RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_1841
CTACGCGCTGGCCAGCCATGTGACTGCCTTCCTCCCCTGCGGGCAGCAGCTGAGCAGCTACGGCAGAAGGATCTGAGGAT

TTCCCAGCTGCAAGCGGAACTCCGACGGCCACCCCCTGCCCCTGCCCAGCCCCCTGAACCCGAGGCCCTGCCTACTATCT

ATGTTGTTACCCCCACCTATGCCAGGCTGGTACAGAAGGCAGAGTTGGTACGGCTGTCCCAGACACTGAGCCTGGTGTCC

CGGCTGCATTGACTGCTGGTGGAGGATGCTGAGGGTCCCACCCCGCTGGTCTCAGGGCTGCTGGCTGCCTCTGGCCTCCT

CTTCACACACCTGGTGGTCCTCACGCCCAAAGCCCAGTGGCTTCGGGAGGGCAAGCCTGGCTGGGTTCATCCCCATGGTG

TCGAGCAGCGGAACAAGGCCCTGGACTGGCTCCGGGGCAGAGGGAGTGCTGTGGGTGGGGAGAAGGACCCATCACCACCA

GGGACCCAAGGAGTCGTGTACTTTGCTGACAGTGGCAACACCTACAGCTGGGAGCTGTTTGAGGAGATGCGCTGGACCCG

TGGTGTCTCAGTGTGGCCTGTGGGGCTGGTGGGTGGCCTGCGAGTCAAGGACCCTCAGGTACAGGACAGCCGGGTAGTGG

GCTTCCACACAGCATGGGAGCCCAACAGGCCCTTCCCTGTGGGTATGGCCGGATTTGCTGTGGCCCTGCCCTTGCTGTTA

GCTAAGCCCAATGCCCAGTTTGATTCCACTGCTCCCCGGAGCCACCTGGAGAGCAGTCTTCTAAGCCACCTTGTGGATCC

CAAGGACCTGGAGCCATGGGCTGCCAACTGCACTCGGATACTGGTGTGACATACACGGACAGCGAAGCCCAAGATGAAGC

AGGAGGAGCAGCTGCAGCGGCAGGGCCAGGGCTCAGACCCAGCAATTGAGGTG

ORF - retro_ptro_1841 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	91.96 %
Parental protein coverage:	92.84 %
Number of stop codons detected:	2
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalVQLGQPCDCLPPLRAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQKAELV
		...GQPCDCLPPLRAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQKAELV
RetrocopyLRAGQPCDCLPPLRAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQKAELV
ParentalRLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQRLREGEPGWVHPRGVEQRNKA
		RLSQTLSLV.RLH.LLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQ.LREG.PGWVHP.GVEQRNKA
RetrocopyRLSQTLSLVSRLH*LLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQWLREGKPGWVHPHGVEQRNKA
ParentalLDWLRGRGGAVGGEKDPPPPGTQGVVYFADDDNTYSRELFEEMRWTRGVSVWPVGLVGGLRFEGPQVQDG
		LDWLRGRG.AVGGEKDP.PPGTQGVVYFAD..NTYS.ELFEEMRWTRGVSVWPVGLVGGLR...PQVQD.
RetrocopyLDWLRGRGSAVGGEKDPSPPGTQGVVYFADSGNTYSWELFEEMRWTRGVSVWPVGLVGGLRVKDPQVQDS
ParentalRVVGFHTAWEPNRPFPVDMAGFAVALPLLLDKPNAQFDSTAPRGHLESSLLSHLVDPKDLEPRAANCTRV
		RVVGFHTAWEPNRPFPV.MAGFAVALPLLL.KPNAQFDSTAPR.HLESSLLSHLVDPKDLEP.AANCTR.
RetrocopyRVVGFHTAWEPNRPFPVGMAGFAVALPLLLAKPNAQFDSTAPRSHLESSLLSHLVDPKDLEPWAANCTRI
ParentalLVWHTRTEKPKMKQEEQLQRQGRGSDPAIEV
		LV.HTRT.KPKMKQEEQLQRQG.GSDPAIEV
RetrocopyLV*HTRTAKPKMKQEEQLQRQGQGSDPAIEV

							

							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 .27 RPM	49 .87 RPM
SRP007412_cerebellum	0 .14 RPM	20 .58 RPM
SRP007412_heart	0 .03 RPM	3 .06 RPM
SRP007412_kidney	0 .10 RPM	21 .31 RPM
SRP007412_liver	0 .03 RPM	15 .94 RPM
SRP007412_testis	0 .95 RPM	2 .63 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_1841 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1841 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_1841 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2724
Gorilla gorilla	retro_ggor_1896
Pongo abelii	retro_pabe_2266

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000149541	1 retrocopy	retro_hsap_2724,
Gorilla gorilla	ENSGGOG00000013604	1 retrocopy	retro_ggor_1896,
Nomascus leucogenys	ENSNLEG00000003956	1 retrocopy	retro_nleu_589,
Pongo abelii	ENSPPYG00000025907	1 retrocopy	retro_pabe_2266,
Pan troglodytes	ENSPTRG00000039665	1 retrocopy	retro_ptro_1841 ,

	RetrogeneDB ID:	retro_ptro_1841
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	3:164240246..164241179(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	B3GAT3P1
	Ensembl ID:	ENSPTRG00000039665
	Aliases:	None
	Description:	Pan troglodytes beta-1,3-glucuronyltransferase 3 (glucuronosyltransferase I) (B3GAT3), mRNA. [Source:RefSeq mRNA;Acc:NM_001242626]

Parental	VQLGQPCDCLPPLRAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQKAELV
	...GQPCDCLPPLRAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQKAELV
Retrocopy	LRAGQPCDCLPPLRAAAEQLRQKDLRISQLQAELRRPPPAPAQPPEPEALPTIYVVTPTYARLVQKAELV

Parental	RLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQRLREGEPGWVHPRGVEQRNKA
	RLSQTLSLV.RLH.LLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQ.LREG.PGWVHP.GVEQRNKA
Retrocopy	RLSQTLSLVSRLH*LLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQWLREGKPGWVHPHGVEQRNKA

Parental	LDWLRGRGGAVGGEKDPPPPGTQGVVYFADDDNTYSRELFEEMRWTRGVSVWPVGLVGGLRFEGPQVQDG
	LDWLRGRG.AVGGEKDP.PPGTQGVVYFAD..NTYS.ELFEEMRWTRGVSVWPVGLVGGLR...PQVQD.
Retrocopy	LDWLRGRGSAVGGEKDPSPPGTQGVVYFADSGNTYSWELFEEMRWTRGVSVWPVGLVGGLRVKDPQVQDS

Parental	RVVGFHTAWEPNRPFPVDMAGFAVALPLLLDKPNAQFDSTAPRGHLESSLLSHLVDPKDLEPRAANCTRV
	RVVGFHTAWEPNRPFPV.MAGFAVALPLLL.KPNAQFDSTAPR.HLESSLLSHLVDPKDLEP.AANCTR.
Retrocopy	RVVGFHTAWEPNRPFPVGMAGFAVALPLLLAKPNAQFDSTAPRSHLESSLLSHLVDPKDLEPWAANCTRI

Parental	LVWHTRTEKPKMKQEEQLQRQGRGSDPAIEV
	LV.HTRT.KPKMKQEEQLQRQG.GSDPAIEV
Retrocopy	LV*HTRTAKPKMKQEEQLQRQGQGSDPAIEV

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

RetrogeneDB ID:

retro_ptro_1841