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: 75.0 %
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






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 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

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_439 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_439 retrocopy.

TSS - click to see more details



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 libraries 428 libraries 66 libraries 1 library 1 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)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

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
retro_amel_771,
Canis familiaris ENSCAFG000000108654 retrocopies
retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Callithrix jacchus ENSCJAG000000039906 retrocopies
retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Echinops telfairi ENSETEG000000091844 retrocopies
retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Homo sapiens ENSG000001443817 retrocopies
retro_hsap_1006, retro_hsap_2770, retro_hsap_2987, retro_hsap_3151, retro_hsap_3494, retro_hsap_3930, retro_hsap_4018,
Gorilla gorilla ENSGGOG000000082676 retrocopies
retro_ggor_1927, retro_ggor_2069, retro_ggor_2361, retro_ggor_2698, retro_ggor_800, retro_ggor_985,
Loxodonta africana ENSLAFG000000000531 retrocopy
retro_lafr_476,
Macropus eugenii ENSMEUG000000119872 retrocopies
retro_meug_1688, retro_meug_224,
Myotis lucifugus ENSMLUG000000008714 retrocopies
retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta ENSMMUG000000104891 retrocopy
retro_mmul_83,
Monodelphis domestica ENSMODG000000122893 retrocopies
retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furoENSMPUG000000078183 retrocopies
retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Mus musculus ENSMUSG00000025980 5 retrocopies
retro_mmus_1225, retro_mmus_2494, retro_mmus_3206, retro_mmus_439 , retro_mmus_706,
Nomascus leucogenys ENSNLEG000000068747 retrocopies
retro_nleu_1349, retro_nleu_2238, retro_nleu_229, retro_nleu_657, retro_nleu_675, retro_nleu_691, retro_nleu_787,
Otolemur garnettii ENSOGAG000000340535 retrocopies
retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Pongo abelii ENSPPYG000000130465 retrocopies
retro_pabe_2040, retro_pabe_2244, retro_pabe_2476, retro_pabe_2887, retro_pabe_848,
Rattus norvegicus ENSRNOG000000145259 retrocopies
retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Xenopus tropicalis ENSXETG000000075091 retrocopy
retro_xtro_63,


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