RetrogeneDB ID:

retro_rnor_2430

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:7:17348360..17349181(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Pcgf6
Ensembl ID:ENSRNOG00000020250
Aliases:Pcgf6, Rnf134
Description:Polycomb group RING finger protein 6 [Source:UniProtKB/Swiss-Prot;Acc:Q5XI70]


Retrocopy-Parental alignment summary:






>retro_rnor_2430
CCCCTGGAGTTGGAGCCAGAGCACAGTCTGGGCCTCTTGTGAGTCCACTTCGAGAACTATGATGAGGAGTTGGAAGAAGA
TTAGGAGATGGAGGAGGAGAAAGACCAGGAGGAAGAGATGAGCCACTTCTCTCTGAGTCTGGAGTCCGGATGTGCAAACT
CCTAGGACCAGGAGAAGAGCCTGATGAACCTGACTGAGCTGACGCCCTACATCTTGTGCTCCATTCGCAAAGGTTAATTG
ATACATGCCACCACTATTGCAGAATGTCTCCACACCTTTTGTAAAAGCTGCATTGTGAGACATTTTTACTATAGCAACAG
ATGCCCCAAATGCAACATAGTAGTCCACCAGACTCAGCCTCTTTATAATATAAGGTTGGACCGGCAGTTACAAGACAAAG
TATATAAATTAGTAATCAATCTAGCGGAAAGAGGAAAAAAGCAAAAGCACGACTTCTATAAAGAAAGAGGTCTAGAAGTC
CCTAAGCCTGCTCTTACACAGCCAGTCGCTGCAAACAAAGGAAGAACCCAGAAAATCCTAGAGTCAGTGTTTTGTATTCC
ACCTGATGTTTTATTGATGTTGAGTTCATTGATGCTAATGAAGACAGAGGACATTTTAAGCCATTGGAAAAGAAGTTTGT
GCATGTTTCAGGAGAAGCAACTACTGGGTATGTAGAAAAATTTCTTGGAAGAAAATTGTGTCTTGATCCAGCTTGTCAGG
TAGATAACATCTGTGGGGATCACTTATTGGAGCGGTACCAAACTCTGCAGGAAATCCGATGTTCAATACGTGACACAGCA
ATGCAGGATGGTCTACCTGTT

ORF - retro_rnor_2430 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.14 %
Parental protein coverage: 78.63 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPPELEPERSLGRLRGRFEDYDEELEEDEEMEEEEEEEEEMSHFSLRLESGRADSEDEEERLINLVELTPY
P.ELEPE.SLG.L...FE.YDEELEED.EMEEE...EEEMSHFSL.LESG.A.S.D.E..L.NL.ELTPY
RetrocopyPLELEPEHSLGLL*VHFENYDEELEED*EMEEEKDQEEEMSHFSLSLESGCANS*DQEKSLMNLTELTPY
ParentalILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLYNIRLDRQLQDIVYKLVVN
ILCSI.KG.LI.ATTI.ECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLYNIRLDRQLQD.VYKLV.N
RetrocopyILCSIRKG*LIHATTIAECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLYNIRLDRQLQDKVYKLVIN
ParentalLEEREKKQMHDFYKERGLEVPKPAVPQPVPASKGRTKKALESVFRIPPELDVSLLL-EFIGANEDTGHFK
L.ER.KKQ.HDFYKERGLEVPKPA..QPV.A.KGRT.K.LESVF.IPP..DV.L.L.EFI.ANED.GHFK
RetrocopyLAERGKKQKHDFYKERGLEVPKPALTQPVAANKGRTQKILESVFCIPP--DVLLML<EFIDANEDRGHFK
ParentalPLEKKFVRVSGEATIGHVEKFLRRKMGLDPACQVDIICGDHLLERYQTLREIRRAIGDTAMQDGLLV
PLEKKFV.VSGEAT.G.VEKFL.RK..LDPACQVD.ICGDHLLERYQTL.EIR..I.DTAMQDGL.V
RetrocopyPLEKKFVHVSGEATTGYVEKFLGRKLCLDPACQVDNICGDHLLERYQTLQEIRCSIRDTAMQDGLPV

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 11 .29 RPM
SRP017611_kidney 0 .00 RPM 6 .28 RPM
SRP017611_liver 0 .00 RPM 7 .06 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2430 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2430 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2430 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Echinops telfairi ENSETEG000000044171 retrocopy
Myotis lucifugus ENSMLUG000000049851 retrocopy
Rattus norvegicus ENSRNOG00000020250 2 retrocopies
retro_rnor_2429, retro_rnor_2430 ,



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