RetrogeneDB ID: retro_ocun_143

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:48138714..48142032(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000008471
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: IPO5
• Ensembl ID: ENSOCUG00000003898
• Aliases: None
• Description: importin 5 [Source:HGNC Symbol;Acc:6402]

Sequence

>retro_ocun_143
ATGGCGGCGGCCGGGGCTGCAGGGGTGCCGGCGGCCGTGTCAGAAAAGCAAGAGTTTTACCAGCTTCTGAAGAACCTGAT
CAATCCAAGCTGTATGGTGCGGAGACAAGCAGAGGAAATATATGAAAATATCCCAGGTCTGTGTAAAACTACATTCCTCT
TAGATGCCGTCAGAAATAGAAGAGCGGGTTATGAGGTGAGACAAATGGCTGCCGCACTGCTACGACGGCTTTTGTCCTCT
GGGTTTGAGGAGGTGTATCCAAATCTGCCTTCTGATGTGCAGAGGGATGTCAAGATTGAGCTGATACTGGCTGTTAAGTT
AGAAACGCATGCTAGCATGAGGAAAAAACTTTGTGATATTTTTGCGGTGCTGGCCAGGAATTTGATTGATGAGGATGGCA
CCAACCACTGGCCAGAAGGTCTGAAGTTTCTTATTGATTCTGTCTACTCTAAAAATGTGGTTCTGTGGGAAGTTGCACTT
CACGTTTTCTGGCACTTTCCTGGGATTTTTGGGAACCAGGAGCGGCACGATTTGGATATCATCAAACGGTTATTGGACCA
GTGTATTCAAGATCAAGAACATCCAGCAATCAGGACATTATCCGCTAGAGCTGCTGCTGCGTTTGTCCTTGCTAACGAGA
ATAATGTTGCTCTTTTCAAAGACTTTGCAGACTTGCTTCCTGGAATCTTACAGGCTGTTAATGACTCATGCTACCAAGAT
GATGATTCAGTGCTAGAATCCCTTGTTGAAATTGCGGATACGGTACCTAAGTACTTGGGTCCTTACTTGGAAGATACCCT
ACAATTGAGTCTGAAGTTATGTGGAGATTCTAGGCTCAGTAATCTGCAACGCCAGCTGGCCCTCGAAGTAATAGTGACTT
TGTCTGAAACTGCAACCCCAATGTTGAAAAAACATACAAATATTATTGCACAGGCAATTCCTTTTATATTAGCAATGATG
GTTGATCTACAAGATGATGAGGACTGGGTAAATGCTGATGAAATGGAGGAAGATGATTTTGACAGCAATGCAGTTGCTGC
TGAGAGTGCACTAGACAGACTGGCTTGTGGACTTGGTGGAAAAATTGTTTTACCAATGACCAAGGAGCATATCCTGCAGA
TGCTTCAGAGCCCTGACTGGAAATACCGACATGCCGGATTAATGGCCTTATCTGCCATTGGAGAAGGATGCCATCAGCAA
ATGGAACCAATTCTAGATGAGACAGTTAACTCTGTTCTGCTTTTTCTTCAGGATCCTCATCCAAGGGTGAGGGCTGCAGC
CTGTACTACACTTGGACAGATGGCTACAGACTTTGCGCCCAGTTTCCAAAAGAAATTCCATGAAACAGTCATTGCAGCTC
TGTTGCGTACCATGGAAAATCAAGGTAATCAGCGTGTGCAGTCACATGCGGCTTCTGCTCTTATTATTTTTATTGAAGAC
TGCCCCAAATCATTGCTAGTTCTGTATTTGGATAATATGGTAAAAAATCTACATTCCATCTTGGTGATTAAACTTCAGGA
