RetrogeneDB ID:

retro_mmus_439

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:1:49399405..49400729(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Hspd1
Ensembl ID:ENSMUSG00000025980
Aliases:Hspd1, 60kDa, Hsp60
Description:heat shock protein 1 (chaperonin) [Source:MGI Symbol;Acc:MGI:96242]


Retrocopy-Parental alignment summary:






>retro_mmus_439
ATGCCTCATCTATTCACAGTCCTTTGCCAGATGAGACCAGTGTCCCCAGCACTGGCTCCTCATCTCACTTGGGCCTATGC
CAAAGATATAAAATTTGGTGCGGATGCTTGAGCCTTAATGCTTCAAGGTATAGATCTTTTAGCTGATGCTATAGCTGTTA
CAGTGGGGTCAAAGCAAAGAACAGTGCTTATTGAATGGAGTTGGGGAAGTCCCAAATTAATAAAAGATAGGGTCACTGGC
CCAAAGTCAATTTCATAAAGGATAAATACAAAAATATCGGACATAAACTTGTTCAGGTTGTTGCCAATAACACAAACGAA
GAGGCTGGGGATGGTATTACCACTACCACTGTTCTGGCATGGTCTATTGCCAAGGAGGACTTTGAGAAGTGCAGCAAAGG
GCCATGAGAAATCAAAAGAAATGTGATGTTGGGTGTTAATGCTGTAATTACTGAACTTAAGAAACAATATAAACCTGTGA
CATCCCCTGATGAAATTGCTCAGGTTGCTACAATTTCTGGAAATAGAGACAAAGACATTTAAAATATCATTTCTGATAGA
ATGGAAAAGGTTGAAGAAAGGGTGTCATCACAGTGAAGGTTGGAAAAATCCTGAATGATGAAGTAGAAATTATTGAAGGC
ATGAAGTTTGATAGAGGATATATTTCTCTAGAATTTTATTAACACATCATAAGGTCAAAAAGTGTGAATTCCAAGATGCC
TATGTTTTTGTTGAGTGAAATGAAATTTTCTAGTGTCCAGTCCATTGTATCTGCTCTTAAAATTGTTAATGCTCATCAGA
TGCCCTTGGTAATAATTGCTGAAGATATTGATAGAGTAGCTCTAAGATCACTGATTTTGAACAAGCTAAAAGTTTGTCTT
CAGGTTGGAACAGTCAAAGCTCCAGGGTTTGGTGACAATCAGAAAAAACAGTTTAAAGATAATAGCTAATGCTACTAGTG
GTACAATGTTTTGAGAAGAGGGATTGAATCAAAACCTTGGAGATGTTCACGCTCATGTCATAGGAAAACTTGGAGAGGTC
CTTTTCACCAAAGAAGATGCCATGCTTTTGAAAGGAAAAGGTGACAAGGTTCACATTGAAAAACATATTCAAGAAATCAC
TGAACAGCTAGACATCACAACTGGTCAATATAAAAAGGAAAACTGAACAAGGGACTTGCTAAACTTTCAGATGGAGTAGG
TGTTTTGAAGGTTAGAGGAACAATTGATGTTGAAATGAAGGAGAAGACAGTTACAGATGCTCTCAGTGCTGCAAGAGCAG
CTGTTGAAGAATGCATTGTTCTTGGAGAAGGCTCTGCTTTGTTG

ORF - retro_mmus_439 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75. %
Parental protein coverage: 77.66 %
Number of stop codons detected: 5
Number of frameshifts detected 7


Retrocopy - Parental Gene Alignment:

