...FKDNS.LY.VMEYVPGGEMFSHLRR.G.FSEP
RetrocopyKILHKQKLVKLKQVEHTLNEKRILQAIDFPFLVKLQFSFKDNSYLYLVMEYVPGGEMFSHLRRVGSFSEP
ParentalHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDHQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIIL
		HA.FYAAQ.VL.F.YLHSLDLI.RDLKPENLLID.QGY..VTDFGFAKRVKGRTWTLCGTP.YLAPEIIL
RetrocopyHACFYAAQVVLAFQYLHSLDLIHRDLKPENLLIDQQGYLRVTDFGFAKRVKGRTWTLCGTPQYLAPEIIL
ParentalSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRF
		SKGYNKAVDWWALGVLIYEM..G.PPF.AD.PIQIYEKIVSG.VRFPS..SSDLKDLLR.LLQVDLTKRF
RetrocopySKGYNKAVDWWALGVLIYEMTVGFPPFYADEPIQIYEKIVSGRVRFPSKLSSDLKDLLRSLLQVDLTKRF
ParentalGNLKNGVSDIKTHKWFATTDWIAIYQRKVEAPFIPKFRGSGDTSNFDDYEEEDIRVSITEKCAKEFGEF
		GNL.NGV.DIK.HKWFATT.WIAIY..KVEAPFIPK..G.GD.SNFDDYEEE..R.SI.EKCAKEF.EF
RetrocopyGNLRNGVGDIKNHKWFATTSWIAIYEKKVEAPFIPKYTGPGDASNFDDYEEEELRISINEKCAKEFSEF

							

							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 .50 RPM	183 .12 RPM
SRP007412_cerebellum	1 .82 RPM	179 .48 RPM
SRP007412_heart	0 .66 RPM	14 .12 RPM
SRP007412_kidney	0 .40 RPM	13 .42 RPM
SRP007412_liver	0 .31 RPM	5 .84 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_61 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_61 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_pabe_61 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_46
Pan troglodytes	retro_ptro_80
Gorilla gorilla	retro_ggor_2856
Macaca mulatta	retro_mmul_186

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000003457	1 retrocopy	retro_mmul_186,
Nomascus leucogenys	ENSNLEG00000009888	1 retrocopy	retro_nleu_2469,
Pongo abelii	ENSPPYG00000001209	1 retrocopy	retro_pabe_61 ,
Rattus norvegicus	ENSRNOG00000004978	1 retrocopy	retro_rnor_519,
Tarsius syrichta	ENSTSYG00000000380	2 retrocopies	retro_tsyr_1640, retro_tsyr_1802,

	RetrogeneDB ID:	retro_pabe_61
Retrocopy location	Organism:	*Orangutan (Pongo abelii)*
	Coordinates:	9:63705788..63706841(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSPPYG00000019273
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	PRKACB
	Ensembl ID:	ENSPPYG00000001209
	Aliases:	None
	Description:	cAMP-dependent protein kinase catalytic subunit beta isoform 2 [Source:RefSeq peptide;Acc:NP_001127665]

Parental	SSDASACSSSEISVKEFLAKAKEDFLKKWENPTQNNAGLEDFERKKTLGTGSFGRVMLVKHKATEQYYAM
	...A......E.S..EFL.KA..DFL..W.NP.QN.A....FER..TLGTGSFGRVMLV.H..T...YAM
Retrocopy	NAPAKKDTEQEKSATEFLVKARGDFLYRWGNPAQNTASSDQFERLRTLGTGSFGRVMLVRHRETGGHYAM

Parental	KILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVRLEYAFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEP
	KIL.KQK.VKLKQ.EHTLNEKRILQA..FPFLV.L...FKDNS.LY.VMEYVPGGEMFSHLRR.G.FSEP
Retrocopy	KILHKQKLVKLKQVEHTLNEKRILQAIDFPFLVKLQFSFKDNSYLYLVMEYVPGGEMFSHLRRVGSFSEP

Parental	HARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDHQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIIL
	HA.FYAAQ.VL.F.YLHSLDLI.RDLKPENLLID.QGY..VTDFGFAKRVKGRTWTLCGTP.YLAPEIIL
Retrocopy	HACFYAAQVVLAFQYLHSLDLIHRDLKPENLLIDQQGYLRVTDFGFAKRVKGRTWTLCGTPQYLAPEIIL

Parental	SKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRF
	SKGYNKAVDWWALGVLIYEM..G.PPF.AD.PIQIYEKIVSG.VRFPS..SSDLKDLLR.LLQVDLTKRF
Retrocopy	SKGYNKAVDWWALGVLIYEMTVGFPPFYADEPIQIYEKIVSGRVRFPSKLSSDLKDLLRSLLQVDLTKRF

Parental	GNLKNGVSDIKTHKWFATTDWIAIYQRKVEAPFIPKFRGSGDTSNFDDYEEEDIRVSITEKCAKEFGEF
	GNL.NGV.DIK.HKWFATT.WIAIY..KVEAPFIPK..G.GD.SNFDDYEEE..R.SI.EKCAKEF.EF
Retrocopy	GNLRNGVGDIKNHKWFATTSWIAIYEKKVEAPFIPKYTGPGDASNFDDYEEEELRISINEKCAKEFSEF

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

RetrogeneDB ID:

retro_pabe_61