RetrogeneDB ID:

retro_mmus_3528

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:141980721..141982318(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000080775
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Hsp90ab1
Ensembl ID:ENSMUSG00000023944
Aliases:Hsp90ab1, 90kDa, AL022974, C81438, Hsp84, Hsp84-1, Hsp90, Hspcb
Description:heat shock protein 90 alpha (cytosolic), class B member 1 [Source:MGI Symbol;Acc:MGI:96247]


Retrocopy-Parental alignment summary:






>retro_mmus_3528
CAGTACTTAGAGGAGAGGAGGGTCAAGGAAGTGGTGAAGAAACATTCGCAGTTCATAGGCTATCCAATCACCCTCTATTT
GGAGAAGGAGAGGGAGAAGGAGATCAGTGATGATAAGGCAGAGGAAGAGAAAGGTGAAAAAGAGGAGGAAGATAAGCAGG
ATGAGGAGAAGCCTAAGATTGAATATGTGGGATCTGATGAGGAAGATGACAGTGGCAAAGACAAGAAAAAGAAAACAAAG
AAGATCAAGGAGAAGTACATTGACCAGGAGGAGCTGAACAAGAGAGCCTATTTGGACCAGAAATCCAGATGACATCACTC
AAGAGGAGTATGGTGAATTCTATAAGAGCCTCAACAATGATTGGAAGGACCAGTTGGCACTCAAACACTTCTCTGTAGAA
GGTCAATTGGAATTCAGGGCATTGCTCTTCATTCCCCAGCTAGCGCCCTTTGACATTTTTGAGAAGAAGAACAACAACAA
CATCACATTGTATGTCCGCTGTGTGTTCATCATAGACAGCTGTAATGAGCTGATATCTGAGTCCCTCAACTTTATCTGTG
GTGTGGTTGTCTCTGAGGACCTGTGTCTGAACATCTCCAGAGAATTGCTCCAGCAGAACAAGATCCTGAAAGTCACCCAC
AAAAATACTATGAAGAAGTGCCTTGAGCTCTTCTCTGAATTGGCTGAAGACAAAGAGAACTACAAGAAGTTCTATGAGGC
TTTCTCCAAGAATTTAAAGCTTGGAATTCATGAAGATTCCACTAACTGTCACTGCCTCTCTGAGCTCCTTCTCTATCACA
CCTCTCAGTCTGGAGATGATATGACTTTCCTGTCAGAGTATGTGTCTTGCATGAAGGAGACCAAGAAGTCCATCTACTAT
ATCACTGGAGAGAGCAAAGAGCAAGTGGCCAACACTGCCTTTGTGGAGCGTGTGAGGAAGTAGGGCTTTGAGGTGGTGTA
AATGACTAAGCCTAGTGATGAGGACTGTGTGCAGCAGCTCAAGGAGTTTGATGGGAAGAGTCTGGTCTCGGTGACTAAGG
AGGGCCGGGAGCTACCAGAGCATGAGGAAGAGAAGAAGAAAATAGAGGAGAGCAAGGTAAAGTTTGAGAATCTCTGCAAG
CTCCTGAAAGAGCTCTTGGAGAAGAAGGTTGAAAAAGTGACAATCTCCAATAGGCTTGTATCTTCACCCTGCTGCATTGT
GACAAGCACCTATAGCTGGACAGTCAACATGGAGCAGATCATGAAGGCCCTGGCACTGTGAAACAACTCTACGATGGGCT
ACATGATGGCCAAAAAACACCTGGTGTTAAACCCTGACTACCCCATCGTGGAAACCCTGCAGCAGAAGGCTGAGGCAGAC
AAAAACGACAAAGCTGCCAAGAACCTGGTGGTGCTGCTGTTTGAAACTGCTCTGCTCTCTTCTGGTTTCTCACTTGAGGA
TCCCCAAACCCACTCCAACTGCATCTACCACATGATTAAACTAGGCCTGGGCATCGATGAAGATGAGGTCACTGCAGAGG
AGCCCAGTGCTGCTGTTCCTGATGAGATCCCCCCACTGGAAGGTGATGAGAATGCCTCGAGCATGGAAGAAGTGGAT

