RetrogeneDB ID: retro_rnor_240

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:255232606..255235924(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000026931
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ipo5
• Ensembl ID: ENSRNOG00000010989
• Aliases: Ipo5, Kpnb3, Ranbp5
• Description: Protein Ipo5 [Source:UniProtKB/TrEMBL;Acc:D4A781]

Sequence

>retro_rnor_240
ATGGCGGCGGCCGGGTCTGCAGGGTTGCCGGCGACCATATCGGATAAGCAGGAGTTTTACCAGCTTCTGAAGAACCTGAT
CAATCCAAGCTGTATGGTGCGGAGGCAAGCCGAGGAGGTCTATGAGAATATCCCAGGTCTGTGTAAGACTACATTCCTCT
TAGATGCCGTCCGAAATAGAAGAGCAGGTTATGAGGTGAGACAAATGGCTGCCGCACTGCTACGACGGCTTTTGTCCTCT
GGGTTTGAGGAGGTCTATCCAAATCTACCTTCTGAAGTGCAGAGGGATNCTNNNNNTNNNNNNNNNNNNNNCGTTAAGTT
AGAAACACATGCTAGCATGAGGAAAAAGCTTTGTGATATTTTTGCGGTGCTGGCCAGGAATTTGATAGATGAGAATGGCA
CTAACCATTGGCCAGAAGGTCTGAAATTCCTCATTGATTCGATCCACTCTAAAAATGTGGTTCTGTGGGAAGTTGCACTT
CACGTTTTCTGGCACTTTCCTGGGATTTTTGGGAACCAAGATCGTCACGACTTGGATATCATCAAGAGGTTGTTGGACCA
GTGTATTCAAGATCAAGAGCATCCAGCCATCAGGACATTATCTGCTAGAGCTGCGGCTGCGTTTGTCCTTGCTAATGAAA
ACAATATTGCTCTTTTCAAAGACTTTGCAGATTTGCTTCCTGGAATCTTACAGGCTGTGAATGATTCCTGCTACCAGGAT
GATGATTCCGTGCTAGAATCCCTTGTTGAGATTGCAGATACTGTACCTAAGTACTTGGGTCCCTATTTAGAAGATACTCT
GCAGTTGAGCCTGAAGTTATGTGGAGACTCTAGGCTTAGCAATCTGCAACGCCAGCTGGCTTTGGAAGTAATAGTGACCT
TATCGGAAACTGCGACTCCGATGTTGAAAAAGCATACGAATATTATCGCACAGGCTGTGCCTCATATATTAGCAATGATG
GTTGATCTTCAAGATGACGATGACTGGGTAAATGCTGATGAAATGGAAGAAGATGATTTTGACAGCAACGCCGTTGCTGC
TGAGAGCGCCCTAGACAGACTGGCTTGTGGACTTGGTGGAAAAGTAGTTTTGCCGATGACCAAGGAGCATATCATGCAAA
TGCTTCAGAGCCATGACTGGAAATGTCGACATGCCGGATTAATGGCCTTATCAGCCATCGGAGAAGGTTGCCATCAGCAA
ATGGAACCAATTCTAGATGAAACGGTTAACTCGGTTTTGCTTTTTCTTCAGGATCCTCATCCAAGGGTAAGGGCTGCTGC
CTGTACTACACTTGGACAGATGGCTACAGATTTTGCACCTAGTTTCCAAAAGAAATTCCATGAAATAGTGATTACAGCTT
TGTTGCGAACCATGGAAAACCAAGGTAATCAGCGTGTGCAATCTCAGGCCGCTTCTGCTCTTGTTATTTTTATTGAAGAC
