RetrogeneDB - Retrocopy retro_ocun

                        
>retro_ocun_676
AAACAGAGGTATGCAAAGGAACAGAGCATCATGAATGAAGGCAGCACCAACTTATCGTCGCTGCAGATGAAGAAGGCAAA

TGTGGCCTTTTGTTTGCTTTTGGCAGGATCAAGATGAAGAAACTGCCAAGTTTGACAAGACTGTGAGAGGCCAGAGTAGC

AGTCAGCCTTGGGACAATGATGCAGTACGTGTAAACCCCTGCTCCTTGATCCCCACACCCAACAAGGAAGAGGATGAACT

AGTACATGCATATCCCACATTTGATCCTCAGGGTGTCATACCATCCAGAGCCTCACTGCTGCCTGTACTGAACTGGGCAG

AGAGAGGAAGTCTGGAAAGTCATGTTACACGAGGAAAAGAAGTACTTAGGGGATAAGCACTTTTGCAGCAACATCCTCTT

CTGCAGCCTAAAACGCGAGCGATTCTTCTGGACTGGTTAACGGAGGTACGTGATGTCTATAAACTCCACAGGAAGACATT

TTACTTGACACAGGGTTTCTTTGATCAGTGTGTGGCAACACAAGAAAATATTGTAAAAACACTTGTTCAGCTTACTGGAA

TTTCATCTTTATTCACTGCTGCTAAACATGAGGAAATCTATTCTCCCAAGTTGCATCAGTTTTCTTGTGTTACAGACAGG

GCTTGTCCAGGTGATGGAATAGTTACCATGGAATTAGCAACAATGAAGGCCTGTAAGTGGCAATTAAGTCTCCTGAGCCC

CTGTGTCTTAGCTGAATGTATACAGACAGGATGCCTATCTAAATGATGAGTATGAAGTGCTACTGCCACAGTATCCCCAG

GAAATCTTTATAGCAACTGCAGAACTTTTGATCTCTGTCCCAGACATTGACTACTGAGGATTTTTATATAATATTCTTGC

TGTTTCTGCCTTATGTCATTTCTTTTCATCTGAATTGATACAAAAAGTTTCAGAGTATCAGTGGTGTGACACAGAGAAGT

GCATTAAGTGGATAGTTCCACTTGCCATGGTCATCGAAGAGTTAGGAAGTTCCAACTTAAGCACTTC

ORF - retro_ocun_676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	62.54 %
Parental protein coverage:	83.9 %
Number of stop codons detected:	3
Number of frameshifts detected:	3

Retrocopy - Parental Gene Alignment:

                                ParentalKERDAKERGTMKDDGGSDFSVRSRKRKANVAVFL-QDPDEQIAKIDRTVRGQCGSQPWDSDAVRADPCSS
K.R.AKE...M........S....K........L.QD.DE..AK.D.TVRGQ..SQPWD.DAVR..PCS.
RetrocopyKQRYAKEQSIMNEGSTNLSSLQMKKANVAFCLLL>QDQDEETAKFDKTVRGQSSSQPWDNDAVRVNPCSL
ParentalIPTPDKEEDEPVYANSTFDPHSLAPARASPLPVLNWANREEVWKIMLNKEKKYLRDQHFLQRHPLLQPKM
IPTP.KEEDE.V.A..TFDP....P.RAS.LPVLNWA.R...........K..LR....LQ.HPLLQPK.
RetrocopyIPTPNKEEDELVHAYPTFDPQGVIPSRASLLPVLNWAERGSL-ESHVTRGKEVLRG*ALLQQHPLLQPKT
ParentalRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENIVKTLLQLIGISSLFIAAKLEEIYPPKLHQFA
RAILLDWL.EV..VYKLHR.TFYL.Q.FFD...ATQENIVKTL.QL.GISSLF.AAK.EEIY.PKLHQF.
RetrocopyRAILLDWLTEVRDVYKLHRKTFYLTQGFFDQCVATQENIVKTLVQLTGISSLFTAAKHEEIYSPKLHQFS
ParentalYVTDGACSGDEILTMELVIMKALKWHLSPLT-IVSWLNVYMQVAYLNDVCEVLLPQYPQQIFTQIAELLD
.VTD.AC.GD.I.TMEL..MKA.KW.LS.L...VS.LNVY.Q.AYLND..EVLLPQYPQ.IF...AELL.
RetrocopyCVTDRACPGDGIVTMELATMKACKWQLSLLS>PVS*LNVYRQDAYLNDEYEVLLPQYPQEIFIATAELL-
ParentalLCVLDVGCLEFSYGVLAASALYHFSSSELMQKVSGYQWCDIEKCVKWMVPFAMVIRETGSS-KLKHF
..V.D.....F.Y..LA.SAL.HF.SSEL.QKVS.YQWCD.EKC.KW.VP.AMVI.E.GSS..LKHF
RetrocopyISVPDIDY*GFLYNILAVSALCHFFSSELIQKVSEYQWCDTEKCIKWIVPLAMVIEELGSS<QLKHF

