RetrogeneDB ID:

retro_mmus_614

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:10:3139465..3141067(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Cpne3
Ensembl ID:ENSMUSG00000028228
Aliases:Cpne3, 5430428M23Rik, 5730450C07Rik, C85108, CPN3
Description:copine III [Source:MGI Symbol;Acc:MGI:1917818]


Retrocopy-Parental alignment summary:






>retro_mmus_614
ATGGCTGCCCAGTATGTCACAAAATTGGAACTAAACATTTCCTATAACAAACTTTTGGATGTAGATGTAACATCAAAGTC
AGATCCTTTATGTGTGTTGTTTTTGAACATGAGTGGTCAACAGTGGTATGAGGTTGAAGGGAAAGAAGCATTAAGAATTC
TTTGAATCTCAAATTTTCTAAGACGTTTCTTATTGATTACTACTTTGACATGGTTCAGAAATTGAAATTTTGCGTCTATA
GCATTGACAAGAAAACTATTGAGTCGAGTGATGATGACTTCTTGGGAGAATGTGGAGTCACTCTTGGACAAATAGTTTAC
AGTAAGAAGATAACTTAATCACTGGTGCTCAAAAATGGCAAACCTTCAGGGAGAGGGAGCATTGCAATTTCAGTAGAAGA
AATAAAGGACAACAGAGTGGTATTGTCTGAAGTAGAAGCCAGAAAACTGGATAATAAGGATCTGTTTGGGAAGTCAGATC
CATACTTGGAGTTTCACAAGCAGACATCAGAGAGCCACTGGCTGATGGTTCACTGAACAGGAGTTATAAAAAAACAACCT
GAATCCCACGGGGAAGCCTTTTAAAATCTCCAGTCTCCTTAACTCTCTGTGCTATGAAAAAGTGGACAAAACCATTAAGG
TAGAGTATTATGATTATGACAATGATGGCTCACATAATCTCATTGGAACTTTTCAAACCACCATGACAAAACTCAAAGAA
GCCTCCAGAAACTCATCAGTTGAATATTAATGCATAAATGAAAAAAAGAGACAGAAGAAAGAAAGCTACAAGAATTCAGG
TGTTATCAGCGTGAAGCATCATGAGATTACTGTAGAATGCACATTTCTTGACTACATCATGGGAAGGTGTCAGCTCAATT
TTACTGCGGGAATGGACTTCACTGGCTCTAATGGTGACCCCAGTTCTCCAGACTCCCTGCATTACATCAGCCCTAATAGT
GTTAATGAGTATTTGAGTGCCATCTGCTCAGTGGGATTGGCAATTCAAGATTATGATGTTGATAAAATGTCTCCAGCTTT
TGGCTTTGAAGCTCAGGTGCCCCCTCAGTGGCAGGTGTCTCATGAATTCCCAATGGACTTTAACCCCTCGAACCCCTATT
GCAATGGAATCAAGGCATTATAGAGGCTTATCAGACCTGTCTTCCTCAGATAAGACTCTGTGGATCAACTAATTTTTCTC
CAATTATAACCACGTGGCCAGGTTTGCAGCTGCAGCCACACAGCAGCAGACCACTTCTCAATACTTTCTGCTTGTATCCA
TCACCGATGGCGTGATCGCAGACCTTGATGAAACCAGACAGGCAATCGTCAATGCAGCCAAGCTGCCCATGTCTATCATC
ATTGTGGGACTTCGGAGAGCTGACTTCAGTGCCATGGAGTTTCTAGATGGTGATGGTGGAAGGCTCCGTGCCCCATCAGG
TGAGGTGACCATAAGAGATATTGTTCAGTCTGTGCCTTTCAGACAGTTCAGAATGCTCCAAAAGAAACACTTGCTCAGTG
TGTCTTGGCAGAAATTCCCTAGCAGGTGGTGGGCTACTTCAACACATACAAACTCCTTCCTCCCAAAAACCCAGCTGTGA
AG

