RetrogeneDB ID:

retro_mmus_2900

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:7:14306044..14307663(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Phf20
Ensembl ID:ENSMUSG00000038116
Aliases:Phf20, 6820402O20Rik
Description:PHD finger protein 20 [Source:MGI Symbol;Acc:MGI:2444148]


Retrocopy-Parental alignment summary:






>retro_mmus_2900
GACTGTTTGAAATTTTTCCGCAAGGCTAAATTGCTGCACTATCATATGACGTATTTCCATGGGATGGAGAAGTCACCAGA
GCCAGAGGAGGGCCCAGGGAAGACGCATGTATAGACTCGGGGCTCTGCGGTGCCTGACAAGGCCAGCCAGGAGAGCCTAA
CCAGGAAGCGGGTCTCTGCCAGTTCCCCCACTGCAAAAGAGAAGGAAAAGACTAAAGAGAAGAAATTCAAAGAACTTGTG
AGAGTGAAGCCAAAGAAGAAAAAGAAAACCAAGCCTGAATGTCCCTGCAGTGAGGACATCAGTGATACTTCCCAGGAACC
TTCTCCACCCAAAACATTTGCTGTCACCAGGTGTGGGTCTTCACACAAGTCTGGGGTCCATTGGAGCCCGCAGCTCCATG
GGTCAGATAATGGAAACCACAAAGGGAAATTGAAAACTTGTGAGGAGGATAATTTGAGCGAGTCCTCTTCCGAGAGTTTT
CTTTGGAATGATGAGGAATATGGTCAAGATGTTGATGTGGCCACCAATCCAGGTGAGGAGCTTGAGGACAACGACCGCTA
TGATTTTGAGGTGGTCCGCTGCATCTGTGAAGTGCAGGAGGAAAATGACTTCATGATTCAGTGTGAAGAGTGCCAGTGCT
GGCAGCACGGGGTCTGCAAGGGCTTCCTGGAAGAAAATGTGCCTGAGAAATACACCTGCTATGTTTGCCAAGACCCTCCA
GGTCAGAGGCCTGGCTTCAAGTACTGGTATGACAAGGAGTGGCTGAGCCGGGGACACATGCATGACCTGGAGTTTCTGGA
ACAGAACTACTCCCACCAGAATGCCAGGAAGATCGTGGCCACCCACCAGCTGCTCGGGGACGTGCCGAGAGTGATCCAAG
TGCTGCACGGCCTGCAGCTCAAGATGAGCATTCTGCAAAGCAGAGAGCATCCTGATCTGCGGCTATGGTGCCAGCCCTGG
AAACAGCACTCGGGGGAGGGAATAGCACATCCCAGACACATCCACATCACAGACTCCAGGAGCGAGGAGTCCCCAAGCTA
TAGAACTTTGAATGGGGCGGTGGAGAAGCCATCGCCCCTGCCCCGATCTGTGGAGGAATCTTACATCACCAGTGAGCATT
GCTACCAGAAACCTCGTGCTTATTATCCTGCTGTGGAGCAGAGGCTAGTCGTGGAGAAGAGAGGCTCTGCCCTTGATGCT
GCAGTCAGCCCCTCTGTGAGAACGGCGATGACTCCCTCTCCTCTCGCCTAGGCTGGCCCATCGACCAAGACAGGAGCAGA
GGCGACATAGATCCCAAACCCAGCTCCCCAAAGGTGAGAGAGTACATTTCCAAGAATGTCTTGCTAGAAGAGATGCCTGC
GAGGAAGCTGCTGGACAGAGGTGGAGAAGGGCTGGTGAGCTCTCAGCACCAGTGGCAGTTCAACCTGCTCACACATGTGG
AGCAGGATGAGGTGAGGAACCAGATGGACTCCATTGAGAAGGAGCTGGACATGGTGGAGAGCTGGCTAGACTACACTGGG
GAGCTGGAGCCCCCAGAGCCACTGGCCAGGCTTCTGCAGCTCAAGCAGCTGCTGACTGACCTGGGCAAGGTTCAGCAGAT
CGCCCTCTGCTGCTGGACA