TGCCCCAAATCATTGCTAATCCTATATTTGGAAAATATGGTAAAAAGTCTCCAATCCATCTTGGTAATTAAACTTCAAGA
GCTGATTCGGAATGGAACCAAGTTGGCCTTAGAACAACTCGTGACAACCATTGCCTCGGTGGCAGATGTAATAGAAGAAA
ACTTTATTCCATATTATGATATATTTATGCCCTCACTCAAACACGTTGTTGAGCTCGCTGTTCAAAAGGAACTTAAGCTT
CTTCGAGGAAAAACTATTGAGTGCATTAGCCATGTTGGACTGGCTGTGGGGAAGGAAAAATTTATGCAAGATGCATCGAA
TGTGATGCAGATACTGTTGAAGACACAATCAGACTTAAATAACATGGAAGAAGACGACCCTCAGACTTCTTACATGGTTT
CAGCGTGGGCCAGAATGTGTAAGATCCTTGGAAAAGACTTTGAACAATATCTCCCGCTGGTTATTGAGCCTCTTATCAAG
ACTGCTTCAGCTAAGCCTGATGTCGCACTCTTAGACACACAGGATGTGGAGAACATGAGTGATGACGAGGGCTGGCAGTT
TGTAAACCTCGGAGACCAGCAAAGCTTTGGCATTAAAACTTCAGGACTTGAAGCAAAAGCAACTGCTTGCCAGATGTTGG
TTTACTATGCTAAGGAGTTAAGAGAAGGATTTGTGGAATACACAGAGCAAGTTGTGAAGATGATGGTTCCTCTGCTGAAG
TTTTATTTTCATGACAATGTTCGCATGGCAGCAGCAGAAGCCATGCCCTTTCTCTTAGAATGTGCAAGAATTCGTGGCTC
AGAGTATCTTTCACAGATGTGGCAGTTTATATGTGATCCCTTAATCAAGGCGATTGGAACCGAACCCGACACAGATGTGC
TCTCAGAAATAATGAATTCTTTTGCCAAGTCCATTGAGGTAATGGGAGATGGTTGTCTCAACGATGAACACTTGGAAGAG
CTGGGAGGAATTTTGAAGGCAAAACTTGAAGGGCACTTTAAAAACCAAGAGTTACGGCAAGTAAAAAGGCAAGAAGAAAA
TTATGACCAGCAGGTTGAAATGTCTCTTCAAGATGAGGATGAATGTGATGTTTACATTCTGACCAAAGTATCAGATATTT
TGCACTCATTATTTAGTACTTACAAGGAAAAAATTTTGCCATGGTTTGAACAGCTACTCCCATTAATTGTAAATCTAATT
TGTTCAAGTAGGCCATGGCCAGACAGACAGTGGGGACTATGCATATTTGATGACATCATAGAGCACTGCAGTCCAACCTC
ATTCAAATATGTCGAGTATTTTCGGTGGCCAATGCTACTCAATATGCGAGACAACAACCCTGAAGTCAGGCAAGCTGCTG
CCTATGGACTGGGAGTTATGGCACAGTTTGGTGGAGATGATTATCGTTCTTTGTGTTCAGAAGCCGTCCCACTCTTGGTA
AAAGTTATTAAGTGTGCAAATTCCAAAACCAAAAAAAATGTGATTGCTACAGAGAACTGCATCTCAGCAATCGGAAAGAT
TATGAAGTTTAAGCCCAACTGTGTAAACGTGGATGAAGTTCTCCCACACTGGCTATCATGGCTTCCGCTGCATGAAGATA
AAGAAGAAGCTATTCAGACTTTGAATTTTCTCTGTGACCTAATTGAAAGTAACCACCCAGTTGTAATTGGTCCGAATAAT
TCCAATCTTCCCAAAATCATCAGTATAATTGCAGAAGGAAAAATTAATGAAACTATTAGCCTTGAAGATCCCTGTGCCAA
ACGCCTAGCTAACGTTGTCCGTCAGATACAGACTTCTGAAGAATTGTGGTTGGAATGCACATCCCAACTGGATGATGAAC
AGCAGGAAGCTTTACAAGAGTTACTCAGTTCTGCTTGA

