RetrogeneDB - Retrocopy retro_ocun

						
>retro_ocun_1669
CTTCAGGGACTGGAATATAGAGGATACGATTCTGCTGGTGTGGGAGTTGATGGAGGCAATGACAAAGAACTGGGAAGCCA

ATGCCTGCAAAATCCAGCTCATTAAGAAGAAAGGAAAAGTTAAGGCACTGGATGAAGAAGTCTACAAACAACAGGCTATG

GATTTGGATATAGAATTTGATGTCCACCTTGGAATGGCTCATACCTGTTGGGCAACACATGGAGAACCCAATCCTGTCAA

TAGCCACCCGCAGCGCTCTGATAAAAATAGCGAATTTATTGTCATTCACAATGGAATCATCACTAACTACAAAGACTTGA

AAAAGTTTTTGGAGAGCAAAGGCTATGGCTTTGAAACTGAAACAGACACAGAGACAATCGCCAAGCTTGTTTAGTATATG

TATGACAATCGGGAAAGTCAAGATATCAGTTCTACAACCTTGGTGGAGACAGTTATCCAACAACTGGAAGGTTCTTTTGC

ACTTGTGTTTAAGAGCGTTCATTTCCCTGGTCAAGCAGTTGGCACAAGGTGAGGTAGCCCTCTGCTGACTGGTGTACAGA

GTGAACATAAAATTTCTATTGATCACATTCTGATACTGTACAGAAGAGGCAAAGACAAGAAGGGGAGCTGCAATCTCTCA

TGTGGACAGCACAACTTGCCTTTTCCCTGTTGAAGAAAAAGCAGTGGAATATTACTTTGCTTCTGATGCAAGTGCTGCCA

TAGAACATACCAACCACGTCATCTTTCTAGAAGATGATGATGTTGCAGCAGTGGTGGATGGCCGTTTTTCTATCCATCGA

ATTAAATGGACTGCAGGAGATCACCCTGGATGAGCTGTGCAAACCCTGCAGATGGAACTCCTACAGATCATAAAGGGCAA

TTTCAGTTCATTTATGCAGAAGGAAATTTTTGAGCAGCCAGAGTCCATGATGAACACAATGAAAGGAAGAATCAACTTTA

ATGACTATGCTGTGAATCTGGGTGGTATGAAGGATCACATTAAGGAGATCCAGAGGTGTCAGTTCTGATCCCTGTTGCCT

GTGGAACGAGTTACCATGCTGGAGTAGCAACACATCCAGTTCTGGAGGAGCTGACAGAGTTGCCTGTGATGGTGGAAGTA

GCCAGTGACTTCTTGGAGAGAAACACGCCAGTCTTTCAAGATGACATTTGCTTTTTCATCAGTCAGTCAGGT

ORF - retro_ocun_1669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	86.78 %
Parental protein coverage:	78.04 %
Number of stop codons detected:	3
Number of frameshifts detected	3

Retrocopy - Parental Gene Alignment:

									ParentalLQRLEYRGYDSAGVGVDGGNDKD-WEANACKIQLIKKKGKVKALDEEVHKQQDMDLDIEFDVHLGIAHTR
		LQ.LEYRGYDSAGVGVDGGNDK..WEANACKIQLIKKKGKVKALDEEV.KQQ.MDLDIEFDVHLG.AHT.
RetrocopyLQGLEYRGYDSAGVGVDGGNDKE>WEANACKIQLIKKKGKVKALDEEVYKQQAMDLDIEFDVHLGMAHTC
ParentalWATHGEPNPVNSHPQRSDKNNEFIVIHNGIITNYKDLKKFLESKGYDFESETDTETIAKLVKYMYDNRES
		WATHGEPNPVNSHPQRSDKN.EFIVIHNGIITNYKDLKKFLESKGY.FE.ETDTETIAKLV.YMYDNRES
RetrocopyWATHGEPNPVNSHPQRSDKNSEFIVIHNGIITNYKDLKKFLESKGYGFETETDTETIAKLV*YMYDNRES
ParentalQDISFTTLVERVIQQLEGAFALVFKSVHFPGQAVGTRRGSPLLIGVRSEHKLSTDHIPILYRTGKDK-KG
		QDIS.TTLVE.VIQQLEG.FALVFKSVHFPGQAVGTR.GSPLL.GV.SEHK.S.DHI.ILYR.GKDK..G
RetrocopyQDISSTTLVETVIQQLEGSFALVFKSVHFPGQAVGTR*GSPLLTGVQSEHKISIDHILILYRRGKDK>RG
ParentalSCNLSRVDSTTCLFPVEEKAVEYYFASDASAVIEHTNRVIFLEDDDVAAVVDGRLSIHRIKRTAGDHPGR
		....S.VDSTTCLFPVEEKAVEYYFASDASA.IEHTN.VIFLEDDDVAAVVDGR.SIHRIK.TAGDHPG.
RetrocopyAA-ISHVDSTTCLFPVEEKAVEYYFASDASAAIEHTNHVIFLEDDDVAAVVDGRFSIHRIKWTAGDHPG*
ParentalAVQTLQMELQQIMKGNFSSFMQKEIFEQPESVVNTMRGRVNFDDYTVNLGGLKDHIKEIQRCR-RLILIA
		AVQTLQMEL.QI.KGNFSSFMQKEIFEQPES..NTM.GR.NF.DY.VNLGG.KDHIKEIQRC...LI..A
RetrocopyAVQTLQMELLQIIKGNFSSFMQKEIFEQPESMMNTMKGRINFNDYAVNLGGMKDHIKEIQRCQ<VLIPVA
ParentalCGTSYHAGVATRQVLEELTELPVMVELASDFLDRNTPVFRDDVCFFISQSG
		CGTSYHAGVAT..VLEELTELPVMVE.ASDFL.RNTPVF.DD.CFFISQSG
RetrocopyCGTSYHAGVATHPVLEELTELPVMVEVASDFLERNTPVFQDDICFFISQSG