ORF - retro_mmus_2900 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.56 %
Parental protein coverage: 54.46 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalDCLKFFRKAKLLHYHMKYFHGMEKSPEPEEGPGKTHVQTRGSAVPDKTSQESLTRKRVSASSPTAKEKEK
DCLKFFRKAKLLHYHM.YFHGMEKSPEPEEGPGKTHV.TRGSAVPDK.SQESLTRKRVSASSPTAKEKEK
RetrocopyDCLKFFRKAKLLHYHMTYFHGMEKSPEPEEGPGKTHV*TRGSAVPDKASQESLTRKRVSASSPTAKEKEK
ParentalTKEKKFKELVRVKPKKKKKKKKKTKPECPCSEDISDTSQEPSPPKTFAVTRCGSSHKPGVHMSPQLHGSD
TKEKKFKELVRVKP....KKKKKTKPECPCSEDISDTSQEPSPPKTFAVTRCGSSHK.GVH.SPQLHGSD
RetrocopyTKEKKFKELVRVKP----KKKKKTKPECPCSEDISDTSQEPSPPKTFAVTRCGSSHKSGVHWSPQLHGSD
ParentalNGNHKGKLKTCEEDNLSESSSESFLWSDEEYGQDVDVTTNPDEELEGDDRYDFEVVRCICEVQEENDFMI
NGNHKGKLKTCEEDNLSESSSESFLW.DEEYGQDVDV.TNP.EELE..DRYDFEVVRCICEVQEENDFMI
RetrocopyNGNHKGKLKTCEEDNLSESSSESFLWNDEEYGQDVDVATNPGEELEDNDRYDFEVVRCICEVQEENDFMI
ParentalQCEECQCWQHGVCMGLLEENVPEKYTCYVCQDPPGQRPGFKYWYDKEWLSRGHMHGLAFLDQNYSHQNAR
QCEECQCWQHGVC.G.LEENVPEKYTCYVCQDPPGQRPGFKYWYDKEWLSRGHMH.L.FL.QNYSHQNAR
RetrocopyQCEECQCWQHGVCKGFLEENVPEKYTCYVCQDPPGQRPGFKYWYDKEWLSRGHMHDLEFLEQNYSHQNAR
ParentalKIVATHQLLGDVQRVIQVLHGLQLKMSILQSREHPDLQLWCQPWKQHSGEGRAHPRHIHITDARSEESPS
KIVATHQLLGDV.RVIQVLHGLQLKMSILQSREHPDL.LWCQPWKQHSGEG.AHPRHIHITD.RSEESPS
RetrocopyKIVATHQLLGDVPRVIQVLHGLQLKMSILQSREHPDLRLWCQPWKQHSGEGIAHPRHIHITDSRSEESPS
ParentalYRTLNGAVEKPSPLPRSVEESYITSEHCYQKPRAYYPAVEQRLVVETRGSALDAAVS-PLCENGDDSLSP
YRTLNGAVEKPSPLPRSVEESYITSEHCYQKPRAYYPAVEQRLVVE.RGSALDAAVS.PLCENGDDSLS.
RetrocopyYRTLNGAVEKPSPLPRSVEESYITSEHCYQKPRAYYPAVEQRLVVEKRGSALDAAVS<PLCENGDDSLSS
ParentalRLGWPIDQDRSRGDIDPKPSSPKVREYISKNVLPEETPARKLLDRGGEGLVSSQHQWQFNLLTHVESLQD
RLGWPIDQDRSRGDIDPKPSSPKVREYISKNVL.EE.PARKLLDRGGEGLVSSQHQWQFNLLTHVE..QD
RetrocopyRLGWPIDQDRSRGDIDPKPSSPKVREYISKNVLLEEMPARKLLDRGGEGLVSSQHQWQFNLLTHVE--QD
ParentalEVTHRMDSIEKELDVLESWLDYTGELEPPEPLARLPQLKHCIKQLLTDLGKVQQIALCCST
EV...MDSIEKELD..ESWLDYTGELEPPEPLARL.QLK....QLLTDLGKVQQIALCC.T
RetrocopyEVRNQMDSIEKELDMVESWLDYTGELEPPEPLARLLQLK----QLLTDLGKVQQIALCCWT

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 .05 RPM 72 .78 RPM
SRP007412_cerebellum 0 .00 RPM 92 .57 RPM
SRP007412_heart 0 .00 RPM 20 .02 RPM
SRP007412_kidney 0 .04 RPM 35 .48 RPM
SRP007412_liver 0 .00 RPM 13 .90 RPM
SRP007412_testis 0 .00 RPM 35 .13 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2900 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2900 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_2900 retrocopy 5' end.

Lab - click to see more details

retro_mmus_2900 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2900 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 ENSMUSG00000038116 1 retrocopy
retro_mmus_2900 ,


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