RetrogeneDB ID:

retro_mmus_1299

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:14:92602559..92604388(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Hspa5
Ensembl ID:ENSMUSG00000026864
Aliases:Hspa5, AL022860, AU019543, Bip, D2Wsu141e, D2Wsu17e, Grp78, Hsce70, SEZ-7, Sez7, baffled, mBiP
Description:heat shock protein 5 [Source:MGI Symbol;Acc:MGI:95835]


Retrocopy-Parental alignment summary:






>retro_mmus_1299
GGACCTGCAGTTGGCATTGATCTTGGGACCACCTACTCCTGTGTGGGTGTCTTCCATCATGGAAAGGTGGAAATTATTGC
CAATGACCAGGGTAACCGCACCGCGCCGAGCTACGTTGCTTTCACCGGCACAGAGAGATTAATTCAGGATGCGGCCAAGA
ATCAGGTTGCAAAGAACCCCACCAACACAGTTTTTGATGCCAAACGTCTGGTCGGGCGTAGGTTTGATGATGCTGTTGTT
CAGTCTGATATGAAGCACTGGCCCTTCATGGTGGTGAATGATGCAGGCAGGCCCAAGGTCCAAGTGGAATACAAAGGGGA
GACAACAAGTTTCTACCCAGAGAAAGTGTCCTCCACGGTTCTGACAAAGATGAAGGAAATTGCAGAAGCGTACCTCGGAA
AGACTGTTATCAATGCTGTGGTCACAGTGCCGGCTTACTTCAATGACTCTCAGCGACAGGCAACAAAAGATGCTGGAACT
ATTGCTGGCCTCAATGTACTTCGAATCATCAATGAACCAACTGCTGCTGCTATTGCTTATGGCTTAGATAAGAAGGTTGG
AGCTGAAAGGAATGTGCTCATTTTTGACTTGGGAGGTGGCACTTTTGATGTGTCAATCCTGACTATTGAGGATGGAAGTT
TTGAAGTCAAATCAACAGCTGGAGACACCCACTTAGGTGGAGAAAGTTTTGACAACCGAATGGTCAATCATTTCATTGCT
GAGTTTAAGCGAAAGCACAAGGAAGATGTCAGTGAGAACAAGAGAGCTGTCCGCCGTCTCCGCACCGCCTGCGAGCCAAG
CGCACCCTTTCCTCCAGCACCCAGGCCAGTATTGAGATTGATTCTCTCTATGAGGGAATTGACTTCTATACCTCCATTAC
CCGGGCTCGATTTGAGGAGTTGAATGCTGACCTGTTCCGTGGCCCACTGGACCCTGTAGAGAAAGCCCTTCGAGATGCCA
AACTGGACAAGTCACAGATCCATGATATTGTCTTGGTGGGTGGTTCTACCAGAATCCCCAAGATTCAGAAATTTCTGCAA
GACTTCTTCAATGGAAAAGAGCTGAACAAGAGCATTAACCCCGATGAAGCTGTTGCCTATGGTGCAGCTGTCCAGGCAGC
CATTCTATCTGGAGACAAGTCTGAGAACGTTCAGGATTTGCTGCTCTTGGATGTCACTCCTCTTTCCCTTGGTATTGAAA
CTGCTGGCAGAGTCATGACTGTCCTCATCAAGTGCAATACCACCATCCCTACCAAGCAGACACAGACTTTCACCACCTAC
TCTGACAACCAGCCTGGTGTACTCATTCAGGTGTATGAAGGTGAAAGGGCCATGACCAAGGACAACAACCTGCTTGGAAA
GTTCGAGCTCACGGGCATCCCTCCAGCACCCCGTGGGGTTCCTCAGATTGAGGTTACTTTTGACATCGATGCCAATGGCA
TCCTCAATGTTTCTGCTGTAGTTAAGAGCACAGGAAAGAAGAAAAAGATCACCATCACCAATGACAGGGGCCACTTGAGT
AAGGAAGATATTGAGCGCATGGTCCAAGAAGCTGAAAAGTACAAAGCTGAGGATGAGAAGCAGAGAGATAAAGTTTCCTC
CAAGAATTCACTGGAGTCCTATGCCTTCAACATGAAAGCAACTGTGGAAGATGAGAAACTTCAAGGCAAGATCAATGATA
AAGACAAGCAGATTCTTGACAAGTGCAATGAAATCATCAGCTGGCTGGATAAGAACCAGACTGCAGAGAAGGAAGAATTT
GAGCATCAGCAGAAAGAACTGGAGAAAGTCTGCAACCCTATCATTACCAAGCTGTACCAGAGTGCTGGT