ORF - retro_mmus_614 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.81 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMAAQCVTKVELNVSCNNLLDADVTSKSDPLCVLFLNTSGHQWYEVE-RTERIKNSLNPKFSKTFVIDYYF
MAAQ.VTK.ELN.S.N.LLD.DVTSKSDPLCVLFLN.SG.QWYEVE.R...IKNSLN.KFSKTF.IDYYF
RetrocopyMAAQYVTKLELNISYNKLLDVDVTSKSDPLCVLFLNMSGQQWYEVE<RERSIKNSLNLKFSKTFLIDYYF
ParentalEVVQKLKFGIYDIDNKTIELSDDDFLGECEVTLGQIVSSKKLTRPLVLKNGKPAGKGSITISAEEIKDNR
..VQKLKF..Y.ID.KTIE.SDDDFLGEC.VTLGQIV.SKK.T..LVLKNGKP.G.GSI.IS.EEIKDNR
RetrocopyDMVQKLKFCVYSIDKKTIESSDDDFLGECGVTLGQIVYSKKIT*SLVLKNGKPSGRGSIAISVEEIKDNR
ParentalVVLFEMEARKLDNKDLFGKSDPYLEFHKQTSDGHWLMVHRTEVIK-NNLNPMWKPFKIS--LNSLCYGDM
VVL.E.EARKLDNKDLFGKSDPYLEFHKQTS..HWLMVH.T.VIK.NNLNP..KPFKIS..LNSLCY...
RetrocopyVVLSEVEARKLDNKDLFGKSDPYLEFHKQTSESHWLMVH*TGVIK>NNLNPTGKPFKISSLLNSLCYEKV
ParentalDKTIKVECYDYDNDGSHDLIGTFQTTMTKLKEASRSSPVEYECINEKKRQKKKSYKNSGVISVKHCEITV
DKTIKVE.YDYDNDGSH.LIGTFQTTMTKLKEASR.S.VEY.CINEKKRQKK.SYKNSGVISVKH.EITV
RetrocopyDKTIKVEYYDYDNDGSHNLIGTFQTTMTKLKEASRNSSVEY*CINEKKRQKKESYKNSGVISVKHHEITV
ParentalECTFLDYIMGGCQLNFTVGVDFTGSNGDPSSPDSLHYISPNGVNEYLTAIWSVGLVIQDYDADKMFPAFG
ECTFLDYIMG.CQLNFT.G.DFTGSNGDPSSPDSLHYISPN.VNEYL.AI.SVGL.IQDYD.DKM.PAFG
RetrocopyECTFLDYIMGRCQLNFTAGMDFTGSNGDPSSPDSLHYISPNSVNEYLSAICSVGLAIQDYDVDKMSPAFG
ParentalFGAQVPPQWQVSHEFPMNFNPSNPYCNGI-QGIVEAYRTCLPQIRLYGPTNFSPII-NHVARFAAAATQQ
F.AQVPPQWQVSHEFPM.FNPSNPYCNGI.QGI.EAY.TCLPQIRL.G.TNFSPII.NHVARFAAAATQQ
RetrocopyFEAQVPPQWQVSHEFPMDFNPSNPYCNGI<QGIIEAYQTCLPQIRLCGSTNFSPII<NHVARFAAAATQQ
ParentalQTASQYFVLLIITDGVITDLDETRQAIVNAAKLPMSIIIVGVGGADFSAMEFLDGDGGSLRAPSGEVAIR
QT.SQYF.L..ITDGVI.DLDETRQAIVNAAKLPMSIIIVG...ADFSAMEFLDGDGG.LRAPSGEV.IR
RetrocopyQTTSQYFLLVSITDGVIADLDETRQAIVNAAKLPMSIIIVGLRRADFSAMEFLDGDGGRLRAPSGEVTIR
ParentalDIVQFVPFRQF-QNAPKEALAQCVLAEIPQQVVGYFNTYKLLPPKNPAVK
DIVQ.VPFRQF.QNAPKE.LAQCVLAEIP.QVVGYFNTYKLLPPKNPAVK
RetrocopyDIVQSVPFRQF<QNAPKETLAQCVLAEIP*QVVGYFNTYKLLPPKNPAVK

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 16 .33 RPM
SRP007412_cerebellum 0 .00 RPM 17 .06 RPM
SRP007412_heart 0 .00 RPM 24 .13 RPM
SRP007412_kidney 0 .00 RPM 51 .47 RPM
SRP007412_liver 0 .00 RPM 47 .71 RPM
SRP007412_testis 0 .00 RPM 4 .85 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_614 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_614 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_614 retrocopy 5' end.

Lab - click to see more details

retro_mmus_614 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_614 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 ENSMUSG00000028228 1 retrocopy
retro_mmus_614 ,


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