GTTGATTCGCAATGGAACTAAGTTGGCTTTAGAACAACTTGTGACAACCATTGCCTCAGTTGCCGATACAATAGAAGAAA
AATTTGTCCCATATTATGATATATTTATGCCCTCACTAAAGCACATTGTTGAGCTTGCCATTCAGAAGGACCTCAAGCTT
CTGAGAGGAAAAACTATTGAGTGCATTAGCCATGTTGGCCTTGCTGTTGGGAAGGAAAAATTTTTGCAGGATGCATCAAA
TGTGATGCAGCTGTTGTTGAAGACACAATCAGATTTAAATAATATGGAAGATGATGACCCTCAGACCTCGTACATGGTTT
CAGCTTGGGCTAGAATGTGTAAAATTCTTGGAAAAGATTTTCAACAGTACCTACCACTGGTTATTGAGCCTCTTATTAAG
ACTGCTTCGGCTAAACCTGATGTTGCTCTCCTAGACACACAAGATGTTGAGAACATGAGTGATGATGATGGCTGGCAATT
TGTGAATCTTGGAGACCAGCAAAGTTTTGGAATTAAAACTTCAGGACTTGAAGCAAAAGCAACTGCTTGTCAGATGTTGG
TTTACTATGCTAAGGAGTTAAAAGAAGGATTTGTGGAATATACAGAACAAGTTGTGAAACTTATGGTTCCTTTACTGAAA
TTTTATTTCCATGACAATGTTCGAGTGGCAGCAGCAGAATCCATGCCTTTTCTCCTGGAATGTGCAAAACTGCATAGCCC
AGAGTATCTTTCACAGATGTGGCAGTTTATATGTGATCCCTTAATCAAGGCTATTGGGACTGAACCTGATACAGATGTAC
TCTCAGAAATAATGAATTCTTTCGCAAAGTCCATTGAAGTAATGGGAGATGGTTGCCTTAATGATGAACATTTGGAAGAA
CTGGGAGGAATATTGAAAGCAAAACTTGAGGGACACTTTAAAAACCAAGAATTGCGACAGGTGAAGAGACAGGAAGAAAA
CTATGACCAACAGGTTGAGATGTCTCTGCAAGATGAGGATGAATGTGATGTTTATATTCTGACCAAAGTATCAGATATTT
TGCACTCATTATTTAGTACTTACAAGGAAAAGATTTTACCATGGTTTGAACAGTTACTTCCATTAATTGTCAATCTAATT
TGTTCAAGTAGGCCATGGCCAGACAGGCAGTGGGGACTGTGCATATTTGATGATATCATAGAGCACTGCAGTCCAACTTC
ATTTAAATATGTAGAATATTTTCGGTGGCCAATGCTGCTAAATATGAGAGATAACAACCCTGAAGTCAGGCAAGCTGCTG
CTTATGGCCTGGGTGTTATGGCACAGTTTGGTGGCGATGATTATCGTTCTTTATGTTCAGAAGCTGTTCCACTGCTGGTA
AAAGTTATTAAGTGTGCAAATTCCAAAACCAAAAAAAATGTCATTGCTACAGAGAACTGTATCTCAGCAATAGGGAAGAT
TTTGAAGTTTAAGCCTAACTGTATAAATGTGGATGAAGTTCTTCCACATTGGTTATCATGGCTTCCACTGCATGAAGATA
AAGAGGAAGCTCTTCAGACTTTGAGTTTTCTCTGTGACTTAATTGAAAGTAACCACCCAGTTGTAATTGGTCCAAATAAT
TCCAATCTCCCCAAAATAATTAGTATAATTGCCGAAGGAAAAATTAATGAGACTATTAACTTTGAAGATCCTTGTGCCAA
ACGCCTAGCTAATGTCATCCGACAGGTACAGACTTCTGAAGAATTATGGTTGGAATGCATATCCCAACTCAATGATGAAC
AACAGGAAGCCTTACAGGAGTTGCTAAATTTTGCTTGA

