RetrogeneDB ID:

retro_rnor_533

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:1:232986592..232987190(+)
Located in intron of:ENSRNOG00000020440
Retrocopy
information
Ensembl ID:ENSRNOG00000036633
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RGD1359508
Ensembl ID:ENSRNOG00000038330
Aliases:None
Description:UPF0462 protein C4orf33 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q5M845]


Retrocopy-Parental alignment summary:






>retro_rnor_533
GTGGATTGTAAAATTGAATACACTTGGGATAGTTTTCCAGTAAGTCAGGAGCCAGTGCGTGCCAGGCTGAATCCATGTGA
CAAGGGATTGAAGATGGAGGTTACTGCTCCATATTTCAGTGATCCTCTAGCCCCTCTTGGAGAACCAGGAAAGCCTTTCA
GTGAACTGTGGAATTATGAAGTTGTGGAAGCATTCTTCTTGAATGATACCACTGAGCAGTATTTAGAAGTTGAACTTTGT
CCACATGGACAACATTTAGTTCTTTTACTTCCTGGAAGAAAAAATGTTTGGGAAAAAAGAGCTTGCATTATCATTCAAAG
TGTCCAGAGGAGAGACTCATTGGGAAGGTGAAGCTTATCTTCCTTGGGGTTATTTTCCATCTAATGTGACACGATTCAAC
TCATTTGCAATCCATGGATCAAATGATAGAAGAGTTTATGAAGCGCTTTACCCTGCGCCACAACCTGAGCTGCAACAAGG
ACAAAATCCTGACTTCCATCGTCTAAAATATTTCAAGCCTTTCAGTTTTAACACACTGCTTGGAGAAGAGTGGAAGCAGC
CAGAATCAGACCTGTGGCTGATAGAGAAATCCGATGTA

ORF - retro_rnor_533 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.5 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMDFKIEYTWDSFPVSHEPVRIRLNPCDKGLKMEVSAPFFNDPPAPLGEPGKPFSELWNYEVVEAFFLNNT
.D.KIEYTWDSFPVS.EPVR.RLNPCDKGLKMEV.AP.F.DP.APLGEPGKPFSELWNYEVVEAFFLN.T
RetrocopyVDCKIEYTWDSFPVSQEPVRARLNPCDKGLKMEVTAPYFSDPLAPLGEPGKPFSELWNYEVVEAFFLNDT
ParentalTEQYLEVELCPHGQHLVLLLSGRRNVW-KKELALSFKVSRGETHWEGEAFLPWSYFPSKVTRFNSFAIHG
TEQYLEVELCPHGQHLVLLL.GR.NVW.KKELALSFKVSRGETHWEGEA.LPW.YFPS.VTRFNSFAIHG
RetrocopyTEQYLEVELCPHGQHLVLLLPGRKNVW>KKELALSFKVSRGETHWEGEAYLPWGYFPSNVTRFNSFAIHG
ParentalSNDKRVYEALYPVPQPELQQGQNPDFHRLEYFKPFSFNTLLGEEWKQPESDLWLIEKSDI
SND.RVYEALYP.PQPELQQGQNPDFHRL.YFKPFSFNTLLGEEWKQPESDLWLIEKSD.
RetrocopySNDRRVYEALYPAPQPELQQGQNPDFHRLKYFKPFSFNTLLGEEWKQPESDLWLIEKSDV

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 2 .37 RPM
SRP017611_kidney 0 .00 RPM 4 .88 RPM
SRP017611_liver 0 .00 RPM 3 .43 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_533 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_533 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_533 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Mus musculus ENSMUSG000000257661 retrocopy
Otolemur garnettii ENSOGAG000000103681 retrocopy
Rattus norvegicus ENSRNOG00000038330 1 retrocopy
retro_rnor_533 ,
Tupaia belangeri ENSTBEG000000147661 retrocopy



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