Alignment

ORF - retro_rnor_240 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.39 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAAAEQQQFYLLLGNLLSPDNVVRKQAEETYENIPGRSKITFLLQAIRNTTAAEEARQMAAVLLRRLL
          ..A.....Q.FY.LL.NL..P...VR.QAEE.YENIPG..K.TFLL.A.RN..A..E.RQMAA.LLRRLL
Retrocopy LPATISDKQEFYQLLKNLINPSCMVRRQAEEVYENIPGLCKTTFLLDAVRNRRAGYEVRQMAAALLRRLL

Parental  SSAFDEVYPALPSDVQTAIKSELLMIIQMETQSSMRKKICDIAAELARNLIDEDGNNQWPEGLKFLFDSV
          SS.F.EVYP.LPS.VQ.............ET..SMRKK.CDI.A.LARNLIDE.G.N.WPEGLKFL.DS.
Retrocopy SSGFEEVYPNLPSEVQRDXXXXXXXXVKLETHASMRKKLCDIFAVLARNLIDENGTNHWPEGLKFLIDSI

Parental  SSQNMGLREAALHIFWNFPGIFGNQQQHYLDVIKRMLVQCMQDQEHPSIRTLSARATAAFILANEHNVAL
          .S.N..L.E.ALH.FW.FPGIFGNQ..H.LD.IKR.L.QC.QDQEHP.IRTLSARA.AAF.LANE.N.AL
Retrocopy HSKNVVLWEVALHVFWHFPGIFGNQDRHDLDIIKRLLDQCIQDQEHPAIRTLSARAAAAFVLANENNIAL

Parental  FKHFADLLPGFLQAVNDSCYQNDDSVLKSLVEIADTVPKYLRPHLEATLQLSLKLCGDTNLNNMQRQLAL
          FK.FADLLPG.LQAVNDSCYQ.DDSVL.SLVEIADTVPKYL.P.LE.TLQLSLKLCGD..L.N.QRQLAL
Retrocopy FKDFADLLPGILQAVNDSCYQDDDSVLESLVEIADTVPKYLGPYLEDTLQLSLKLCGDSRLSNLQRQLAL

Parental  EVIVTLSETAAAMLRKHTNIIAQTIPQMLAMMVDLEEDEDWANADELEDDDFDSNAVAGESALDRMACGL
          EVIVTLSETA..ML.KHTNIIAQ..P..LAMMVDL..D.DW.NADE.E.DDFDSNAVA.ESALDR.ACGL
Retrocopy EVIVTLSETATPMLKKHTNIIAQAVPHILAMMVDLQDDDDWVNADEMEEDDFDSNAVAAESALDRLACGL

Parental  GGKLVLPMIKEHIMQMLQNADWKYRHAGLMALSAIGEGCHQQMEGILNEIVNFVLLFLQDPHPRVRYAAC
          GGK.VLPM.KEHIMQMLQ..DWK.RHAGLMALSAIGEGCHQQME.IL.E.VN.VLLFLQDPHPRVR.AAC
Retrocopy GGKVVLPMTKEHIMQMLQSHDWKCRHAGLMALSAIGEGCHQQMEPILDETVNSVLLFLQDPHPRVRAAAC

Parental  NAVGQMATDFAPGFQKKFHEKVIAALLQTMEDQGNQRVQAHAAAALINFTEDCPKSLLIPYLDNLVKHLH
          ...GQMATDFAP.FQKKFHE.VI.ALL.TME.QGNQRVQ..AA.AL..F.EDCPKSLLI.YL.N.VK.L.
Retrocopy TTLGQMATDFAPSFQKKFHEIVITALLRTMENQGNQRVQSQAASALVIFIEDCPKSLLILYLENMVKSLQ

Parental  SIMVLKLQELIQKGTKLVLEQVVTSIASVADTAEEKFVPYYDLFMPSLKHIVENAVQKELRLLRGKTIEC
          SI.V.KLQELI..GTKL.LEQ.VT.IASVAD..EE.F.PYYD.FMPSLKH.VE.AVQKEL.LLRGKTIEC
Retrocopy SILVIKLQELIRNGTKLALEQLVTTIASVADVIEENFIPYYDIFMPSLKHVVELAVQKELKLLRGKTIEC

Parental  ISLIGLAVGKEKFMQDASDVMQLLLKTQTDFNDMEDDDPQISYMISAWARMCKILGKEFQQYLPVVMGPL
          IS..GLAVGKEKFMQDAS.VMQ.LLKTQ.D.N.ME.DDPQ.SYM.SAWARMCKILGK.F.QYLP.V..PL
Retrocopy ISHVGLAVGKEKFMQDASNVMQILLKTQSDLNNMEEDDPQTSYMVSAWARMCKILGKDFEQYLPLVIEPL

