RetrogeneDB ID:

retro_rnor_497

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:1:168600982..168601519(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Prdx2
Ensembl ID:ENSRNOG00000003520
Aliases:Prdx2, Tdpx1
Description:Peroxiredoxin-2 [Source:UniProtKB/Swiss-Prot;Acc:P35704]


Retrocopy-Parental alignment summary:






>retro_rnor_497
ATGGCCTCCAGCAACGCACACAGCAGAAAGCCTGCCCCTGACTTCATAGCCACCTTGGTGGTAGATGGTGCCTTTAAGGA
AATCAAGCTTTCAGACTACAGAGGGAAGTACGTGGTCCTCTTTTTCTAACCACTGGACTTCACTTTTGTTTGCCCCACGG
AGGTCATCCCTTTTAGCAACCATGCTGAGGACTTCCGAAAGCTGGACTGCGAGGTGCCGGGAGCATCTGTGGACTCTCAG
TTCACCCACCTGGCGTGGATTAATACCCCACGGAAGGAGGGAGACGTGGGCCCCCTGAATATCCCTCTGCTTGCTGATGT
GACTAAAAGCTTGTCCCAGAATTACGGCGTGTTGAAAAATGATGAGGGCATCGCTGACAGGGGCCTCTTTATCATCAATG
CCAAGGGTGTGCTTCGCCAGATCACAGTCAACAGCCTATCTGTAGGACGCTCTGTAGATGAGGCTCTGCACCTTGTCCAG
GCCTTCCAGTATACAGACGAGCATGGGGAAGTCTGTCCTGCTGGCTGGAAGCCCGGC

ORF - retro_rnor_497 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.39 %
Parental protein coverage: 90.4 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMASGNAHIGKPAPDFTATAVVDGAFKEIKLSDYRGKYVVLFFYPLDFTFVCPTEIIAFSDHAEDFRKLGC
MAS.NAH..KPAPDF.AT.VVDGAFKEIKLSDYRGKYVVLFF.PLDFTFVCPTE.I.FS.HAEDFRKL.C
RetrocopyMASSNAHSRKPAPDFIATLVVDGAFKEIKLSDYRGKYVVLFF*PLDFTFVCPTEVIPFSNHAEDFRKLDC
ParentalEVLGVSVDSQFTHLAWINTPRKEGGLGPLNIPLLADVTKSLSQNYGVLKNDEGIAYRGLFIIDAKGVLRQ
EV.G.SVDSQFTHLAWINTPRKEG..GPLNIPLLADVTKSLSQNYGVLKNDEGIA.RGLFII.AKGVLRQ
RetrocopyEVPGASVDSQFTHLAWINTPRKEGDVGPLNIPLLADVTKSLSQNYGVLKNDEGIADRGLFIINAKGVLRQ
ParentalITVNDLPVGRSVDEALRLVQAFQYTDEHGEVCPAGWKPG
ITVN.L.VGRSVDEAL.LVQAFQYTDEHGEVCPAGWKPG
RetrocopyITVNSLSVGRSVDEALHLVQAFQYTDEHGEVCPAGWKPG

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 130 .92 RPM
SRP017611_kidney 0 .00 RPM 105 .44 RPM
SRP017611_liver 0 .00 RPM 35 .30 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_497 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_497 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_497 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 22 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000123073 retrocopies
Canis familiaris ENSCAFG000000171633 retrocopies
Ciona intestinalis ENSCING000000030021 retrocopy
Callithrix jacchus ENSCJAG000000048824 retrocopies
Dipodomys ordii ENSDORG000000090051 retrocopy
Felis catus ENSFCAG000000004731 retrocopy
Homo sapiens ENSG000001678153 retrocopies
Gorilla gorilla ENSGGOG000000250893 retrocopies
Macaca mulatta ENSMMUG000000056892 retrocopies
Monodelphis domestica ENSMODG000000069781 retrocopy
Mustela putorius furoENSMPUG000000045912 retrocopies
Mus musculus ENSMUSG000000051612 retrocopies
Nomascus leucogenys ENSNLEG000000128002 retrocopies
Otolemur garnettii ENSOGAG000000249982 retrocopies
Pongo abelii ENSPPYG000000096073 retrocopies
Pan troglodytes ENSPTRG000000105413 retrocopies
Rattus norvegicus ENSRNOG00000003520 2 retrocopies
retro_rnor_2288, retro_rnor_497 ,
Rattus norvegicus ENSRNOG000000171948 retrocopies
Sorex araneus ENSSARG000000001461 retrocopy
Sarcophilus harrisii ENSSHAG000000155961 retrocopy
Sus scrofa ENSSSCG000000137362 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000258621 retrocopy



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