							

							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
SRP017611_brain	0 .33 RPM	12 .14 RPM
SRP017611_kidney	0 .41 RPM	20 .17 RPM
SRP017611_liver	0 .23 RPM	2 .70 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_1669 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1669 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ocun_1669 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000029568	1 retrocopy	retro_ocun_1669 ,

	RetrogeneDB ID:	retro_ocun_1669
Retrocopy location	Organism:	*Rabbit (Oryctolagus cuniculus)*
	Coordinates:	GL018752:598277..599469(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	GFPT1
	Ensembl ID:	ENSOCUG00000029568
	Aliases:	None
	Description:	glutamine--fructose-6-phosphate transaminase 1 [Source:HGNC Symbol;Acc:4241]

Parental	LQRLEYRGYDSAGVGVDGGNDKD-WEANACKIQLIKKKGKVKALDEEVHKQQDMDLDIEFDVHLGIAHTR
	LQ.LEYRGYDSAGVGVDGGNDK..WEANACKIQLIKKKGKVKALDEEV.KQQ.MDLDIEFDVHLG.AHT.
Retrocopy	LQGLEYRGYDSAGVGVDGGNDKE>WEANACKIQLIKKKGKVKALDEEVYKQQAMDLDIEFDVHLGMAHTC

Parental	WATHGEPNPVNSHPQRSDKNNEFIVIHNGIITNYKDLKKFLESKGYDFESETDTETIAKLVKYMYDNRES
	WATHGEPNPVNSHPQRSDKN.EFIVIHNGIITNYKDLKKFLESKGY.FE.ETDTETIAKLV.YMYDNRES
Retrocopy	WATHGEPNPVNSHPQRSDKNSEFIVIHNGIITNYKDLKKFLESKGYGFETETDTETIAKLV*YMYDNRES

Parental	QDISFTTLVERVIQQLEGAFALVFKSVHFPGQAVGTRRGSPLLIGVRSEHKLSTDHIPILYRTGKDK-KG
	QDIS.TTLVE.VIQQLEG.FALVFKSVHFPGQAVGTR.GSPLL.GV.SEHK.S.DHI.ILYR.GKDK..G
Retrocopy	QDISSTTLVETVIQQLEGSFALVFKSVHFPGQAVGTR*GSPLLTGVQSEHKISIDHILILYRRGKDK>RG

Parental	SCNLSRVDSTTCLFPVEEKAVEYYFASDASAVIEHTNRVIFLEDDDVAAVVDGRLSIHRIKRTAGDHPGR
	....S.VDSTTCLFPVEEKAVEYYFASDASA.IEHTN.VIFLEDDDVAAVVDGR.SIHRIK.TAGDHPG.
Retrocopy	AA-ISHVDSTTCLFPVEEKAVEYYFASDASAAIEHTNHVIFLEDDDVAAVVDGRFSIHRIKWTAGDHPG*

Parental	AVQTLQMELQQIMKGNFSSFMQKEIFEQPESVVNTMRGRVNFDDYTVNLGGLKDHIKEIQRCR-RLILIA
	AVQTLQMEL.QI.KGNFSSFMQKEIFEQPES..NTM.GR.NF.DY.VNLGG.KDHIKEIQRC...LI..A
Retrocopy	AVQTLQMELLQIIKGNFSSFMQKEIFEQPESMMNTMKGRINFNDYAVNLGGMKDHIKEIQRCQ<VLIPVA

Parental	CGTSYHAGVATRQVLEELTELPVMVELASDFLDRNTPVFRDDVCFFISQSG
	CGTSYHAGVAT..VLEELTELPVMVE.ASDFL.RNTPVF.DD.CFFISQSG
Retrocopy	CGTSYHAGVATHPVLEELTELPVMVEVASDFLERNTPVFQDDICFFISQSG

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

RetrogeneDB ID:

retro_ocun_1669