Parental  MKTASIKPEVALLDTQDMENMSDDDGWEFVNLGDQQSFGIKTAGLEEKSTACQMLVCYAKELKEGFVEYT
          .KTAS.KP.VALLDTQD.ENMSDD.GW.FVNLGDQQSFGIKT.GLE.K.TACQMLV.YAKEL.EGFVEYT
Retrocopy IKTASAKPDVALLDTQDVENMSDDEGWQFVNLGDQQSFGIKTSGLEAKATACQMLVYYAKELREGFVEYT

Parental  EQVVKLMVPLLKFYFHDGVRVAAAESMPLLLECARVRGPEYLTQMWHFMCDALIKAIGTEPDSDVLSEIM
          EQVVK.MVPLLKFYFHD.VR.AAAE.MP.LLECAR.RG.EYL.QMW.F.CD.LIKAIGTEPD.DVLSEIM
Retrocopy EQVVKMMVPLLKFYFHDNVRMAAAEAMPFLLECARIRGSEYLSQMWQFICDPLIKAIGTEPDTDVLSEIM

Parental  HSFAKCIEVMGDGCLNNEHFEELGGILKAKLEEHFKNQELRQVKRQDEDYDEQVEESLQDEDDNDVYILT
          .SFAK.IEVMGDGCLN.EH.EELGGILKAKLE.HFKNQELRQVKRQ.E.YD.QVE.SLQDED..DVYILT
Retrocopy NSFAKSIEVMGDGCLNDEHLEELGGILKAKLEGHFKNQELRQVKRQEENYDQQVEMSLQDEDECDVYILT

Parental  KVSDILHSIFSSYKEKVLPWFEQLLPLIVNLICPHRPWPDRQWGLCIFDDIIEHCSPASFKYAEYFLRPM
          KVSDILHS.FS.YKEK.LPWFEQLLPLIVNLIC..RPWPDRQWGLCIFDDIIEHCSP.SFKY.EYF..PM
Retrocopy KVSDILHSLFSTYKEKILPWFEQLLPLIVNLICSSRPWPDRQWGLCIFDDIIEHCSPTSFKYVEYFRWPM

Parental  LQYVCDNSPEVRQAAAYGLGVMAQYGGDNYRPFCTEALPLLVRVIQSADSKTKENVNATENCISAVGKIM
          L....DN.PEVRQAAAYGLGVMAQ.GGD.YR..C.EA.PLLV.VI..A.SKTK.NV.ATENCISA.GKIM
Retrocopy LLNMRDNNPEVRQAAAYGLGVMAQFGGDDYRSLCSEAVPLLVKVIKCANSKTKKNVIATENCISAIGKIM

Parental  KFKPDCVNVEEVLPHWLSWLPLHEDKEEAVQTFSYLCDLIESNHPIVLGPNNTNLPKIFSIIAEGEMHEA
          KFKP.CVNV.EVLPHWLSWLPLHEDKEEA.QT...LCDLIESNHP.V.GPNN.NLPKI.SIIAEG...E.
Retrocopy KFKPNCVNVDEVLPHWLSWLPLHEDKEEAIQTLNFLCDLIESNHPVVIGPNNSNLPKIISIIAEGKINET

Parental  IKHEDPCAKRLANVVRQVQTSGGLWTECIAQLSPEQQAAIQELLNSA
          I..EDPCAKRLANVVRQ.QTS..LW.EC..QL..EQQ.A.QELL.SA
Retrocopy ISLEDPCAKRLANVVRQIQTSEELWLECTSQLDDEQQEALQELLSSA

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	22.72 RPM	136.82 RPM
SRP017611_kidney	18.14 RPM	97.07 RPM
SRP017611_liver	11.43 RPM	59.37 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_240 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_240 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_240 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_57
Pan troglodytes	retro_ptro_49
Gorilla gorilla	retro_ggor_47
Mus musculus	retro_mmus_251

---

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,