RetrogeneDB ID: retro_ocun_1688

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018773:989346..991386(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000007047
• Aliases: None
• Description: None

Sequence

>retro_ocun_1688
ATGCCTGCAGAGTCTGGAAAGAGACAAACCCAGAAACATTTCCTGGCCTCAGCAGCCGCTATCTTCTTAAAGAGAGCTAC
CACACTCTTTGCTTGTACGTGTCCAGGATTAAGCCTGAATGTGTCACCTGCAGTGCCCATCTACAATGAATTTATGTTTC
TCTTTGTTCTGGCCAGTTACAGTAGGGCCACCTTCATGGACCCAGGCATTTTCCCCTGAGCTGAGGAAGATGAGGACAAG
GAAGATTTTCAAGCTCCCCTTTACAAAGCAGTGGAGATGAAGGGCATCGAGGTGCTCATGAAAGGGTGTGCCACCAGCCA
CTTCTACTGTCCTCGGCATTCCCACACAGTGTCTGTGATAATTGTGTGGAGGAATTTGATCATCCCTGCCCCTGGGTGAA
CAACTGTATTGGTCATTGGAACTACCGTTATTTCTTCCTCTTCTTCCTTTCCTTGACAGCCCACTCTAAGGGTGTATTTG
GCCTTGGCTTCCTTTGTGTCCTCTACCACATAGAGGAGCTCTCAGGGGTCTTCACAGCTGTCACAATGGAGTGATGTATG
TGGCTGGCCTATTCTTCATCCCTGTAGCTGGCCTCACAGGGTTTCATGTGGTGTTGGTGGCCTGGGGACGCACAGCCAAT
GAAAAGGTTATGGGTAAATTCCGGGGAGGTGTGAACCCCTTCACCATTGGCTGCTGTAACAATGTTGGCTGTGTAATTTG
CAATTCCTCAGCACCCAGATATTTGGAAAGACCAAAAAAAGAAGACAATTGTAATCAGACCTCCCTTCCTTCAGCCAGAA
GTGTCAGATGTCAGATTACTGTAACGATCATGGATAATGGCATCCAGGGAGAGCTCAGGAGAACTAAGTCTAAGGGAAGC
TTGGAAATAACAGAGAGCCAGTCTGCAAATGCCAAACCCTGGCCTCCTCCTACGCCAGACCTGAGCAGTTACATGGGACT
GCAAACACACCTCAGCCTGGCTACTAATGGATATAGCAGCCTTTTGGGCAAGGACAGCCCTCCCACACCAACCATGTACA
AGTATCGGCCAGGTTATAGTAGCAGCAGTACATCAGCTGCCCTGCCTCATTCCTCCAGCACCAAGTTTGTCATGGGGACA
GTTTGAAGGAGCCCATCCTCAACTGCAGAGAGCAGCCATCATCCCAGTTACCACTCAGAGCCCAGCTTGGAACCAGAGAG
CTTCTGTTCTCCCACCTTTGGCAAAAGCTTTCACTTCAACCCACTTTCCAGTGACTTTTGTTCCTCCAGCCTCAAGTCAG
CCCAGAGAACAGGTTTTGTGCTGGACCAGTTGCAGTCCATTCATTGAGAAGGCATCACTTCCACCTCCTTTAAGAGCCTA
GCCAACCAGGCATGCAATGGAAGCCTGTCTTATGACAGCCTGCTCTCTTCTTCAGACAGCCCTGATTTCAAATCAGTGCA
GGCAGGGCCTGAGGCAGACCTGGCTTTAAGCTATACCTCTCCCTTCCTGTCAGCCCGCCTGGCCCAACAATGGGAAGCCA
AGAGGCATCCACATTTGGTGCCAATAGGCCCAACATGAGAGCCCTCACCAGTCCGTTATTACAATCTGTGGTGCCATATT
GTGGCCTTCCTCCAAGAATGAGAGAAGCTGCTGCACCAGTCACCCCCTCTCCCAGGCCATGAGTAAGAACCAAGATTGGG
AAACTCAGGCATTCAATCAACAGCTGGCTCAGGCAATGCCCTCATACAAGTTCCTTCTCAGATGATTCGAAGGGATCACC
ATTGGGCAAGACTCCACTTGGACACCCAGCTTTCCCACATTTTGGGAAGCCAGAAAGGCTAATGGCCCGGGGATTAGGGT
CCCCTGAACCAGGTCCAATCACCCCATATCTGGGCCATTCAACATCTTACAGCAGCCAAAAAGCCCCACCTGGTGTCTCT
AAGACAGAGGAAGTGGACTTTCAGCCACTACAGATGCCTAAAGGTGAAGTACAGCTCAAGACCGCTCACAGCAAATCCAA
CGGGCAACCCAAGAGCACATGCTCAGCCTTCCCTGGCCCC

Alignment

ORF - retro_ocun_1688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.3 %
• Parental protein coverage: 73.11 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MPAESGKRFKPSKYVPVSAAAVFLVGATTLFFAFTCPGLSLNVSPAVPIYNAIMFLFVLANFSMATFMDP
          MPAESGKR....K....SAAA.FL..ATTLF.A.TCPGLSLNVSPAVPIYN..MFLFVLA..S.ATFMDP
Retrocopy MPAESGKR-QTQKHFLASAAAIFLKRATTLF-ACTCPGLSLNVSPAVPIYNEFMFLFVLASYSRATFMDP