ParentalMLRLPTVLRQMRPVSRALAPHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
M..L.TVL.QMRPVS.ALAPHLT.AYAKD.KFGADA.ALMLQG.DLLADA.AVT.G.K.RTV.IE.SWGS
RetrocopyMPHLFTVLCQMRPVSPALAPHLTWAYAKDIKFGADA*ALMLQGIDLLADAIAVTVGSKQRTVLIEWSWGS
ParentalPKVTKDGVTVAKSID-LKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVE
PK..KD.VT..KSI...KDKYKNIG.KLVQ.VANNTNEEAGDG.TT.TVLA.SIAKE.FEK.SKG..P.E
RetrocopyPKLIKDRVTGPKSIS<IKDKYKNIGHKLVQVVANNTNEEAGDGITTTTVLAWSIAKEDFEKCSKG--P*E
ParentalIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKDIGNIISDAMKKVG-RKGVITVKDGKTLN
I.R.VML.V.AVI.ELKKQ.KPVT.P.EIAQVATIS.N.DKDI.NIISD.M.KV..RKGVITVK.GK.LN
RetrocopyIKRNVMLGVNAVITELKKQYKPVTSPDEIAQVATISGNRDKDI*NIISDRMEKVE<RKGVITVKVGKILN
ParentalDELEIIEGMKFDRGYISP-YFINTSKGQ-KCEFQDAYV-LLSEKKISSVQSIVPALEIANAHRKPLVIIA
DE.EIIEGMKFDRGYIS...FINTS.GQ.KCEFQDAYV.LLSE.K.SSVQSIV.AL.I.NAH..PLVIIA
RetrocopyDEVEIIEGMKFDRGYISL>NFINTS*GQ>KCEFQDAYV>LLSEMKFSSVQSIVSALKIVNAHQMPLVIIA
ParentalEDVDGEALSTLVLNRLKVGLQVVAVKAPGFGDN-RKNQLKDMAIATGGAVFGEEGLNLNLEDVQAHDLGK
ED.D..AL..L.LN.LKV.LQV..VKAPGFGDN.RKN.LK..A.AT.G..F.EEGLN.NL.DV.AH..GK
RetrocopyEDIDRVALRSLILNKLKVCLQVGTVKAPGFGDN>RKNSLKIIANATSGTMF*EEGLNQNLGDVHAHVIGK
ParentalVGEVIVTKDDAMLLKGKGDKAHIEKRIQEITEQLDITTSEYEKE-KLNERLAKLSDGVAVLKVGGTSDVE
.GEV..TK.DAMLLKGKGDK.HIEK.IQEITEQLDITT..Y.KE.KLN..LAKLSDGV.VLKV.GT.DVE
RetrocopyLGEVLFTKEDAMLLKGKGDKVHIEKHIQEITEQLDITTGQYKKE<KLNKGLAKLSDGVGVLKVRGTIDVE
ParentalVNEKKDRVTDALNATRAAVEEGIVLGGGCALL
..EK...VTDAL.A.RAAVEE.IVLG.G.ALL
RetrocopyMKEK--TVTDALSAARAAVEECIVLGEGSALL

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
SRP007412_brain 0 .00 RPM 93 .17 RPM
SRP007412_cerebellum 0 .00 RPM 79 .33 RPM
SRP007412_heart 0 .00 RPM 210 .75 RPM
SRP007412_kidney 0 .00 RPM 298 .39 RPM
SRP007412_liver 0 .00 RPM 313 .50 RPM
SRP007412_testis 0 .00 RPM 22 .73 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_439 was not detected
No EST(s) were mapped for retro_mmus_439 retrocopy.


TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_74689576 libraries428 libraries66 libraries1 library1 library

The graphical summary, for retro_mmus_439 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

retro_mmus_439 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_439 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 18 parental genes, and 74 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137701 retrocopy
Canis familiaris ENSCAFG000000108654 retrocopies
Callithrix jacchus ENSCJAG000000039906 retrocopies
Echinops telfairi ENSETEG000000091844 retrocopies
Homo sapiens ENSG000001443817 retrocopies
Gorilla gorilla ENSGGOG000000082676 retrocopies
Loxodonta africana ENSLAFG000000000531 retrocopy
Macropus eugenii ENSMEUG000000119872 retrocopies
Myotis lucifugus ENSMLUG000000008714 retrocopies
Macaca mulatta ENSMMUG000000104891 retrocopy
Monodelphis domestica ENSMODG000000122893 retrocopies
Mustela putorius furoENSMPUG000000078183 retrocopies
Mus musculus ENSMUSG00000025980 5 retrocopies
Nomascus leucogenys ENSNLEG000000068747 retrocopies
Otolemur garnettii ENSOGAG000000340535 retrocopies
Pongo abelii ENSPPYG000000130465 retrocopies
Rattus norvegicus ENSRNOG000000145259 retrocopies
Xenopus tropicalis ENSXETG000000075091 retrocopy



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