Alignment

ORF - retro_ocun_143 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.31 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETYENIPGQSKITFLLQAIRNTAAAEEARQMAAVLLRRLLSSAFDEVYPALPSEVQTAIKSELLMIIQME
          E.YENIPG..K.TFLL.A.RN..A..E.RQMAA.LLRRLLSS.F.EVYP.LPS.VQ...K.EL......E
Retrocopy EIYENIPGLCKTTFLLDAVRNRRAGYEVRQMAAALLRRLLSSGFEEVYPNLPSDVQRDVKIELILAVKLE

Parental  TQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFDSVSSQNMGLREAALHIFWNFPGIFGNQQQHYL
          T..SMRKK.CDI.A.LARNLIDEDG.N.WPEGLKFL.DSV.S.N..L.E.ALH.FW.FPGIFGNQ..H.L
Retrocopy THASMRKKLCDIFAVLARNLIDEDGTNHWPEGLKFLIDSVYSKNVVLWEVALHVFWHFPGIFGNQERHDL

Parental  DVIKRMLVQCMQDQEYPLIRTLSARATAAFILANEHNVTLFKHFADLLPGFLQAVNDSCYQNDDSVLKSL
          D.IKR.L.QC.QDQE.P.IRTLSARA.AAF.LANE.NV.LFK.FADLLPG.LQAVNDSCYQ.DDSVL.SL
Retrocopy DIIKRLLDQCIQDQEHPAIRTLSARAAAAFVLANENNVALFKDFADLLPGILQAVNDSCYQDDDSVLESL

Parental  VEIADTVPKYLRPHLEATLQLSLKLCGDTSLNNMQRQLALEVIVTLSETAAAMLRKHTSIVAQTIPQMLA
          VEIADTVPKYL.P.LE.TLQLSLKLCGD..L.N.QRQLALEVIVTLSETA..ML.KHT.I.AQ.IP..LA
Retrocopy VEIADTVPKYLGPYLEDTLQLSLKLCGDSRLSNLQRQLALEVIVTLSETATPMLKKHTNIIAQAIPFILA

Parental  MMVDLEEDEDWANADELEDDDFDSNAVAGESALDRMACGLGGKLVLPMIKEHIMQMLQNPDWKYRHAGLM
          MMVDL..DEDW.NADE.E.DDFDSNAVA.ESALDR.ACGLGGK.VLPM.KEHI.QMLQ.PDWKYRHAGLM
Retrocopy MMVDLQDDEDWVNADEMEEDDFDSNAVAAESALDRLACGLGGKIVLPMTKEHILQMLQSPDWKYRHAGLM

Parental  ALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAACNAVGQMATDFAPGFQKKFHEKVIAALLQTM
          ALSAIGEGCHQQME.IL.E.VN.VLLFLQDPHPRVR.AAC...GQMATDFAP.FQKKFHE.VIAALL.TM
Retrocopy ALSAIGEGCHQQMEPILDETVNSVLLFLQDPHPRVRAAACTTLGQMATDFAPSFQKKFHETVIAALLRTM

Parental  EDQGNQRVQAHAAAALINFTEDCPKALLIPYLDNLVKHLHSIMVLKLQELIQKGTKLVLEQVVTSIASVA
          E.QGNQRVQ.HAA.ALI.F.EDCPK.LL..YLDN.VK.LHSI.V.KLQELI..GTKL.LEQ.VT.IASVA
Retrocopy ENQGNQRVQSHAASALIIFIEDCPKSLLVLYLDNMVKNLHSILVIKLQELIRNGTKLALEQLVTTIASVA

Parental  DTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIECISLIGLAVGKEKFMQDASDVMQLLLKTQTD
          DT.EEKFVPYYD.FMPSLKHIVE.A.QK.L.LLRGKTIECIS..GLAVGKEKF.QDAS.VMQLLLKTQ.D
Retrocopy DTIEEKFVPYYDIFMPSLKHIVELAIQKDLKLLRGKTIECISHVGLAVGKEKFLQDASNVMQLLLKTQSD

Parental  FNDMEDDDPQISYMISAWARMCKILGKEFQQYLPVVMGPLMKTASIKPEVALLDTQDMENMSDDDGWEFV
          .N.MEDDDPQ.SYM.SAWARMCKILGK.FQQYLP.V..PL.KTAS.KP.VALLDTQD.ENMSDDDGW.FV
Retrocopy LNNMEDDDPQTSYMVSAWARMCKILGKDFQQYLPLVIEPLIKTASAKPDVALLDTQDVENMSDDDGWQFV

Parental  NLGDQQSFGIKTAGLEEKSTACQMLVCYAKELKEGFVEYTEQVVKLMVPLLKFYFHVKRVRVAAAESMPL
          NLGDQQSFGIKT.GLE.K.TACQMLV.YAKELKEGFVEYTEQVVKLMVPLLKFYFH...VRVAAAESMP.
Retrocopy NLGDQQSFGIKTSGLEAKATACQMLVYYAKELKEGFVEYTEQVVKLMVPLLKFYFH-DNVRVAAAESMPF

Parental  LLECARVRGPEYLTQMWHFMCDALIKAIGTEPDSDVLSEIMHSFAKCIEVMGDGCLNNEHFEELGGILKA
          LLECA....PEYL.QMW.F.CD.LIKAIGTEPD.DVLSEIM.SFAK.IEVMGDGCLN.EH.EELGGILKA
Retrocopy LLECAKLHSPEYLSQMWQFICDPLIKAIGTEPDTDVLSEIMNSFAKSIEVMGDGCLNDEHLEELGGILKA