Parental  GIFPRAEEDEDKEDDFRAPLYKTVEIKGIQVRMKWCATCRFYRPPRCSHC-SVCDNCVEEFDHHCPWVNN
          GIFP.AEEDEDKED.F.APLYK.VE.KGI.V.MK.CAT..FY.P.R.SH..SVCDNCVEEFDH.CPWVNN
Retrocopy GIFP*AEEDEDKED-FQAPLYKAVEMKGIEVLMKGCATSHFYCP-RHSHT<SVCDNCVEEFDHPCPWVNN

Parental  CIGRRNYRYFFLFLLSLTAHIMGVFGFGLLYVLYHIEKLSGVCTAVTM-AVMCVAGLFFIPVAGLTGFHV
          CIG..NYRYFFLF.LSLTAH..GVFG.G.L.VLYHIE.LSGV.TAVTM..VM.VAGLFFIPVAGLTGFHV
Retrocopy CIGHWNYRYFFLFFLSLTAHSKGVFGLGFLCVLYHIEELSGVFTAVTM<GVMYVAGLFFIPVAGLTGFHV

Parental  VLVARGRTTNEQVTGKFRGGVNPFTNGCCNNVSRVLCSSPAPRYL-GRPKK-EKTIVIRPPFLRPEVSDG
          VLVA.GRT.NE.V.GKFRGGVNPFT.GCCNNV..V.C.S.APRYL.G..KK..KTIVIRPPFL.PEVSD.
Retrocopy VLVAWGRTANEKVMGKFRGGVNPFTIGCCNNVGCVICNSSAPRYL<GKTKK<KKTIVIRPPFLQPEVSDV

Parental  -QITVKIMDNGIQGELRRTKSKGSLEITESQSADAEPPPPPKPDLSRYTGLRTHLSLATNEADSSLLGKD
          .QITV.IMDNGIQGELRRTKSKGSLEITESQSA.A.P.PPP.PDLS.Y.GL.THLSLATN...SSLLGKD
Retrocopy <QITVTIMDNGIQGELRRTKSKGSLEITESQSANAKPWPPPTPDLSSYMGLQTHLSLATN-GYSSLLGKD

Parental  SPPTPTMYKYRPGYSSSSTSAAMPHSSSAK-LSRGDSLKE-PTSIAESSRHPSYRSEPSLEPESFRSPTF
          SPPTPTMYKYRPGYSSSSTSAA.PHSSS.K....GDSLKE.P.S.AESS.HPSY.SEPSLEPESF.SPTF
Retrocopy SPPTPTMYKYRPGYSSSSTSAALPHSSSTK<VCHGDSLKE>PSSTAESSHHPSYHSEPSLEPESFCSPTF

Parental  GKSFHFDPLSSGSRSSSLKSAQGTGFELGQLQSIRSEGTTSTSYKSLANQTRNGSLSYDSLLTPSDSPDF
          GKSFHF.PLSS...SSSLKSAQ.TGF.L.QLQSI..EG.TSTS.KSLANQ..NGSLSYDSLL..SDSPDF
Retrocopy GKSFHFNPLSSDFCSSSLKSAQRTGFVLDQLQSIH*EGITSTSFKSLANQACNGSLSYDSLLSSSDSPDF

Parental  ESVQAGPEPDPPLGYTSPFLSARLAQQREAERHPRLVPTGPPHREPSPVRYDNLSRHIVASLQEREKLLR
          .SVQAGPE.D..L.YTSPFLSARLAQQ.EA.RHP.LVP.GP...EPSPVRY.NL..HIVA.LQE.EKLL.
Retrocopy KSVQAGPEADLALSYTSPFLSARLAQQWEAKRHPHLVPIGPT-*EPSPVRYYNLWCHIVAFLQE*EKLLH

Parental  QSPPLPVREEEPGLGDSGIQSTPGSGHA-PRTSSSSDDSKRSPLGKTPLGRPAVPRFGKPEGLRGRGLGS
          QSPPLP..E.EP.LG.SGIQST.GSG.A.P.TSS.SDDSK.SPLGKTPLG.PA.P.FGKPE.L..RGLGS
Retrocopy QSPPLPGHE*EPRLGNSGIQSTAGSGNA<PHTSSFSDDSKGSPLGKTPLGHPAFPHFGKPERLMARGLGS

Parental  PEPGPTAPYLGRSTSYSSQKAPPGVSETEEVALQPLLTPKDEVQLKTAYSKSNGQPKSIGSASPGP
          PEPGP..PYLG.STSYSSQKAPPGVS.TEEV..QPL..PK.EVQLKTA.SKSNGQPKS..SA.PGP
Retrocopy PEPGPITPYLGHSTSYSSQKAPPGVSKTEEVDFQPLQMPKGEVQLKTAHSKSNGQPKSTCSAFPGP

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	131.79 RPM
SRP017611_kidney	0.00 RPM	141.49 RPM
SRP017611_liver	0.00 RPM	49.64 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1688 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1688 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1688 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000014912	1 retrocopy	retro_lafr_266,
Oryctolagus cuniculus	ENSOCUG00000007047	1 retrocopy	retro_ocun_1688 ,