RetrogeneDB ID:

retro_mmus_2460

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:4:52360825..52361628(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000083338
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Pold3
Ensembl ID:ENSMUSG00000030726
Aliases:Pold3, 2410142G14Rik, C85233, P66, P68
Description:polymerase (DNA-directed), delta 3, accessory subunit [Source:MGI Symbol;Acc:MGI:1915217]


Retrocopy-Parental alignment summary:






>retro_mmus_2460
CTAATCTCTAAAGCTGCTACTAAAACCCAAGACACCAACAAGGAAACCGAAACAGAGGCCGGAGAAGTAACAAGCGCCGT
CTTCCGCTGGGGGCAAAGCACTACTAGGAAAAGGGAACTTTTTTTGAAAAGTTGCAATGAATAAATTTAAAGTCAATTTG
GATTCAGAACAAGCAGTAAAGGAAGAAAAAACACCGGAGCAACCTCCAGTGTCTGTCACTGAACCAAAGCTGGCAGCTCC
CCCAGCTCTGAAGAAATCCAGCAGAAAGTCCGAGCCTGCGAAGGTGCAGGAGAGGGAGAAAAGCAACAGGGGCAAGCGAG
CATACTTATCTGATGAGGAAGCATAGGAAACCGAAAAGCTGAAGAAAAAGAGAAGAAGAATCAAGCTTCCTCAGTCTGAT
AGCAGTGAAGATGAAGTCTTTGCAAACTCTCCTGAGATGTCTGAAGCCGGCTCGCCATCTCCAGTTCCTGTATCTCCACC
TCTTGATCCTAGGCCCCAAAACTGAGCCTCCTCCTGTCAAGCGTTCAGGTGGAGACAATAAGAGAAAACGAAAGCGTGTA
CTGAAATCTAAACCCTTTGTGGATGAAGAAGGCTGCGTAGTGACTGAGAAAGTCTATGAGAGTGAGTCCTGCACAGACAG
TGAGGAGGACCTTAAGAAGAAGCCGGCCTCAGCACACAGACCCTCTGCTGTCGCTGTGAAAAGGGAGCCCAGAGAAGACT
CAGAGAAGAGCCCCAGGAAAAGGGCTGCGGCTCTGGGTAAATCCAACAGACAAGTGTCCATTACTGGTTTCTTCCAGAAA
AAG

ORF - retro_mmus_2460 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.05 %
Parental protein coverage: 58.13 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLISKAATKTQDTNKETKPEAREVTSA-SSAGGKAP-GKGSVMSNFFGKAAMNKLKVNLDSEQAVKEEKTV
LISKAATKTQDTNKET..EA.EVTSA.SSAGGKA..GKG....NFF.K.AMNK.KVNLDSEQAVKEEKT.
RetrocopyLISKAATKTQDTNKETETEAGEVTSA>SSAGGKALLGKG----NFF*KVAMNKFKVNLDSEQAVKEEKTP
ParentalEQPPVSVTEPKLAAPPAQKKSSRKSEPGKVQQKEKS-RGKRVDLSDEEAKETEHLKKKRRRIKLPQSDSS
EQPPVSVTEPKLAAPPA.KKSSRKSEP.KVQ..EKS.RGKR..LSDEEA.ETE.LKKKRRRIKLPQSDSS
RetrocopyEQPPVSVTEPKLAAPPALKKSSRKSEPAKVQEREKSNRGKRAYLSDEEA*ETEKLKKKRRRIKLPQSDSS
ParentalEDEVFEDSPEMYEADSPSPPPVSPPPDPMP-KTEPPPVKRSSGETKRRRKRVLKSKTFVDEEGCIVTEKV
EDEVF..SPEM.EA.SPSP.PVSPP.DP.P.KTEPPPVKRS.G..KR.RKRVLKSK.FVDEEGC.VTEKV
RetrocopyEDEVFANSPEMSEAGSPSPVPVSPPLDPRP>KTEPPPVKRSGGDNKRKRKRVLKSKPFVDEEGCVVTEKV
ParentalYESESCTDSEEELKMKPASAHKPPAAAVKREPREE-RKGPKKGAAALGKANRQVSITGFFQKK
YESESCTDSEE.LK.KPASAH.P.A.AVKREPRE...K.P.K.AAALGK.NRQVSITGFFQKK
RetrocopyYESESCTDSEEDLKKKPASAHRPSAVAVKREPREDSEKSPRKRAAALGKSNRQVSITGFFQKK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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
SRP007412_brain 0 .00 RPM 23 .13 RPM
SRP007412_cerebellum 0 .00 RPM 22 .80 RPM
SRP007412_heart 0 .00 RPM 10 .09 RPM
SRP007412_kidney 0 .00 RPM 20 .54 RPM
SRP007412_liver 0 .00 RPM 9 .04 RPM
SRP007412_testis 0 .05 RPM 132 .14 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2460 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2460 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_2460 retrocopy 5' end.

Lab - click to see more details

retro_mmus_2460 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2460 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Mus musculus ENSMUSG00000030726 1 retrocopy
retro_mmus_2460 ,


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