RetrogeneDB ID:

retro_rnor_860

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:12:12857102..12858446(+)
Located in intron of:ENSRNOG00000049143
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Hsp90aa1
Ensembl ID:ENSRNOG00000007219
Aliases:Hsp90aa1, Hsp86, Hsp90, Hspca
Description:Heat shock protein HSP 90-alpha [Source:UniProtKB/Swiss-Prot;Acc:P82995]


Retrocopy-Parental alignment summary:






>retro_rnor_860
TACATTGATCAAGAAGAACTCAACAAAACAAAGCCAAATTGTACAAGAAATCCTGATGACATTACATAAGAATATGGACA
GTTCTTCAAAAGCTTAGCCAACGATTGGGAAGAACATTGGGCAGTAAAGAATTTTTCTGTTGAAGGATAATTAGAATCCC
GGGTCATTCTTTTTGTACCAAGATGGGCTCCTTTTGATCTGTTTGAAAACAGAAAGAAAAAGAAGAACATCAAGTTGTAT
GTTTGTAGTATTTTTATCATGGATAACTATGAGGAGTTAATCTCTGAGTATCTGAATTTCATCAGAGGGGTGGTGGATTT
TGTGGATCTCCCTCTAAATATTTCCCATGAAATGCTGCAACAAAGCAAAATTCTGGAAGTTATCAGAAAGAATTTCGTCA
AGAAATTCTTAGAACTATTTACTGAACTGGCTGAAGATAAAGAGAACTACAAAAAGTGTTATGAGCAATCCTCAAAAATT
ATAAAGTTTGGAATTCATGAAGACTCTCAAAATTGGAAGAAGCCTTCAGAGCTGTTGAGATACTACACATCTGCTTCTGG
GGATGAGATGGTTTCTCTGAAGGACTACTGCACCAGAATGAAGGAAAACCAGAAGCACATCTATTTTTATCACAGGTGAG
ACCAAGGACCAGGTTGATAACTCAGCCTTTGTGGAACCTCTTCAAAAGCATAGCTTAGAAGTAATCTATATGATTGAGCC
CATTGATGAGTATTGTGTGCAACAGCTGAAGGAATTTGAGGACAAGACCTTGATGTCAGTTACAAAACAAGGACAGGAAC
TTCCAGGGAATGAAGAGAAAAAGAAGAAAAAAGGAGAAAAAAAGACAAAATTTAAGAACCTGTGAAAAATTATGAAAGAT
ATTTTGGAGAAAAGGGTTGAAAAAGTGGTTGTGTCAAACCAATTGGTGACATCCCTATGCTGTATTGTCACAAGCACATA
TGGGCAAACAGAAAATATGGAAGAATCATGAAAGTTCAAGCATCAAGCACTCAAAGACAACTCAACAATGAGTTACATGG
CAGCAAAGACACACTTGGAGATAAACCCTGACCACTCCATTATTGAAACAAAGCAAAAGGCAGAGGCTGAAAAGAATGAC
AAGTCATGAAGGATCTGGTCATCTTGATGTATGAAAATGCACTCCTGTCTTCTAGCATCTGCCTGGAAGATCCCCAAACC
CATGCTAACAGGATCTACACTATGATCAAGTTTTGTTTAGGTACTGATGAGGATGATCCTACAGTGGATGATACCAATGC
TGTTGTAACTGAAGAAATGCCACCCCTGGAGGGAGATGATGACACATCATGCATGGAAGAAGTA

ORF - retro_rnor_860 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.31 %
Parental protein coverage: 61.12 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalYIDQEELNKTKPIWTRNPDDITNEEYGEFYKSLTNDWEEHLAVKHFSVEGQLEFRALLFVPRRAPFDLFE
YIDQEELNKTKP..TRNPDDIT.E.YG.F.KSL.NDWEEH.AVK.FSVEG.LE.R..LFVPR.APFDLFE
RetrocopyYIDQEELNKTKPNCTRNPDDIT*E-YGQFFKSLANDWEEHWAVKNFSVEG*LESRVILFVPRWAPFDLFE
ParentalNRKKKNNIKLYVRRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKKCLEL
NRKKK.NIKLYV...FIMDN.EELI.EYLNFIRGVVD..DLPLNIS.EMLQQSKIL.VIRKN.VKK.LEL
RetrocopyNRKKKKNIKLYVCSIFIMDNYEELISEYLNFIRGVVDFVDLPLNISHEMLQQSKILEVIRKNFVKKFLEL
ParentalFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKDYCTRMKENQKHIYF
FTELAEDKENYKK.YEQ.SK.IK.GIHEDSQN.KK.SELLRYYTSASGDEMVSLKDYCTRMKENQKHIYF
RetrocopyFTELAEDKENYKKCYEQSSKIIKFGIHEDSQNWKKPSELLRYYTSASGDEMVSLKDYCTRMKENQKHIYF
Parental-ITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQLKEFEGKTLVSVTKEGLELPEDEEEKKKQE
.ITGETKDQV.NSAFVE.L.KH.LEVIYMIEPIDEYCVQQLKEFE.KTL.SVTK.G.ELP..........
Retrocopy>ITGETKDQVDNSAFVEPLQKHSLEVIYMIEPIDEYCVQQLKEFEDKTLMSVTKQGQELPGNXXXXXXXX
ParentalEKKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVTSTYGWTANMERI--MKAQALRDNSTMGYMAA
.....F.NL.KIMKDILEK.VEKVVVSN.LVTS.CCIVTSTYG.T.NME.....K.QAL.DNSTM.YMAA
RetrocopyXXXXXFKNL*KIMKDILEKRVEKVVVSNQLVTSLCCIVTSTYGQTENMEES*KFKHQALKDNSTMSYMAA
ParentalKKHLEINPDHSIIETLRQKAEADKNDKS-VKDLVILLYETALLSSGFSLEDPQTHANRIYRMIKLGLGID
K.HLEINPDHSIIET..QKAEA.KNDKS..KDLVIL.YE.ALLSS...LEDPQTHANRIY.MIK..LG.D
RetrocopyKTHLEINPDHSIIET-KQKAEAEKNDKS<MKDLVILMYENALLSSSICLEDPQTHANRIYTMIKFCLGTD
ParentalEDDPTVDDTSAAVTEEMPPLEGDDDTSRMEEV
EDDPTVDDT.A.VTEEMPPLEGDDDTS.MEEV
RetrocopyEDDPTVDDTNAVVTEEMPPLEGDDDTSCMEEV

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






(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 .07 RPM 533 .11 RPM
SRP017611_kidney 0 .00 RPM 216 .81 RPM
SRP017611_liver 0 .81 RPM 71 .00 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_860 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_860 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_860 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 13 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000062701 retrocopy
Canis familiaris ENSCAFG000000180361 retrocopy
Callithrix jacchus ENSCJAG000000339458 retrocopies
Cavia porcellus ENSCPOG000000020151 retrocopy
Homo sapiens ENSG000000808242 retrocopies
Macaca mulatta ENSMMUG000000110732 retrocopies
Monodelphis domestica ENSMODG000000133023 retrocopies
Mus musculus ENSMUSG000000212701 retrocopy
Nomascus leucogenys ENSNLEG000000159253 retrocopies
Pongo abelii ENSPPYG000000061531 retrocopy
Pan troglodytes ENSPTRG000000067362 retrocopies
Rattus norvegicus ENSRNOG00000007219 1 retrocopy
retro_rnor_860 ,
Rattus norvegicus ENSRNOG000000198346 retrocopies



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