RetrogeneDB - Retrocopy retro_ocun

						
>retro_ocun_765
AAAGAAGTTGACAAAGTTCAATAACAGTCCAGATAGGGACATGAAGGAAACAGAGACATTGTTACAGAACCACATAAGGC

AGAGGAGGAAAATGAGAAGGCCAATGACAGAGACACCAGAGAAGTGGATTTGCTGGCCAATGAAGTAGAAGACTTTGAGA

AGAAAAAGGTTGCTGCTTGAGCTCTCACTGGGATCCTGGCCTCTCACCCCAACAGAAATGATGCCCACGTCATCAACCTT

TCACTCACCTTTCACGGCCAAGATCTGCTCAGTTACGCCAAACTGGAATTAAACTTGGGTTATCGGTATGGCCTCATTGG

CTCAAATGGAATTGGGAAGTCCATATTAGTGTCTGCTATTGGGGAAATAGGAAGTGCCTATCCCTGAACACATCGGCACC

TAGCATATGACTTGAGACAGGCCTCCTAGTGACAAGACACCCTGGAAACATTTAGAGAAAGTTGACACAGAGCAGGCCAT

GCTGGAGAGGGAGGCTGAGCTGTTAGCTCATGAGGACACAGAGTGTGAAAAGCTCATGGAGATCTATGAGCACCTGAAGG

AGCTGCATGACAAGGTAGAGATGAGGGCCTCATAGATTTTAGCACAGACTGGGTTTTATGCCTGCCATGCAGTGCAAGAA

GCTAAAAGACTTTACTGGCAGCTAGAAGATGAGGGTTACCCCCACAGGAGACCACTTTATTTGGCCCTTTATAATGCTCC

TGGATGCGCCACCAACTGCTTGGACCTATATATATGAGTGTGGTTGGAAGAACTAAAAACCTTCAAAAATGTGCTGGTTC

TTATGTCGCATTCCATGAGCTTTCTGAATGGTGTCTGTACCAACATCACTTCACGTGTGCGAGAAGCTGAAATATTATAT

GAGTAACTACTATCGTATGTGAAGAACAGCTGGAGCTGGAGGAGAACCAGATGACGAGGTTTCACTGGGAACAAGATCAG

ATTTGTACACATGAACAGCTGTGTTGCTAGGTTTGGTCATGGCAGTGCCAGGCTA

ORF - retro_ocun_765 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	66.67 %
Parental protein coverage:	52.55 %
Number of stop codons detected:	9
Number of frameshifts detected	7

Retrocopy - Parental Gene Alignment:

									ParentalKEAAKARQRPKKGHEENGDAVTEPQVAEEKNE-ANGREATEVDLLTKELEDFELKKAAARAVTGVLASHP
		KE..K.......GHE.N.D.VTEP..AEE.NE.AN.R...EVDLL..E.EDFE.KK.AA.A.TG.LASHP
RetrocopyKEVDKVQ*QSR*GHEGNRDIVTEPHKAEEENEKANDRDTREVDLLANEVEDFEKKKVAA*ALTGILASHP
ParentalNSTDVHIINLSLTFHGQELLSDTKLELNSGRRYGLIGLNGIGKSMLLSAI-GKREVPIPEHIDIYHLTRE
		N..D.H.INLSLTFHGQ.LLS..KLELN.G.RYGLIG.NGIGKS.L.SAI.GK.EVPIPEHI...H.T..
RetrocopyNRNDAHVINLSLTFHGQDLLSYAKLELNLGYRYGLIGSNGIGKSILVSAI>GK*EVPIPEHIGT*HMT*D
ParentalMPPSDKTPLQCVMEVDTERAMLEREAERLAHEDAECEKLMELYERLEELDADKAEMRASRIL-HGLGFTP
		.PPSDKTP......VDTE.AMLEREAE.LAHED.ECEKLME.YE.L.EL..DK.EMRAS.IL.H.LGF.P
RetrocopyRPPSDKTPWKHLEKVDTEQAMLEREAELLAHEDTECEKLMEIYEHLKELH-DKVEMRAS*IL>HRLGFMP
ParentalAMQRKKLKDFSGGWRMRVALARALFIRPFMLLLDEP-TNHLDLDACVWLEEELKTFKRILVLVSHSQDFL
		AMQ.KKLKDF.G...MRV......FI.PF..LLD.P.TN.LDL...VWL.EELKTFK..LVL.SHS..FL
RetrocopyAMQCKKLKDFTGS*KMRVTPTGDHFIWPFIMLLDAP<TNCLDLYI*VWL-EELKTFKNVLVLMSHSMSFL
ParentalNGVCTNI-IHMHNKKLKYYTGNYDQ-YVKT-RLELEENQMKRFHWEQDQI-AHMKNYIARFGHGSAKL
		NGVCTNI..H....KLKYY..NY...YVK...LELEENQM.RFHWEQDQI..HM....ARFGHGSA.L
RetrocopyNGVCTNI>LHV-CEKLKYYMSNYYR<YVKN<QLELEENQMTRFHWEQDQI>VHMNSCVARFGHGSARL

