RetrogeneDB - Retrocopy retro_ocun

						
>retro_ocun_1261
CATCAGCCTGCTCAACCCTTTAAATGTACAATTTCAGAATCCTGCGATGGGATTAGGGAAGAGTTTCAGTTTTTACAGGC

TCAATACCACAGTTTGAAGCTGGAATGTGAGAAACTCGCCAGTGAGAAGACGGAGATACAGCGGCATTACGTCATGTACT

AGGAAATGTCCTGTGGGTTGAATTTAGAAATGCACAAGCAGGCAGAGGTTGTCAAGAGGCTGAATGCTATCGGAGCACAA

GTCATCCCTTTCCTGTCCCAAGAGCACCAGCAGCAAGTGGTGCAGGCTGTGGAATGGGCCAAGTAGGTGACCACGGCAGA

ACTGAACGCCATCATTGGGCAACAACTCCAGGCTCAGCATTTATCACATGGACAGGGGCTGCCAGTGCCTCTGATCCACA

CCCTTCTGGGCTTCAGCCACCTGCTGTTGCACCCATTGGCAGCAGTGCCGGACTTCTGGCCCTCTGTAGTGCCCTAGGAG

GCCAGTCTCACCTTCCAATTAAAGATGAGGAGAAGCACCAGGAAAACGATCACCCAGGAGACGGAGACTCCATCAAGAGC

TCGTCTGTATCCCCGTCAGCCAGGTTCCACGCTTAGAAGCACAGAAACTCCACAGACTGCTCCCGGGAGAGCAAAAGCAG

GCAACTGAGGAAAAGGAAATTGTAGCTCATTATGACAGTGATGGTGAGAAGAGTCATGACAACTTGGCAGTTAATGTTTC

CAATGAGGATCCATCTTCCGCCTGGGGGGAGCCCAGCACACTCCCCAAGAGAGAACGGCCTGGCCAAGACACGCCTGCTC

AAGAAAGATGCCCCCGTCAGCCCCGCTTCCATGCCTCTTCCAGCAGTACTCCTTCCTCCAGCTCCAAAGAACTTAGCCTT

AATGAAAAACCTACCACTCCTGTTTCAAAGTCTAATACCTCCACTCCACGAACTGATGCACCCACTCCAGGCAGTAATCC

CACTCCCGGATTGAGGCCTGTACCTGGAAAACTACCAGGAGTTGACCCTTTGGCTTCCAGCCTGAGGACCCCAGTGGCGA

TACCTTGTCCATATCCAACCCCATTTGGGATTGTTCCCCATGCTGGGATGAATGGAGAGCTGACCAGCCCGGAGCCGCCT

ATGCTGGACTGCACTACATCTCCCCTCAGATGAGTGGTGGGATTTGATCCGCATCGTCA

ORF - retro_ocun_1261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	83.5 %
Parental protein coverage:	51.1 %
Number of stop codons detected:	4
Number of frameshifts detected	5

Retrocopy - Parental Gene Alignment:

									ParentalHQPSHPEQFTISESCIRIKEEFQFFRPQYHSLKLECEKLASEKTEMQRHYVMYYEMSYGLNIEMHKQAEI
		HQP..P...TISESC..I.EEFQF...QYHSLKLECEKLASEKTE.QRHYVMY.EMS.GLN.EMHKQAE.
RetrocopyHQPAQPFKCTISESCDGIREEFQFLQAQYHSLKLECEKLASEKTEIQRHYVMY*EMSCGLNLEMHKQAEV
ParentalVKRLNAICAQVIPFLSQEHQQQVVQAVERAKQVTMAELNAIIGQQLQAQHLSHGHGLPVPLT-PHPSGLQ
		VKRLNAI.AQVIPFLSQEHQQQVVQAVE.AK.VT.AELNAIIGQQLQAQHLSHG.GLPVPL..PHPSGLQ
RetrocopyVKRLNAIGAQVIPFLSQEHQQQVVQAVEWAK*VTTAELNAIIGQQLQAQHLSHGQGLPVPLI<PHPSGLQ
ParentalPPAIPPIGSSAGLLALSSALGGQSHLPIKDEKKHHENDHQRDRDSIKSSSVSPSASFRGAEKHRNSTDYS
		PPA..PIGSSAGLLAL.SALGGQSHLPIKDE.KH.ENDH..D.DSIKSSSVSPSA.F..A.KHRNSTD.S
RetrocopyPPAVAPIGSSAGLLALCSALGGQSHLPIKDEEKHQENDHPGDGDSIKSSSVSPSARFH-A*KHRNSTDCS
ParentalSESK-KQKTEEKEIAARYDSDGEKSDDNLVVDVSNEDPSS-PRGSPAHSPRENGLDKTRLLKKDAPISPA
		.ESK.KQ.TEEKEI.A.YDSDGEKS.DNL.V.VSNEDPSS.P.GSPAHSPRENGL.KTRLLKKDAP.SPA
RetrocopyRESK<KQATEEKEIVAHYDSDGEKSHDNLAVNVSNEDPSS>PGGSPAHSPRENGLAKTRLLKKDAPVSPA
ParentalSI-ASSSSTPSSKSKELSLNEKSTTPVSKSNTPTPRTDAPTPGSNSTPGLRPVPGKPPGVDPLASSLRTP
		S..ASSSSTPSS.SKELSLNEK.TTPVSKSNT.TPRTDAPTPGSN.TPGLRPVPGK.PGVDPLASSLRTP
RetrocopySM<ASSSSTPSSSSKELSLNEKPTTPVSKSNTSTPRTDAPTPGSNPTPGLRPVPGKLPGVDPLASSLRTP
ParentalMAVPCPYPTPFGIVPHAGMNGELTSP-GAAYAGLHNISPQMSAAAAAAAA
		.A.PCPYPTPFGIVPHAGMNGELTSP.GAAYAGLH.ISPQMS.....A..
RetrocopyVAIPCPYPTPFGIVPHAGMNGELTSP<GAAYAGLHYISPQMSGGI*SASS

