RetrogeneDB ID: retro_ocun_1798

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018916:271705..272794(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: COIL
• Ensembl ID: ENSOCUG00000011345
• Aliases: None
• Description: coilin [Source:HGNC Symbol;Acc:2184]

Sequence

>retro_ocun_1798
GAAAACAAAAGAAAGGACAAAGCAGCGTGTGGCACAATGGATGGTGATGACCTAGAGACCAAACAGAAGTCACCAAAGAA
ACAGGAGAAATGTGAATACAAAGCAGACCAAGAATCCCAAGACTCCTAAAGCATGCCTGGTAACAGAGTGGACCACCCAC
TCTGCTGTCCTGTAAAAGGTCCTACTGAAAACAGCCTGGCAAAAGCCAGAAGGAAAGCTGGTATAGGCACTGTTTCAAAG
ATGGTCCAGTTCCTCCTCAGACTCCGAGTCTTGCTGCGAATCCACCATGGATGGGCTCAGCAGTGTCACTTTGGAGGTCA
GAAATTCCTCAGAGAAAATTGCCACTGAGTTAGCAAAGGAAGGATACTTTATGAAAGACACAGCAGCAAACAAATTGCCT
GCCAAAGGAGGCTGCAGCCTTCCTGTGATTAGGGCAAGATCACCAGAACACCATCATCTAGTCCAGATTCAAGCTCAGAG
TCTGAGGACCAGTGCCTGCTGACCAAGACATTCCCCAGTGTGCTGCAGGGTTCTTCAAGACAGGTGGCCTCTTCCCAGGG
AGAGGCTGCCCACGTCCATGGCTGTCCTCGCAGGTGCCACCTGCTGCTTGCTGGAAGTATTGTGACTTAAATGGTAGCAT
ACAGGCTCCCTGTCTTCCCTCCATTGCAACTCTCCCCTCCAGGCTAGGAGGAGGATTGGGTCAAGGAGAGCACCTTATTT
CTCGAAAGGGAGTTAGAGGTTGGGGTGTGCCGGGTAGATGATCAGGGCCGAGGCAGTCTGTGTCCAATGTTTTCAACAGA
AATCCCAACTATCAGAAGCAGAAGCAATTAAATGAAGTGATAAACTCATCTACTTTCATCCAGAATCCTCAGAGACACAA
AAGAAGGTTTGTAGCCTGTTACCACTCTCAGCAGCTGTCCCTCAGATCAGAGAAAAGATTGCATTTAAGCTTTTGGAACT
AACATCCAATTACTCTCCTGATGTCTCTGACTACAAGGAAGGAAAATATTAAGCCTCAATCCAGAGATCCAGCAGGCAGA
TATAGAAATTCTTTCATCATTAGCTGCCTTGAAAGAACCTGAGAAATTT

Alignment

ORF - retro_ocun_1798 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68. %
• Parental protein coverage: 63.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  KNKRKNKAACGTMDDNDEETQR-KSPKKKEKCEYKKQTKNSKSPKVPVVKEWTAQN-CSTPKSPAKNSLA
          .NKRK.KAACGTM.D.D.......S..........KQTKN.K.PK...V.EWT....C...K.P..NSLA
Retrocopy ENKRKDKAACGTM-DGDDLETK>RSHQRNRRNVNTKQTKNPKTPKACLVTEWTTHS<CCPVKGPTENSLA

Parental  KARRKAGVGTVSK-DSP-SSSSESESCHESTSDGLSNVTSEARNSSEKIPTELAKEGSSTKNTTANKLPA
          KARRKAG.GTVSK.D.P.SSSS.SESC.EST.DGLS.VT.E.RNSSEKI.TELAKEG...K.T.ANKLPA
Retrocopy KARRKAGIGTVSK<DGP<SSSSDSESCCESTMDGLSSVTLEVRNSSEKIATELAKEGYFMKDTAANKLPA

Parental  KGGFSLTPSQ-GKTTRTSSSSSDSSSESDDQCLLSKS-TPESASGLFKTAGLFPGRGCPGPGLSSQVPPA
          KGG.SL.....GK.TRT.SSS.DSSSES.DQCLL.K...P..A.G.FKT.GLFPGRGCP.P.LSSQVPPA
Retrocopy KGGCSLPVIR<GKITRTPSSSPDSSSESEDQCLLTKT<IPQCAAGFFKTGGLFPGRGCPRPWLSSQVPPA

Parental  ASWKYSDLSGGRQAPGPPSVATLPSSLGRGWGRGEDLLSWKGARGRGAWGRGRGRGQAVSGVVNRNADYQ
          A.WKY.DL.G..QAP..PS.ATLPS.LG.G.G.GE.L.S.KG.RG.G..GR..G..Q.VS.V.NRN..YQ
Retrocopy ACWKYCDLNGSIQAPCLPSIATLPSRLGGGLGQGEHLISRKGVRGWGVPGR*SGPRQSVSNVFNRNPNYQ

Parental  KQKQLNEMITNASTFIQNP-VETHKKDYSLLPLLAAAPQVGEKIAFKLLELTSNYSPDVSDYKEG-KILS
          KQKQLNE.I.N.STFIQNP..ET.KK..SLLPL.AA.PQ..EKIAFKLLELTSNYSPDVSDYKEG.KILS
Retrocopy KQKQLNEVI-NSSTFIQNP<SETQKKVCSLLPLSAAVPQIREKIAFKLLELTSNYSPDVSDYKEG<KILS

Parental  HNPETQQVDIEILSSLPALKEPGKF
          .NPE.QQ.DIEILSSL.ALKEP.KF
Retrocopy LNPEIQQADIEILSSLAALKEPEKF

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	17.05 RPM
SRP017611_kidney	0.00 RPM	14.70 RPM
SRP017611_liver	0.00 RPM	6.78 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1798 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1798 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1798 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008740	1 retrocopy	retro_chof_1121,
Callithrix jacchus	ENSCJAG00000013960	1 retrocopy	retro_cjac_2240,
Dasypus novemcinctus	ENSDNOG00000023961	1 retrocopy	retro_dnov_1986,
Echinops telfairi	ENSETEG00000003687	1 retrocopy	retro_etel_1537,
Nomascus leucogenys	ENSNLEG00000008026	1 retrocopy	retro_nleu_1014,
Oryctolagus cuniculus	ENSOCUG00000011345	1 retrocopy	retro_ocun_1798 ,
Pongo abelii	ENSPPYG00000008248	1 retrocopy	retro_pabe_305,
Tupaia belangeri	ENSTBEG00000008882	4 retrocopies	retro_tbel_2118, retro_tbel_3549, retro_tbel_3961, retro_tbel_838,