RetrogeneDB ID:

retro_mmus_3116

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:8:21598904..21600088(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000082323
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Zmym5
Ensembl ID:ENSMUSG00000040123
Aliases:Zmym5, 9830124H08Rik
Description:zinc finger, MYM-type 5 [Source:MGI Symbol;Acc:MGI:3041170]


Retrocopy-Parental alignment summary:






>retro_mmus_3116
ATGGAAGCTCATCTCACAGATATGGAATCATGTGGGGGTCCAACTAGTTCTTTAGCTGGTTAATCTAGAAACACACATGT
GGAAGATGATAATGTTGTATTTATTGAATCAGTACATCCTCCAATATGTGCTCCAGCAATACCTAATAAAAGAACTTTGT
ATTTGCTTCGTCAAAATATGAAAATCCAGGAGGAACTGATTCCACGATTTCCCCTTCTTGGAGAGATTTGACTTCTCAGA
CGGGAGATATATGTGAAACAATTGTAATTGATGATGAAGGGGACACAGACACAAATAGAGAGGAGGAGAAAAATCCTACC
GACTTTATTGAATGGGGACTGAATGGAAATAAAAATAGTACCAAAAATGTGGATTTCCCCATTGCCAGTCTATCAAGAAG
CAAGACCAAGGCTGCAGTAGGACCTTTTAATCCCGATAGGATTGATGTCACAGATGCATTTCAGAAGGGAAGATTTGTAG
TTCATCACAATCCTGATTCTTATATCTCCCAGTCACCATCATTTCCTCATAACCAGAAACAATGAAAGGTGGATTCTTTA
TCACCAGTGGCCTCACTTCCTAAACAGAATTTCCAGCCGTCAAACCAACAACATCTTACTAAACCTGCTAATAAAATTAC
TTGTGCAAACTGCAAAAATCCTTTACAGAAGGGGCAGACAGCTTATCAATGAACAGGATCAGCTCATCTCTTTTGTTCAA
CCACCTGCCTTTCTTCTTTCTCCCAGAAGTGGACTCAAAGGACACAGAATGTAATGTGTAAAAAAGATTCTCCTGTGAGA
ACCACAACTATTGTTCCTCCAGTGGAGCCAAGCAAGTCCTTACAAGGATTTTATAATGCATCGCCATCTCCCTATGAAAA
CTGCCAGAGTCTTAGGAAAGAAGTTTTTACTAAATCCAGATGTATAATCTGTAATTAATTAGGAGAGGTTCGCCATGAAA
TCAGTGTTAACAGTATAACACATAAACGGTGCAGTAATAATTGCTTTAATGAATACAGATTGACGAATGATCTAACAATG
AACTGCTGTGAACAGCGTAGCAAGTATATGCCCAAGAGTACTGGGCACAGCATTCTGATAACAGGTCAGCAAAAGAGATT
CTGCTGCCAGAATTGTGCTGATGAATATAAAGAGATAATGGAAGCAAAATAAAAAATACTGCTT

ORF - retro_mmus_3116 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.88 %
Parental protein coverage: 62.68 %
Number of stop codons detected: 5
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMEAHLADMESSGGPTSSLAGTSRNTHVEDDDVVFIESVQPPICAPAIPNER-NFVFASSKHENPPGTDST
MEAHL.DMES.GGPTSSLAG.SRNTHVEDD.VVFIESV.PPICAPAIPN.R.NFVFASSK.ENP.GTDST
RetrocopyMEAHLTDMESCGGPTSSLAG*SRNTHVEDDNVVFIESVHPPICAPAIPNKR<NFVFASSKYENPGGTDST
ParentalISPSWRDLTSQKGNLCETIVIDDEGDTDTNGGEEKNPTDFIEWGPNGNKSSTKNVDFPIASLSRSKTKTA
ISPSWRDLTSQ.G..CETIVIDDEGDTDTN..EEKNPTDFIEWG.NGNK.STKNVDFPIASLSRSKTK.A
RetrocopyISPSWRDLTSQTGDICETIVIDDEGDTDTNREEEKNPTDFIEWGLNGNKNSTKNVDFPIASLSRSKTKAA
ParentalVGPFNPGRIDVTDAFQNGRFAVHHNPDSWISQSASFPRNQKQQGVDSLSPVASLPKQIFQPSNQQP-TKP
VGPFNP.RIDVTDAFQ.GRF.VHHNPDS.ISQS.SFP.NQKQ..VDSLSPVASLPKQ.FQPSNQQ..TKP
RetrocopyVGPFNPDRIDVTDAFQKGRFVVHHNPDSYISQSPSFPHNQKQ*KVDSLSPVASLPKQNFQPSNQQHLTKP
ParentalV-KVTCANCKKPLQKGQTAYQRKGSAHLFCSTTCLSSFSHKRTRKTRNVMCKKDSPVRTTTIVPPVESSK
..K.TCANCK.PLQKGQTAYQ..GSAHLFCSTTCLSSFS.K.T..T.NVMCKKDSPVRTTTIVPPVE.SK
RetrocopyANKITCANCKNPLQKGQTAYQ*TGSAHLFCSTTCLSSFSQKWTQRTQNVMCKKDSPVRTTTIVPPVEPSK
ParentalSLQGFYNASLSPYENCQSLRKEVFTKSRCIICNKLGEVRHEISVNSITHKLCSNNCFNEYRLTNGLIMNC
SLQGFYNAS.SPYENCQSLRKEVFTKSRCIICN.LGEVRHEISVNSITHK.CSNNCFNEYRLTN.L.MNC
RetrocopySLQGFYNASPSPYENCQSLRKEVFTKSRCIICN*LGEVRHEISVNSITHKRCSNNCFNEYRLTNDLTMNC
ParentalCEQCSKYMPKSTGHSILITGQQKRFCCQNCADEYKEIMEAKSKLLL
CEQ.SKYMPKSTGHSILITGQQKRFCCQNCADEYKEIMEAK.K.LL
RetrocopyCEQRSKYMPKSTGHSILITGQQKRFCCQNCADEYKEIMEAK*KILL

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 33 .39 RPM
SRP007412_cerebellum 0 .00 RPM 35 .26 RPM
SRP007412_heart 0 .00 RPM 30 .82 RPM
SRP007412_kidney 0 .00 RPM 46 .10 RPM
SRP007412_liver 0 .00 RPM 32 .36 RPM
SRP007412_testis 0 .00 RPM 31 .93 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_3116 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3116 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_3116 retrocopy 5' end.

Lab - click to see more details

retro_mmus_3116 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3116 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Mus musculus ENSMUSG00000040123 4 retrocopies
retro_mmus_3113, retro_mmus_3114, retro_mmus_3115, retro_mmus_3116 ,


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