RetrogeneDB ID:

retro_rnor_2837

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:X:99232409..99233333(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000050970
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Setd8
Ensembl ID:ENSRNOG00000001062
Aliases:Setd8, Pr-set7, RGD1305893
Description:histone-lysine N-methyltransferase SETD8 [Source:RefSeq peptide;Acc:NP_001233594]


Retrocopy-Parental alignment summary:






>retro_rnor_2837
GAGAACTTGTTTGCTGGGCAGTCAAAGATCTGTGCCGTCATGAGTCCAAACAAATGGTCTGGAATTCGCTCTCCACTTCA
GGAAGAGAACTCGGTTGTACATCATGAGGTCAAATTCCCGGGAAAACCATTAGCTGGAATCCTCAGGAAGGGAGAAGAAA
AAAGAAACGCTAGGAATGTTATCCGAAGCACTGTGAAGTCAGATGAACAGAAGAGTAAAGGTACCAGGAGAGGTCCCAGG
GCGCCTTTCCCAAACCAAAAACCTGAAGCAAAAGCACCTCCAAAAGCTCCACCCCCATCACGTGATTATACCAATGTAGC
AGTTGCTAAGCAAGCCCAGAAAAAGCCCCTCAAGGGCAAGCAGGCCCCTAGGGAAAAGTCTCAAGGGAAAACACAGCAGA
ATAGAAAACTCACAGATTTCCACCCTGTGCGAAGGAGCTCCAGGAAGAGCAAAGCTGAGCTGCGGTCTGAAGAAAGGAAG
AAAATAGATGAGCTAATTGAGAGTGGGAAGGAAGAAGGTATGAAGGTTGATCTAATTGATGGCAAAGGCAGGGGCGTGAT
TGCTACCAAGCGGTTCTCCCGGGGAGACTTTGTGGTAGAATACCATGGGGACCTCATTGAAATCACCGATGCCAAGAAGC
GGGAGGCTCTATATGCACAGAACCCCTCCACAGGGTGCTACATGTACTATTTTCAATATCTGAGAAAAACCTACTGCGTG
GATGCCACTCAGGAAACGAATCGCCTGGGGAGACTGATCAATCACAGTAAGTGTGGAAATTGCCAGACCAAACTCCATGA
CATTGATGGCGTGCCTCACCTCATCCTTATTGCCTCCCGAGACATTGCGGCCGGGGAGGAGCTCCTGTACGACTATGGTG
ACCGAAGCAAGGCCTCCATCGAAGCTTACCCTTGGCTGAAGCAC

ORF - retro_rnor_2837 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.23 %
Parental protein coverage: 95.65 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalENVFAGQSKIYAYMSPNKCSGMRSPLQEENSVAHHEVKCPGKPLAGIYRKREEKRNAGNVIRSAVKSEEQ
EN.FAGQSKI.A.MSPNK.SG.RSPLQEENSV.HHEVK.PGKPLAGI.RK.EEKRNA.NVIRS.VKS.EQ
RetrocopyENLFAGQSKICAVMSPNKWSGIRSPLQEENSVVHHEVKFPGKPLAGILRKGEEKRNARNVIRSTVKSDEQ
ParentalKSKDTRRGPLAPFPNQKPEATEPPKTPPPSCDSTSVAVAKQALKKPLKGKQAPRKKSQGKTQQNRKLTDF
KSK.TRRGP.APFPNQKPEA..PPK.PPPS.D.T.VAVAKQA.KKPLKGKQAPR.KSQGKTQQNRKLTDF
RetrocopyKSKGTRRGPRAPFPNQKPEAKAPPKAPPPSRDYTNVAVAKQAQKKPLKGKQAPREKSQGKTQQNRKLTDF
ParentalYPVRRSSRKSKAELQSEERKKIDELIESGKEEGMKIDLIDGKGRGVIATKRFSRGDFVVEYHGDLIEITD
.PVRRSSRKSKAEL.SEERKKIDELIESGKEEGMK.DLIDGKGRGVIATKRFSRGDFVVEYHGDLIEITD
RetrocopyHPVRRSSRKSKAELRSEERKKIDELIESGKEEGMKVDLIDGKGRGVIATKRFSRGDFVVEYHGDLIEITD
ParentalAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATQETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASR
AKKREALYAQ.PSTGCYMYYFQYL.KTYCVDATQETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASR
RetrocopyAKKREALYAQNPSTGCYMYYFQYLRKTYCVDATQETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASR
ParentalDIAAGEELLYDYGDRSKASIEAYPWLKH
DIAAGEELLYDYGDRSKASIEAYPWLKH
RetrocopyDIAAGEELLYDYGDRSKASIEAYPWLKH

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 .43 RPM
SRP017611_kidney 0 .00 RPM 16 .54 RPM
SRP017611_liver 0 .00 RPM 4 .10 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2837 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2837 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2837 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000103711 retrocopy
Homo sapiens ENSG000001839552 retrocopies
Macaca mulatta ENSMMUG000000135141 retrocopy
Mus musculus ENSMUSG000000493272 retrocopies
Otolemur garnettii ENSOGAG000000310931 retrocopy
Pongo abelii ENSPPYG000000050852 retrocopies
Pan troglodytes ENSPTRG000000055981 retrocopy
Rattus norvegicus ENSRNOG00000001062 4 retrocopies
Sarcophilus harrisii ENSSHAG000000153762 retrocopies
Tursiops truncatus ENSTTRG000000158841 retrocopy



Copyright © RetrogeneDB 2014-2017