Parental  KLEEHFKNQELRQVKRQDEDYDEQVEESLQDEDDNDVYILTKVSDILHSIFSSYKEKVLPWFEQLLPLIV
          KLE.HFKNQELRQVKRQ.E.YD.QVE.SLQDED..DVYILTKVSDILHS.FS.YKEK.LPWFEQLLPLIV
Retrocopy KLEGHFKNQELRQVKRQEENYDQQVEMSLQDEDECDVYILTKVSDILHSLFSTYKEKILPWFEQLLPLIV

Parental  NLICPHRPWPDRQWGLCIFDDVIEHCSPASFKYAEYFLRPMLQYVCDNSPEVRQAAAYGLGVMAQYGGDN
          NLIC..RPWPDRQWGLCIFDD.IEHCSP.SFKY.EYF..PML....DN.PEVRQAAAYGLGVMAQ.GGD.
Retrocopy NLICSSRPWPDRQWGLCIFDDIIEHCSPTSFKYVEYFRWPMLLNMRDNNPEVRQAAAYGLGVMAQFGGDD

Parental  YRPFCTEALPLLVRVIQSADSKTKENVNATENCISAVGKIMKFKPDCVNVEEVLPHWLSWLPLHEDKEEA
          YR..C.EA.PLLV.VI..A.SKTK.NV.ATENCISA.GKI.KFKP.C.NV.EVLPHWLSWLPLHEDKEEA
Retrocopy YRSLCSEAVPLLVKVIKCANSKTKKNVIATENCISAIGKILKFKPNCINVDEVLPHWLSWLPLHEDKEEA

Parental  VQTFNYLCDLIESNHPIVLGPNNTNLPKIFSIIAEGEMHEAIKHEDPCAKRLANVVRQVQTSGGLWTECI
          .QT...LCDLIESNHP.V.GPNN.NLPKI.SIIAEG...E.I..EDPCAKRLANV.RQVQTS..LW.ECI
Retrocopy LQTLSFLCDLIESNHPVVIGPNNSNLPKIISIIAEGKINETINFEDPCAKRLANVIRQVQTSEELWLECI

Parental  AQLSPEQQAAIQELLNSA
          .QL..EQQ.A.QELLN.A
Retrocopy SQLNDEQQEALQELLNFA

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	58.83 RPM	177.32 RPM
SRP017611_kidney	20.98 RPM	128.22 RPM
SRP017611_liver	14.57 RPM	78.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_143 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_143 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_143 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003784	1 retrocopy	retro_amel_3,
Bos taurus	ENSBTAG00000039374	1 retrocopy	retro_btau_104,
Canis familiaris	ENSCAFG00000005561	1 retrocopy	retro_cfam_452,
Choloepus hoffmanni	ENSCHOG00000006061	1 retrocopy	retro_chof_11,
Cavia porcellus	ENSCPOG00000004827	2 retrocopies	retro_cpor_265, retro_cpor_57,
Equus caballus	ENSECAG00000014808	1 retrocopy	retro_ecab_37,
Felis catus	ENSFCAG00000025657	1 retrocopy	retro_fcat_24,
Homo sapiens	ENSG00000065150	1 retrocopy	retro_hsap_57,
Gorilla gorilla	ENSGGOG00000008742	1 retrocopy	retro_ggor_47,
Loxodonta africana	ENSLAFG00000016190	1 retrocopy	retro_lafr_22,
Myotis lucifugus	ENSMLUG00000006500	1 retrocopy	retro_mluc_295,
Mus musculus	ENSMUSG00000030662	2 retrocopies	retro_mmus_251, retro_mmus_3683,
Nomascus leucogenys	ENSNLEG00000007831	2 retrocopies	retro_nleu_1610, retro_nleu_2482,
Oryctolagus cuniculus	ENSOCUG00000003898	1 retrocopy	retro_ocun_143 ,
Otolemur garnettii	ENSOGAG00000007570	1 retrocopy	retro_ogar_169,
Pongo abelii	ENSPPYG00000005458	1 retrocopy	retro_pabe_172,
Pan troglodytes	ENSPTRG00000005984	2 retrocopies	retro_ptro_49, retro_ptro_745,
Pteropus vampyrus	ENSPVAG00000004516	1 retrocopy	retro_pvam_8,
Rattus norvegicus	ENSRNOG00000010989	1 retrocopy	retro_rnor_240,
Sus scrofa	ENSSSCG00000009509	1 retrocopy	retro_sscr_24,
Ictidomys tridecemlineatus	ENSSTOG00000011164	1 retrocopy	retro_itri_32,