                            

                            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	10 .76 RPM
SRP017611_kidney	0 .10 RPM	1 .93 RPM
SRP017611_liver	0 .00 RPM	0 .46 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_676 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_676 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ocun_676 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001857	2 retrocopies	retro_cjac_3786, retro_cjac_3996,
Oryctolagus cuniculus	ENSOCUG00000009143	1 retrocopy	retro_ocun_676 ,
Oryctolagus cuniculus	ENSOCUG00000015589	1 retrocopy	retro_ocun_1277,
Oryctolagus cuniculus	ENSOCUG00000028042	1 retrocopy	retro_ocun_169,
Otolemur garnettii	ENSOGAG00000006217	2 retrocopies	retro_ogar_3309, retro_ogar_930,
Sus scrofa	ENSSSCG00000002855	1 retrocopy	retro_sscr_232,
Vicugna pacos	ENSVPAG00000001390	1 retrocopy	retro_vpac_219,

	RetrogeneDB ID:	retro_ocun_676
Retrocopy location	Organism:	*Rabbit (Oryctolagus cuniculus)*
	Coordinates:	13:139438904..139439931(-)
	Located in intron of:	ENSOCUG00000002458
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	CCNE1
	Ensembl ID:	ENSOCUG00000009143
	Aliases:	None
	Description:	cyclin E1 [Source:HGNC Symbol;Acc:1589]

Parental	KERDAKERGTMKDDGGSDFSVRSRKRKANVAVFL-QDPDEQIAKIDRTVRGQCGSQPWDSDAVRADPCSS
	K.R.AKE...M........S....K........L.QD.DE..AK.D.TVRGQ..SQPWD.DAVR..PCS.
Retrocopy	KQRYAKEQSIMNEGSTNLSSLQMKKANVAFCLLL>QDQDEETAKFDKTVRGQSSSQPWDNDAVRVNPCSL

Parental	IPTPDKEEDEPVYANSTFDPHSLAPARASPLPVLNWANREEVWKIMLNKEKKYLRDQHFLQRHPLLQPKM
	IPTP.KEEDE.V.A..TFDP....P.RAS.LPVLNWA.R...........K..LR....LQ.HPLLQPK.
Retrocopy	IPTPNKEEDELVHAYPTFDPQGVIPSRASLLPVLNWAERGSL-ESHVTRGKEVLRG*ALLQQHPLLQPKT

Parental	RAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENIVKTLLQLIGISSLFIAAKLEEIYPPKLHQFA
	RAILLDWL.EV..VYKLHR.TFYL.Q.FFD...ATQENIVKTL.QL.GISSLF.AAK.EEIY.PKLHQF.
Retrocopy	RAILLDWLTEVRDVYKLHRKTFYLTQGFFDQCVATQENIVKTLVQLTGISSLFTAAKHEEIYSPKLHQFS

Parental	YVTDGACSGDEILTMELVIMKALKWHLSPLT-IVSWLNVYMQVAYLNDVCEVLLPQYPQQIFTQIAELLD
	.VTD.AC.GD.I.TMEL..MKA.KW.LS.L...VS.LNVY.Q.AYLND..EVLLPQYPQ.IF...AELL.
Retrocopy	CVTDRACPGDGIVTMELATMKACKWQLSLLS>PVS*LNVYRQDAYLNDEYEVLLPQYPQEIFIATAELL-

Parental	LCVLDVGCLEFSYGVLAASALYHFSSSELMQKVSGYQWCDIEKCVKWMVPFAMVIRETGSS-KLKHF
	..V.D.....F.Y..LA.SAL.HF.SSEL.QKVS.YQWCD.EKC.KW.VP.AMVI.E.GSS..LKHF
Retrocopy	ISVPDIDY*GFLYNILAVSALCHFFSSELIQKVSEYQWCDTEKCIKWIVPLAMVIEELGSS<QLKHF

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

RetrogeneDB ID:

retro_ocun_676