ORF - retro_mmus_3528 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.93 %
Parental protein coverage: 73.76 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKEDEEKPKIEDVGSDEEDD
.YLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDD.AEEEKGEKEEEDK.DEEKPKIE.VGSDEEDD
RetrocopyQYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDKAEEEKGEKEEEDKQDEEKPKIEYVGSDEEDD
ParentalSGKDKK-KKTKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEF
SGKDKK..K..................PIWTRNPDDITQEEYGEFYKSL.NDW.D.LA.KHFSVEGQLEF
RetrocopySGKDKK>RKQRRSRRSTLTRRS*TR-EPIWTRNPDDITQEEYGEFYKSLNNDWKDQLALKHFSVEGQLEF
ParentalRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSK
RALLFIP..APFD.FE.KK..NNI.LYVR.VFI.DSC.ELI.E.LNFI.GVV.SEDL.LNISRE.LQQ.K
RetrocopyRALLFIPQLAPFDIFE-KKNNNNITLYVRCVFIIDSCNELISESLNFICGVVVSEDLCLNISRELLQQNK
ParentalILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSL
ILKV..KN..KKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTN...LSELL.YHTSQSGD.MT.L
RetrocopyILKVTHKNTMKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNCHCLSELLLYHTSQSGDDMTFL
ParentalSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKE
SEYVS.MKET.KSIYYITGESKEQVAN.AFVERVRK.GFEVV.MT.P.DE.CVQQLKEFDGKSLVSVTKE
RetrocopySEYVSCMKETKKSIYYITGESKEQVANTAFVERVRK*GFEVV*MTKPSDEDCVQQLKEFDGKSLVSVTKE
ParentalGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQ
G.ELPE.EEEKKK.EESK.KFENLCKL.KE.L.KKVEKVTISNRLVSSPCCIVTSTY.WT.NME.IMKA.
RetrocopyGRELPEHEEEKKKIEESKVKFENLCKLLKELLEKKVEKVTISNRLVSSPCCIVTSTYSWTVNMEQIMKAL
ParentalALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNR
AL..NSTMGYMMAKKHL..NPD.PIVETL.QKAEADKNDKA.K.LVVLLFETALLSSGFSLEDPQTHSN.
RetrocopyAL*NNSTMGYMMAKKHLVLNPDYPIVETLQQKAEADKNDKAAKNLVVLLFETALLSSGFSLEDPQTHSNC
ParentalIYRMIKLGLGIDEDEVTAEEPSAAVPDEIPPLEGDEDASRMEEVD
IY.MIKLGLGIDEDEVTAEEPSAAVPDEIPPLEGDE.AS.MEEVD
RetrocopyIYHMIKLGLGIDEDEVTAEEPSAAVPDEIPPLEGDENASSMEEVD

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 1 .26 RPM 1372 .48 RPM
SRP007412_cerebellum 2 .61 RPM 1586 .48 RPM
SRP007412_heart 0 .28 RPM 1520 .80 RPM
SRP007412_kidney 2 .81 RPM 1889 .41 RPM
SRP007412_liver 2 .18 RPM 1439 .73 RPM
SRP007412_testis 0 .55 RPM 375 .01 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_3528 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3528 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_155614341 libraries531 libraries190 libraries8 libraries2 libraries

The graphical summary, for retro_mmus_3528 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_3528 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3528 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 12 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000019814 retrocopies
retro_cfam_1108, retro_cfam_411, retro_cfam_562, retro_cfam_881,
Felis catus ENSFCAG000000097641 retrocopy
retro_fcat_1177,
Gorilla gorilla ENSGGOG000000088892 retrocopies
retro_ggor_1011, retro_ggor_701,
Macropus eugenii ENSMEUG000000137351 retrocopy
retro_meug_1896,
Myotis lucifugus ENSMLUG000000052392 retrocopies
retro_mluc_1604, retro_mluc_865,
Macaca mulatta ENSMMUG000000226862 retrocopies
retro_mmul_1319, retro_mmul_1869,
Mus musculus ENSMUSG000000212701 retrocopy
retro_mmus_2139,
Mus musculus ENSMUSG00000023944 3 retrocopies
retro_mmus_1916, retro_mmus_3528 , retro_mmus_856,
Otolemur garnettii ENSOGAG000000119611 retrocopy
retro_ogar_2574,
Pongo abelii ENSPPYG000000166552 retrocopies
retro_pabe_2425, retro_pabe_415,
Rattus norvegicus ENSRNOG000000198346 retrocopies
retro_rnor_1561, retro_rnor_1562, retro_rnor_1787, retro_rnor_597, retro_rnor_598, retro_rnor_87,
Tupaia belangeri ENSTBEG000000148731 retrocopy
retro_tbel_1428,




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