							

							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 .00 RPM	93 .27 RPM
SRP017611_kidney	0 .00 RPM	53 .82 RPM
SRP017611_liver	0 .00 RPM	16 .03 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_765 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_765 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ocun_765 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004830	1 retrocopy	retro_cfam_1612,
Callithrix jacchus	ENSCJAG00000020371	3 retrocopies	retro_cjac_1859, retro_cjac_3526, retro_cjac_381,
Dipodomys ordii	ENSDORG00000012672	1 retrocopy	retro_dord_334,
Echinops telfairi	ENSETEG00000008032	2 retrocopies	retro_etel_1041, retro_etel_1058,
Macaca mulatta	ENSMMUG00000006679	1 retrocopy	retro_mmul_1414,
Oryctolagus cuniculus	ENSOCUG00000000245	1 retrocopy	retro_ocun_765 ,

	RetrogeneDB ID:	retro_ocun_765
Retrocopy location	Organism:	*Rabbit (Oryctolagus cuniculus)*
	Coordinates:	14:100575002..100576017(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	ABCF2
	Ensembl ID:	ENSOCUG00000000245
	Aliases:	None
	Description:	ATP-binding cassette, sub-family F (GCN20), member 2 [Source:HGNC Symbol;Acc:71]

Parental	KEAAKARQRPKKGHEENGDAVTEPQVAEEKNE-ANGREATEVDLLTKELEDFELKKAAARAVTGVLASHP
	KE..K.......GHE.N.D.VTEP..AEE.NE.AN.R...EVDLL..E.EDFE.KK.AA.A.TG.LASHP
Retrocopy	KEVDKVQQSRGHEGNRDIVTEPHKAEEENEKANDRDTREVDLLANEVEDFEKKKVAA*ALTGILASHP

Parental	NSTDVHIINLSLTFHGQELLSDTKLELNSGRRYGLIGLNGIGKSMLLSAI-GKREVPIPEHIDIYHLTRE
	N..D.H.INLSLTFHGQ.LLS..KLELN.G.RYGLIG.NGIGKS.L.SAI.GK.EVPIPEHI...H.T..
Retrocopy	NRNDAHVINLSLTFHGQDLLSYAKLELNLGYRYGLIGSNGIGKSILVSAI>GKEVPIPEHIGTHMT*D

Parental	MPPSDKTPLQCVMEVDTERAMLEREAERLAHEDAECEKLMELYERLEELDADKAEMRASRIL-HGLGFTP
	.PPSDKTP......VDTE.AMLEREAE.LAHED.ECEKLME.YE.L.EL..DK.EMRAS.IL.H.LGF.P
Retrocopy	RPPSDKTPWKHLEKVDTEQAMLEREAELLAHEDTECEKLMEIYEHLKELH-DKVEMRAS*IL>HRLGFMP

Parental	AMQRKKLKDFSGGWRMRVALARALFIRPFMLLLDEP-TNHLDLDACVWLEEELKTFKRILVLVSHSQDFL
	AMQ.KKLKDF.G...MRV......FI.PF..LLD.P.TN.LDL...VWL.EELKTFK..LVL.SHS..FL
Retrocopy	AMQCKKLKDFTGSKMRVTPTGDHFIWPFIMLLDAP<TNCLDLYIVWL-EELKTFKNVLVLMSHSMSFL

Parental	NGVCTNI-IHMHNKKLKYYTGNYDQ-YVKT-RLELEENQMKRFHWEQDQI-AHMKNYIARFGHGSAKL
	NGVCTNI..H....KLKYY..NY...YVK...LELEENQM.RFHWEQDQI..HM....ARFGHGSA.L
Retrocopy	NGVCTNI>LHV-CEKLKYYMSNYYR<YVKN<QLELEENQMTRFHWEQDQI>VHMNSCVARFGHGSARL

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

RetrogeneDB ID:

retro_ocun_765