ORF - retro_mmus_1299 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.66 %
Parental protein coverage: 93.44 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTPEGERLIGDAAKNQLTSNPENTVFDAKR
G..VGIDLGTTYSCVGVF..G.VEIIANDQGNR..PSYVAFT...ERLI.DAAKNQ...NP.NTVFDAKR
RetrocopyGPAVGIDLGTTYSCVGVFHHGKVEIIANDQGNRTAPSYVAFTGT-ERLIQDAAKNQVAKNPTNTVFDAKR
ParentalLIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQVDIGGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTH
L.GR...D..VQ.D.K..PF.VV.....P..QV...G..T..F.PE..S..VLTKMKE.AEAYLGK.V..
RetrocopyLVGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKG-ETTSFYPEKVSSTVLTKMKEIAEAYLGKTVIN
ParentalAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLDKREG-EKNILVFDLGGGTFDVSLLT
AVVTVPAYFND.QRQATKDAGTIAGLNV.RIINEPTAAAIAYGLDK..G.E.N.L.FDLGGGTFDVS.LT
RetrocopyAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILT
ParentalIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREV-EKAKRALSSQHQA
I..G.FEV..T.GDTHLGGE.FD.R...HFI....K...K.....N.......R.....AKR.LSS..QA
RetrocopyIEDGSFEVKSTAGDTHLGGESFDNRMVNHFIAEF-KRKHKEDVSENKRAVRRLRTA<LRAKRTLSSSTQA
ParentalRIEIESFFEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLV
.IEI.S..EG.DF....TRA.FEELN.DLFR....PV.K.L.D..L.KS.I..IVLVGGSTRIPKIQ...
RetrocopySIEIDSLYEGIDFYTSITRARFEELNADLFRGPLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKFL
ParentalKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGD--QDTGDLVLLDVCPLTLGIETVGGVMTKLIPRNTVV
..FFNGKE....INPDEAVAYGAAVQA..LSGD......DL.LLDV.PL.LGIET.G.VMT.LI..NT..
RetrocopyQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGRVMTVLIKCNTTI
ParentalPTKKSQIFSTASDNQPTVTIKVYEGERPLTKDNHLLGTFDLTGIPPAPRGVPQIEVTFEIDVNGILRVTA
PTK..Q.F.T.SDNQP.V.I.VYEGER..TKDN.LLG.F.LTGIPPAPRGVPQIEVTF.ID.NGIL.V.A
RetrocopyPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVSA
ParentalEDKGTGNKNKITITNDQNRLTPEEIERMVNDAEKFAEEDKKLKERIDTRNELESYAYSLKNQIGDKEKLG
..K.TG.K.KITITND...L..E.IERMV..AEK...ED.K........N.LESYA...K....D.EKL.
RetrocopyVVKSTGKKKKITITNDRGHLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVED-EKLQ
ParentalGKLSSEDKETMEKAVEEKIEWLESHQDADIEDFKAKKKELEEIVQPIISKLYGSGG
GK....DK....K...E.I.WL...Q.A..E.F....KELE....PII.KLY.S.G
RetrocopyGKINDKDKQILDKC-NEIISWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAG

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 .07 RPM 254 .63 RPM
SRP007412_cerebellum 2 .26 RPM 314 .11 RPM
SRP007412_heart 0 .40 RPM 480 .28 RPM
SRP007412_kidney 2 .60 RPM 534 .24 RPM
SRP007412_liver 1 .64 RPM 808 .28 RPM
SRP007412_testis 0 .32 RPM 401 .86 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1299 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1299 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_3810744 libraries37 libraries395 libraries229 libraries367 libraries

The graphical summary, for retro_mmus_1299 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_1299 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1299 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 13 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000068801 retrocopy
retro_cjac_2221,
Homo sapiens ENSG000000445741 retrocopy
retro_hsap_3005,
Gallus gallus ENSGALG000000010001 retrocopy
retro_ggal_21,
Gorilla gorilla ENSGGOG000000268791 retrocopy
retro_ggor_2082,
Macropus eugenii ENSMEUG000000167021 retrocopy
retro_meug_522,
Mus musculus ENSMUSG000000156568 retrocopies
retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Mus musculus ENSMUSG000000243591 retrocopy
retro_mmus_3624,
Mus musculus ENSMUSG00000026864 1 retrocopy
retro_mmus_1299 ,
Nomascus leucogenys ENSNLEG000000173481 retrocopy
retro_nleu_751,
Otolemur garnettii ENSOGAG000000067861 retrocopy
retro_ogar_2901,
Pongo abelii ENSPPYG000000196091 retrocopy
retro_pabe_2491,
Pan troglodytes ENSPTRG000000005631 retrocopy
retro_ptro_2033,
Ictidomys tridecemlineatus ENSSTOG000000112434 retrocopies
retro_itri_1686, retro_itri_1687, retro_itri_1689, retro_itri_1879,


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