							

							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	49 .56 RPM
SRP017611_kidney	0 .41 RPM	31 .72 RPM
SRP017611_liver	0 .08 RPM	5 .78 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_1261 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1261 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ocun_1261 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	ENSOCUG00000011891	1 retrocopy	retro_ocun_1261 ,

	RetrogeneDB ID:	retro_ocun_1261
Retrocopy location	Organism:	*Rabbit (Oryctolagus cuniculus)*
	Coordinates:	4:75599617..75600796(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	TLE4
	Ensembl ID:	ENSOCUG00000011891
	Aliases:	None
	Description:	transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila) [Source:HGNC Symbol;Acc:11840]

Parental	HQPSHPEQFTISESCIRIKEEFQFFRPQYHSLKLECEKLASEKTEMQRHYVMYYEMSYGLNIEMHKQAEI
	HQP..P...TISESC..I.EEFQF...QYHSLKLECEKLASEKTE.QRHYVMY.EMS.GLN.EMHKQAE.
Retrocopy	HQPAQPFKCTISESCDGIREEFQFLQAQYHSLKLECEKLASEKTEIQRHYVMY*EMSCGLNLEMHKQAEV

Parental	VKRLNAICAQVIPFLSQEHQQQVVQAVERAKQVTMAELNAIIGQQLQAQHLSHGHGLPVPLT-PHPSGLQ
	VKRLNAI.AQVIPFLSQEHQQQVVQAVE.AK.VT.AELNAIIGQQLQAQHLSHG.GLPVPL..PHPSGLQ
Retrocopy	VKRLNAIGAQVIPFLSQEHQQQVVQAVEWAK*VTTAELNAIIGQQLQAQHLSHGQGLPVPLI<PHPSGLQ

Parental	PPAIPPIGSSAGLLALSSALGGQSHLPIKDEKKHHENDHQRDRDSIKSSSVSPSASFRGAEKHRNSTDYS
	PPA..PIGSSAGLLAL.SALGGQSHLPIKDE.KH.ENDH..D.DSIKSSSVSPSA.F..A.KHRNSTD.S
Retrocopy	PPAVAPIGSSAGLLALCSALGGQSHLPIKDEEKHQENDHPGDGDSIKSSSVSPSARFH-A*KHRNSTDCS

Parental	SESK-KQKTEEKEIAARYDSDGEKSDDNLVVDVSNEDPSS-PRGSPAHSPRENGLDKTRLLKKDAPISPA
	.ESK.KQ.TEEKEI.A.YDSDGEKS.DNL.V.VSNEDPSS.P.GSPAHSPRENGL.KTRLLKKDAP.SPA
Retrocopy	RESK<KQATEEKEIVAHYDSDGEKSHDNLAVNVSNEDPSS>PGGSPAHSPRENGLAKTRLLKKDAPVSPA

Parental	SI-ASSSSTPSSKSKELSLNEKSTTPVSKSNTPTPRTDAPTPGSNSTPGLRPVPGKPPGVDPLASSLRTP
	S..ASSSSTPSS.SKELSLNEK.TTPVSKSNT.TPRTDAPTPGSN.TPGLRPVPGK.PGVDPLASSLRTP
Retrocopy	SM<ASSSSTPSSSSKELSLNEKPTTPVSKSNTSTPRTDAPTPGSNPTPGLRPVPGKLPGVDPLASSLRTP

Parental	MAVPCPYPTPFGIVPHAGMNGELTSP-GAAYAGLHNISPQMSAAAAAAAA
	.A.PCPYPTPFGIVPHAGMNGELTSP.GAAYAGLH.ISPQMS.....A..
Retrocopy	VAIPCPYPTPFGIVPHAGMNGELTSP<GAAYAGLHYISPQMSGGI*SASS

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

RetrogeneDB ID:

retro_ocun_1261