RetrogeneDB ID:

retro_rnor_1527

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:2:123078332..123079182(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Pgk1
Ensembl ID:ENSRNOG00000002467
Aliases:Pgk1, Pgk
Description:Phosphoglycerate kinase 1 [Source:UniProtKB/Swiss-Prot;Acc:P16617]


Retrocopy-Parental alignment summary:






>retro_rnor_1527
ATGTTGCTTTCTAATAAGCTGAGTTTGAACAAGCTGGACATCAAGGGGAAGCATATAGTGATGAGGTTGGACTTCAATGT
TCCTATGAAGAACAACAAAATAACAAATAACTAAAGGATGAAAGACACTGTTCCAAGCATCAAATTTCTGCATGGACAAT
GAAGCCAAGTCAGTTGTCCTTATGAACAACCTAGGCAAGTCAGATGGTGTTCCCGTGCCTGACAAGTACTCTTTAGAGCC
AGTTGCTGCAGAATTCAAATCTCTGCTGGGCAAGGATGTTCTATTCTTGAAGGATTGTGTGGGCCCAGAAGTAGAGAATG
CCTGTGCCAACCCAGCTGCTGGGATTGTCATCCTGCTGGAGAACCTCCGTTTTCATGTAGAGAAAGAAGGGAAGAGAAAC
AATGCTTCTGGGAACAAGGTTAAAGCTGAGCCAGCCAAAATAGATGCTTCCTGAGCCTCACTGTCTAAATTAGGAGATGT
CTATGTAAATGATTCTTTTGGGAGTACGCACTAAGTGCACGGCTCCATGGTGTGTGTGAATCTGCCACAGAAGGCTAGTG
GATTTTTGATGAAGTAGAGCTTAACTACTTTGCCAAGGCTTTGGACAGTCCAGAGCAACATTTCCTGGCTATCTTCAGAG
GAGGTAAGATTGTAGACAAGTTCTAGCTGATCAATAATATGCTAGACAAGGTCAATGAAATGATCATTGGTGGTTTAAAT
GGCTTTTACCTTCCTTAAAGTGCTCAAAAACATGGAAATTAGCACATCTCTGTATGATGACGAAAGAGCCAAGATTGTCA
AGGATCTCATGTCTGATTCTGAGAAAAATACTGTAAACACAATCTTGCCT

ORF - retro_rnor_1527 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.32 %
Parental protein coverage: 67.87 %
Number of stop codons detected: 5
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMSLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKF-CLDNGAKSVVLMSHLGRPDG
M.LSNKL.L.KLD.KGK..VMR.DFNVPMKNN.ITNN.R.K..VPSIKF.C.DN.AKSVVLM..LG..DG
RetrocopyMLLSNKLSLNKLDIKGKHIVMRLDFNVPMKNNKITNN*RMKDTVPSIKF>CMDNEAKSVVLMNNLGKSDG
ParentalVPMPDKYSLEPVAAELKSLLGKDVLFLKDCVGSEVENACANPAAGTVILLENLRFHVEEEGKGKDASGNK
VP.PDKYSLEPVAAE.KSLLGKDVLFLKDCVG.EVENACANPAAG.VILLENLRFHVE.EGK...ASGNK
RetrocopyVPVPDKYSLEPVAAEFKSLLGKDVLFLKDCVGPEVENACANPAAGIVILLENLRFHVEKEGKRNNASGNK
ParentalVKAEPAKIDAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMK-KELNYFAKALESPERPF
VKAEPAKIDA..ASLSKLGDVYVND.FG..H..H.SMV.VNLPQKA.GFLMK..ELNYFAKAL.SPE..F
RetrocopyVKAEPAKIDAS*ASLSKLGDVYVNDSFGSTH*VHGSMVCVNLPQKASGFLMK<VELNYFAKALDSPEQHF
ParentalLAILGGAKVADKIQLINNMLDKVNEMIIGG-GMAFTFLKVLNNMEIGTSLYDEEGAKIVKDLMAKAEKNG
LAI..G.K..DK..LINNMLDKVNEMIIGG..MAFTFLKVL.NMEI.TSLYD.E.AKIVKDLM...EKN.
RetrocopyLAIFRGGKIVDKF*LINNMLDKVNEMIIGG>*MAFTFLKVLKNMEISTSLYDDERAKIVKDLMSDSEKNT
ParentalVKITLP
V...LP
RetrocopyVNTILP

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 .00 RPM 322 .24 RPM
SRP017611_kidney 0 .00 RPM 446 .19 RPM
SRP017611_liver 0 .00 RPM 184 .97 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_1527 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_1527 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1527 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 29 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000176191 retrocopy
Bos taurus ENSBTAG000000008941 retrocopy
Canis familiaris ENSCAFG000000172702 retrocopies
Callithrix jacchus ENSCJAG000000210823 retrocopies
Cavia porcellus ENSCPOG000000237851 retrocopy
Equus caballus ENSECAG000000149841 retrocopy
Felis catus ENSFCAG000000132092 retrocopies
Homo sapiens ENSG000001021442 retrocopies
Gorilla gorilla ENSGGOG000000171113 retrocopies
Loxodonta africana ENSLAFG000000119541 retrocopy
Macropus eugenii ENSMEUG000000047793 retrocopies
Myotis lucifugus ENSMLUG000000177912 retrocopies
Macaca mulatta ENSMMUG000000128741 retrocopy
Monodelphis domestica ENSMODG000000040552 retrocopies
Mus musculus ENSMUSG000000620702 retrocopies
Nomascus leucogenys ENSNLEG000000014233 retrocopies
Oryctolagus cuniculus ENSOCUG000000147261 retrocopy
Otolemur garnettii ENSOGAG000000111041 retrocopy
Procavia capensis ENSPCAG000000021171 retrocopy
Pongo abelii ENSPPYG000000204963 retrocopies
Pan troglodytes ENSPTRG000000220522 retrocopies
Rattus norvegicus ENSRNOG00000002467 7 retrocopies
Sorex araneus ENSSARG000000039561 retrocopy
Sarcophilus harrisii ENSSHAG000000018531 retrocopy
Sus scrofa ENSSSCG000000124401 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000019721 retrocopy
Tupaia belangeri ENSTBEG000000103091 retrocopy
Tarsius syrichta ENSTSYG000000079171 retrocopy
Vicugna pacos ENSVPAG000000012081 retrocopy



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